Zeiss SmartSEM Software Manual PDF

Software Manual
®
SmartSEM V05.06
Operating software for
Scanning Electron Microscopes
Carl Zeiss Microscopy - Electron and Ion beam Microscopy
Software Manual
®
SmartSEM V05.06
Operating software for Scanning Electron
Microscopes
Software Manual SmartSEM® V05.06
Operating software for Scanning Electron Microscopes
Original instructions
Carl Zeiss Microscopy GmbH

Carl-Zeiss-Promenade 10
07745 Jena, Germany
microscopy@zeiss.com
www.zeiss.com/microscopy

Carl-Zeiss-Straße 22
73447 Oberkochen
Document name: Software Manual SmartSEM® V05.06

Revision: en01
Effective from: November 2012
© by Carl Zeiss Microscopy GmbH
346000-8077-000
This document or any part of it must not be translated, reproduced or transmitted in any form or by any means, electronic or
mechanical, including photocopying, recording, or by any information or retrieval system. Violations will be prosecuted.
The use of general descriptive names, registered names, trademarks, etc. in this document does not imply, even in the absence of a
specific statement, that such names are exempt from the relevant protective laws and regulations and therefore free for general use.
Software programs will fully remain the property of Carl Zeiss Microscopy. No program, documentation or subsequent upgrade thereof
may be disclosed to any third party, unless prior written consent of Carl Zeiss Microscopy has been procured to do so, nor may they be
copied or otherwise duplicated, even for the customer’s internal needs apart from a single back-up copy for safety purposes.
Due to an ongoing process of improvement Carl Zeiss Microscopy reserves the right to make modifications of this document without
notice.
Contents
Table of Contents
1. Introduction ................................................................................................ 11
1.1. For your safety ............................................................................................... 11
1.1.1. Intended use .......................................................................................................... 11
1.2. About this manual .......................................................................................... 11
1.2.1. Safety instructions in this manual .......................................................................... 12
1.2.2. Typographical conventions .................................................................................... 13
1.2.3. Definition of terms ................................................................................................. 14
2. Description ................................................................................................. 15
2.1. System requirements ..................................................................................... 15
2.1.1. Operating system .................................................................................................. 15
2.1.2. Dongles ................................................................................................................. 15
2.2. Installation ...................................................................................................... 15
2.3. SmartSEM® program suite ............................................................................ 16
2.4. Available licences .......................................................................................... 19
2.5. Principle of operation .................................................................................... 23
2.6. SmartSEM® user interface ............................................................................ 24
2.7. User access levels ......................................................................................... 26
3. First steps ................................................................................................... 27

3.1. Switching on the SEM/FESEM ...................................................................... 27
3.2. Starting the SmartSEM® user interface ....................................................... 28
3.3. Finding your way in the user interface ........................................................ 30
3.3.1. Showing or hiding toolbars .................................................................................... 30
3.3.2. Showing or hiding the data zone ........................................................................... 31
3.3.3. Showing a full screen image ................................................................................. 31
3.3.4. Docking panels ...................................................................................................... 32
3.3.5. Opening the Panel Configuration Bar .................................................................... 34
3.4. Obtaining the first image ............................................................................... 35
3.4.1. Preparing the sample holder ................................................................................. 36
3.4.2. Loading the specimen chamber ............................................................................ 37
3.4.3. Locating the specimen .......................................................................................... 41
3.4.4. Switching on the gun ............................................................................................. 42
3.4.5. Switching on the EHT ............................................................................................ 43
3.4.6. Generating an image ............................................................................................. 45
3.4.7. Optimising the image ............................................................................................. 47
3.4.8. Saving the image ................................................................................................... 51
3.5. Using the help functions ............................................................................... 53
3.5.1. Calling the SmartSEM® help ................................................................................. 53
3.5.2. Calling the context-sensitive help .......................................................................... 54
Instruction Manual SmartSEM® V05.06 en01 V

Contents
3.5.3. Searching for a topic ............................................................................................. 54

3.5.4. Using the step-by-step guides ............................................................................... 55
3.5.5. Calling the shortcuts help ...................................................................................... 56
3.5.6. Showing information about SmartSEM® ............................................................... 57
3.6. Closing the SmartSEM® software .................................................................58
3.6.1. Logging off ............................................................................................................. 58
3.6.2. Exiting .................................................................................................................... 58
4. Operation ..................................................................................................... 59
4.1. Controlling the vacuum ..................................................................................59
4.1.1. Checking the current vacuum status ..................................................................... 59
4.1.2. Ventilating the specimen chamber ........................................................................ 61
4.1.3. Evacuating the specimen chamber ....................................................................... 63
4.1.4. Working with variable pressure (VP instruments only) .......................................... 64
4.2. Navigating the specimen ...............................................................................66
4.2.1. Moving the specimen with the soft joystick ............................................................ 66
4.2.2. Moving the specimen at high magnifications (Beam Shift) .................................... 67
4.2.3. Improving stage repeatability by activating the function ....................................... 68
4.2.4. Compensating for image drift by shifting the beam (licence: DRIFT CORR) ........ 69
4.2.5. Using fisheye mode (licence: FISHEYE) ............................................................... 72
4.2.6. Using the stage navigation functions ..................................................................... 74
4.2.7. Eucentrically driving a non-eucentric stage (licence: COMPU) ............................. 78
4.2.8. Saving and recalling stage coordinates (licence: STAGECO) ............................... 84
4.2.9. Centering a spot or an area (licence: CENTRE) ................................................... 85
4.2.10. Using Stage Map (licence: CENTRE) .................................................................. 86
4.2.11. Scanning defined image fields (licence: STAGESCAN) ...................................... 87
4.2.12. Toggling between survey view and detail view (licence: SURVEY) .................... 88
4.2.13. Defining a user specific coordinate system (licence: STAGEREG) ..................... 91
4.3. Setting SEM conditions ..................................................................................93
4.3.1. Controlling the gun ................................................................................................ 93
4.3.2. Controlling the EHT ............................................................................................... 95
4.3.3. Blanking the beam ................................................................................................. 97
4.3.4. Modifying the probe current ................................................................................... 98
4.3.5. Aligning the aperture ........................................................................................... 102
4.3.6. Correcting astigmatism ........................................................................................ 103
4.3.7. Showing SEM parameters (SEM status window) ................................................ 104
4.3.8. Recording SEM parameters ................................................................................ 106
4.4. Imaging ..........................................................................................................109
4.4.1. Setting detection parameters ............................................................................... 109
4.4.2. Setting the working distance ................................................................................ 121
4.4.3. Setting scan parameters ...................................................................................... 122
4.4.4. Setting the magnification ..................................................................................... 130
4.4.5. Imaging tilted specimen ....................................................................................... 131
4.4.6. Improving the signal-to-noise ratio (noise reduction) ........................................... 135
VI Instruction Manual SmartSEM® V05.06 en01

Contents
4.4.7. Improving image illumination by using Look Up Tables (LUT) ............................ 138
4.4.8. Processing the image (licence: IMMATH) ........................................................... 143
4.5. Annotating images ....................................................................................... 153
4.5.1. Adding text .......................................................................................................... 153
4.5.2. Adding geometrical objects ................................................................................. 154
4.5.3. Adding EM parameters ........................................................................................ 155
4.5.4. Adding a bitmap or metafile ................................................................................. 156
4.5.5. Zone magnification .............................................................................................. 156
4.5.6. Adding micron markers ....................................................................................... 157
4.5.7. Measuring ............................................................................................................ 158
4.5.8. Editing Annotations ............................................................................................. 161
4.5.9. Displaying crosshairs or graticules (licence: GRATICULE) ................................. 163
4.6. Working with recipes ................................................................................... 166
4.6.1. Saving a user-specific recipe .............................................................................. 166
4.6.2. Saving a common recipe ..................................................................................... 166
4.6.3. Viewing a recipe .................................................................................................. 167
4.6.4. Executing a recipe ............................................................................................... 168
4.6.5. Deleting a recipe ................................................................................................. 168
4.6.6. Creating an ingredient list .................................................................................... 169
4.6.7. Using the MiniBar to work with recipes ............................................................... 172
4.7. Saving and managing images ..................................................................... 173
4.7.1. Saving images ..................................................................................................... 173
4.7.2. Taking videos (licence: AVI capture) ................................................................... 178
4.7.3. Loading images ................................................................................................... 179
4.7.4. Using the Image Gallery ...................................................................................... 180
4.7.5. Printing images .................................................................................................... 181
4.7.6. Copying images to the Windows® buffer (licence: CLIP) .................................... 182
4.7.7. Transmitting data to a FTP server or a network printer (licence: REMARCH) .... 184
4.7.8. Using the Large Image Store Wizard .................................................................. 187
4.8. Managing users ............................................................................................ 190
4.8.1. Managing user profiles ........................................................................................ 190
4.8.2. Managing user accounts (licence: ACCOUNT) ................................................... 198
4.9. Customising the SmartSEM® software ...................................................... 206
4.9.1. Customising joystick and control panel settings .................................................. 206
4.9.2. Setting mouse adjustment preferences ............................................................... 206
4.9.3. Disabling the splash screen on startup ............................................................... 207
4.9.4. Personalising the user interface (User Preferences) ........................................... 208
4.9.5. Customising the data zone .................................................................................. 212
4.9.6. Customising the toolbar ....................................................................................... 215
4.9.7. Customising the magnification display ................................................................ 220
4.9.8. Showing the installed licences ............................................................................ 223
4.10. Remotely controlling the SEM/FESEM ..................................................... 224
4.10.1. Using RS232 (licence: REMCON) ..................................................................... 224
4.10.2. Using Windows XP Remote Desktop Connection (licence: Remote SEM) ....... 225
Instruction Manual SmartSEM® V05.06 en01 VII

Contents
4.11. Communication with additional software .................................................226

4.11.1. Communicating with Camelot software (licence: KNIGHTS CAMELOT) .......... 226
4.11.2. Reading wafer defect files (licence: DEFECT REVIEW) ................................... 227
4.12. Backing up / restoring data .......................................................................228
4.12.1. Creating a backup ............................................................................................. 228
4.12.2. Restoring data ................................................................................................... 230
4.13. Working with optional accessories ...........................................................232
4.13.1. Using the Laser Finder ...................................................................................... 232
4.13.2. Using the Quiet Mode ........................................................................................ 232
4.13.3. Measuring the specimen current ....................................................................... 233
4.13.4. Using the Plasma Cleaner ................................................................................. 234
5. Troubleshooting ....................................................................................... 239

5.1. Initialising the stage .....................................................................................240
5.1.1. Defining the post initialisation position of the stage ............................................. 240
5.2. Changing the joystick TV angle ..................................................................241
5.3. Calibrating OptiProbe ...................................................................................242
5.4. Resetting touch alarm ..................................................................................244
5.5. Checking water flow and temperature ........................................................244
5.6. Checking water flow and temperature (MERLINTM only) ..........................245
5.7. Checking the CAN communication (MERLINTM only) ...............................246
6. Summary of software functions .............................................................. 247

6.1. Menus ............................................................................................................247
6.1.1. Menu File ............................................................................................................. 247
6.1.2. Menu Edit ............................................................................................................ 254
6.1.3. Menu View ........................................................................................................... 259
6.1.4. Menu Beam ......................................................................................................... 262
6.1.5. Menu Detection ................................................................................................... 264
6.1.6. Menu Image ........................................................................................................ 265
6.1.7. Menu Scanning ................................................................................................... 269
6.1.8. Menu Stage ......................................................................................................... 272
6.1.9. Menu Vacuum ..................................................................................................... 275
6.1.10. Menu Tools ........................................................................................................ 278
6.1.11. Menu Help ......................................................................................................... 288
6.2. Panels on the Panel Configuration Bar ......................................................290
6.2.1. Airlock (optional) .................................................................................................. 291
6.2.2. Bakeout ............................................................................................................... 292
6.2.3. Bakeout (MERLINTM only) ................................................................................... 293
6.2.4. Beam Shift ........................................................................................................... 294
6.2.5. BSD Control (optional) ......................................................................................... 294
6.2.6. CAN Communication (MERLINTM only) .............................................................. 295
6.2.7. CZ Detector Calibration (optional) ....................................................................... 295
VIII Instruction Manual SmartSEM® V05.06 en01

Contents
6.2.8. Calibrate Stage Centre ........................................................................................ 296

6.2.9. Calibrate Stigmation ............................................................................................ 296
6.2.10. Colour Mode (licence: Colour Mode) ................................................................. 296
6.2.11. Column Calibration ............................................................................................ 297
6.2.12. Compucentric Height (licence COMPU) ............................................................ 298
6.2.13. Defect Review (licence DEFECT REVIEW) ...................................................... 299
6.2.14. Define User Output Device Magnification ......................................................... 300
6.2.15. Detector Signal Out Configuration (MERLINTM only) ........................................ 300
6.2.16. Drift Correction .................................................................................................. 301
6.2.17. Ext Scan Control ............................................................................................... 303
6.2.18. Image Navigation .............................................................................................. 304
6.2.19. Large Image Store Wizard ................................................................................ 305
6.2.20. Laser Finder (optional) ...................................................................................... 306
6.2.21. Long Distance Measurement ............................................................................ 306
6.2.22. Magnification Calibration ................................................................................... 307
6.2.23. Nano Motor Control ........................................................................................... 307
6.2.24. Peltier Stage ...................................................................................................... 308
6.2.25. Plasma Cleaning ............................................................................................... 309
6.2.26. Rotate/Tilt .......................................................................................................... 312
6.2.27. SEM Controls .................................................................................................... 312
6.2.28. Soft Joystick ...................................................................................................... 312
6.2.29. Specimen Current Monitor ................................................................................ 313
6.2.30. Stage Encoder Calibration ................................................................................ 314
6.2.31. Stage Horizontal Alignment ............................................................................... 314
6.2.32. Stage Limits ....................................................................................................... 314
6.2.33. Stage Nav Settings ............................................................................................ 315
6.2.34. Stage Navigation ............................................................................................... 316
6.2.35. Stage Points List ............................................................................................... 316
6.2.36. Stage Registration (licence STAGEREG) ......................................................... 317
6.2.37. Stage Scanning (licence STAGESCAN) ........................................................... 317
6.2.38. Stage Survey (licence SURVEY) ...................................................................... 318
6.2.39. User Settings ..................................................................................................... 318
6.2.40. VP Control (VP instruments only) ...................................................................... 319
6.2.41. Water Flow/Temperature ................................................................................... 320
6.2.42. Water Flow/Temperature (MERLINTMonly) ....................................................... 321
6.2.43. Windowing ......................................................................................................... 322
6.3. Assignments of toolbar icons (default toolbar) ........................................ 323
6.4. MiniBar icons ................................................................................................ 325
6.5. Annotation icons .......................................................................................... 326
6.6. Shortcuts ...................................................................................................... 329
Instruction Manual SmartSEM® V05.06 en01 IX

Contents
7. Abbreviations ............................................................................................ 331
8. Glossary .................................................................................................... 333
9. Index .......................................................................................................... 335
X Instruction Manual SmartSEM® V05.06 en01

1. Introduction
For your safety
1. Introduction
1.1. For your safety
Read the instructions in this software manual carefully. Keep the software manual nearby the
scanning electron microscope (SEM) or field emission scanning electron microscope (FESEM)
and hand it over to future owners of the
instrument.
1.1.1. Intended use
The SmartSEM® software is intended for the operation of Carl Zeiss SEMs/FESEMs such as SU-
PRA™, ULTRA, and Cross Beam® series.
The SmartSEM® software has to be run exclusively on a personal computer delivered by Carl
Zeiss.
Any other applications are not allowed.
1.2. About this manual
This software manual is designed for operators who have been trained to operate the
SEM/FESEM by an authorised expert. It is assumed that the operator is familiar with Windows®
based programs.
Operators of the SEM/FESEM must not deviate from the instructions provided in this manual.
This software manual contains the following chapters:

• 1. Introduction
Includes general safety information and typographical conventions.
• 2. Description
Describes system requirements, software elements, and operating principles of SmartSEM®.
• 3. First steps
Summarises briefly how to open the SmartSEM® user interface, to navigate and to obtain the
first image.
• 4. Operation
Provides details on software-based operation sequences including user management.
• 5. Troubleshooting
Helps to quickly solve possible problems during operation.
• 6. Summary of software functions
Lists menus and submenus, assignments of toolbar and annotation bar icons as well as short-
cuts.
• 7. Glossary
Alphabetical list and explanation of important technical terms used in this manual.
• 8. Abbreviations
• 9. Index
Instruction Manual SmartSEM® V05.06 en01 11 of 338

1. Introduction
About this manual
1.2.1. Safety instructions in this manual
The safety instructions in this manual follow a system of risk levels, that are defined as follows:
CAUTION
This safety symbol and signal word indicates a potentially hazardous situation.
Disregarding this warning MAY result in minor or moderate injury.
CAUTION
This signal word used without a safety symbol indicates a potentially hazardous situation.
Disregarding this warning MAY result in property damage.
Moreover, you will find the following type of hints:
IMPORTANT
This symbol and signal word draws your attention to important and useful
information.
12 of 338 Instruction Manual SmartSEM® V05.06 en01

1. Introduction
About this manual
1.2.2. Typographical conventions
For the description of software, the following typographical conventions are used:
Typography Meaning
Push <ENTER>. Push the ENTER key on the keyboard.
Type <key1, key2> Type key 1 first, then type key 2 on the keyboard.
Type <Ctrl + Alt + Del>. Simultaneously type CTRL key, ALT key and DEL
key on the keyboard.
Click the High voltage icon. Icons, buttons, and menus are printed in bold.
Select Aperture size from the drop down list.
Select Aperture size 30 µm from the drop-down Values to be selected are printed in italics.
list.
Set FIB Fil V Target to zero.
Text Meaning
Click... Press the left mouse button.
Right-click... Press the right mouse button.
Double-click.... Press the left mouse button twice.

1. Introduction
About this manual
1.2.3. Definition of terms
The following terms are used in this software manual:
SEM Scanning electron microscope, referred to as SEM.
FESEM Field emission scanning electron microscope, referred to as FESEM.
Carl Zeiss service engineer, Specially trained service expert, either Carl Zeiss staff or authorised
Carl Zeiss service staff service partner of Carl Zeiss.
Operator A trained person, who is assigned to operate the SEM/FESEM.
SmartSEM®Administrator Program for user management

2. Description
System requirements
2. Description
2.1. System requirements
2.1.1. Operating system
SmartSEM® V05.06 requires the operating system Windows® XP or Windows® 7.
IMPORTANT
The screenshots shown in this software manual are taken from SmartSEM® V05.06 that
runs on Windows® XP.
If SmartSEM® V05.06 is run on Windows® 7, the screenshots look slightly different.
This does not affect operation of the software.
IMPORTANT
The paths in the software are described for Windows® XP. The only difference on
Windows® 7 is that the software and its components can be found under
“Start/All Programs ...“ instead of “Start/Programs...“.
CAUTION
The integrated personal computer delivered with the SEM/FESEM should mainly be used
to control the SEM/FESEM and to archive images, because the installation of additional
software programs might cause problems.
Before installing additional software programs contact your local Carl Zeiss service engi-
neer for his/her recommendation.
2.1.2. Dongles
To operate the software, a SmartSEM® dongle has to be installed.

For using the optional drift correction licence (DRIFT-CORR), an additional dongle
(called MIL dongle) is required.
IMPORTANT
If a dongle is lost, contact your local Carl Zeiss service engineer to order one.
Microscope type and serial number have to be mentioned in the order.
2.2. Installation
The SmartSEM® software is pre-installed on your SEM/FESEM by the factory.

For possible updates or upgrades or licence installations contact your local Carl Zeiss service en-
gineer for more information.

2. Description
SmartSEM® program suite
2.3. SmartSEM® program suite
The fundamental part of the SmartSEM® program suite is the EM server, which implements the
internal communication between control software and microscope hardware.
Besides EM Server, the SmartSEM® program suite includes several programs and utilities.
Program/Utility Function Remarks
Select Start/Programs/...
ChamberScope Allows to show the chamberscope Option, requires particular

...SmartSEM image and the detector image at the hardware.
same time
FTP Image Archiving For transferring data via FTP Requires REMARCH licence
OptiProbe Calibration Calibration of OptiProbe after cathode

replacement or realigning of the elec-
tron optical column
ReadMe Important information on the current

installed version
RemCon32 Serial interface for remote operation Requires REMCON licence.

via RS232 (e.g. for EDX)
SampleHolderGallery Module to inspect the dimensions of

all possible sample holders as well as
setting the dimensions of the custom
sample holders
SEM Drift Correction Compensates for the drift of the speci- Requires DRIFT-CORR
men by using a reference image and licence.
by controlling the beam shift
Slideshow speed Adjustment of slideshow speed

setting
SmartSEM Administrator User management and instrument

configuration
SmartSEM User Interface Graphical user interface of

SmartSEM®
SmartSEM User Allows recording of important informa-

Accounting tion during individual working sessions
Release Notes Overview on all SmartSEM® versions

including new developments and spe-
cific details
Table 2.1: Overview of the SmartSEM® program suite

2. Description
...SmartSEM Calibration Wizard Service activities For Carl Zeiss service staff
Service only
Gun Monitor Utility for monitoring important para- Refer to section 4.3.8.
meters of the SEM/FESEM.
GUN Service Service activities For Carl Zeiss service staff

only
Piezo Configurator Service activities For Carl Zeiss service staff

only
Service Centre Provides an overview of the state of

the SEM/FESEM
Smart Stage Mapping Service activities For Carl Zeiss service staff
only
Stage Administrator Service activities For Carl Zeiss service staff

only
Upgrade Scangen Service activities For Carl Zeiss service staff

Firmware only
Upgrade Server Database Service activities For Carl Zeiss service staff
only
SmartBackup Tool Utility for backing up configuration and Refer to section 4.12.
calibration data.
Merlin Alignment Wizard Service activities For Carl Zeiss service staff
only
Merlin Database Wizard Service activities For Carl Zeiss service staff
only
Online Help Instructions how to use the applica- Requires the licence Smart-
...SmartStitch tion. Stitch.
(if installed)
SmartStitch Image Stitch- Opens the SmartStitch user interface.
ing Application
Uninstall SmartStitch Removes the application from the PC.
User Documentation Instructions how to use the applica-

tion.

2. Description
...Smart3D Smart3D Opens the Smart3D user interface. Requires particular soft- and
(if installed) hardware.
Smart3D Help Instructions how to use the applica-
tion.
Uninstall Smart3D Removes the application from the PC.

2. Description
Available licences
2.4. Available licences
Software licences are used to enable specific functionality in the SmartSEM® software.
Some licences are provided as standard with a specific model of SEM/FESEM, others are pur-
chased as options. When the SEM/FESEM is delivered, the standard and the additionally pur-
chased licences are already installed.
Licence Sales code Part no. Explanation
- IA - Allows image analysis operations
- QUAD - Enables quad mode on MERLINTM.
- HIGH_KV - License introduced for SUPRA 25 to allow 30 kV

operation
16 Bit TIFF TIFF16 348224-6052 Enables to save TIFF images with a grey value depth /
grey level depth of 16 bit.
3DBSD 3DBSD 351434-6116 Licence for 3DSM
Adjustable Reduced REDUCED 350076-0372 Allows using a scan window with variable size and
Raster position, especially recommended for the adjustment
of parameters such as focus or stigmator.
Advanced Measure- MEASA 348224-6011 Further measuring possibilities such as measuring of

ment rectangles, inserting horizontal/vertical measuring
lines.
Analytical I/F Particle PARTICLE 348224-6032 Specific software for automatic particle analysis.
Scan Application Requires particular hardware.
API (Application Pro- STDAPI 348224-6036 Allows SmartSEM® to be controlled via external pro-
gramming Interface) grams. For example 3D EDS software uses this
functionality
AUTO_CAL AUTO_CAL 348224-6085 AUTO_CAL
AVI Capture AVI 348224-6056 Enables capture of image sequences and storage in
an AVI file.
Cell Counting Software CELL- 348224-6078 Allows counting of cell arrays.

COUNTING Requires particular hardware.
Centre Feature/Stage CENTRE 348224-6005 Enables the point centring (Centre Point) and feature
Map centring (Centre Feature) functions. Enables the func-
tion "stage overview map" (Stage Map).
Colour Mode COLOUR- 348224-6074 Enables functionality that converts the signal from dif-
MODE ferent signal sources in real time and displays it live in
false colours without losing important information.
Compucentric Stage COMPU 348224-6030 Compucentric software enabling tilt/rotation-eucentric

Software control and horizontal alignment of a non-eucentric
stage.
Customer Calibration CUSTOMER_C 351434-6133 Allows the user to change service calibration
Privilege ALIB_PRIV parameters.
Table 2.2: Available software licences

2. Description
Available licences
Cut & Paste CLIP 350076-0370 Enables the user to copy and insert SEM images to
and from the buffer store.
Defect Review DEFECT- 351434-6024 Defect Review is used to find defects on a wafer or a
REVIEW mask based on the results from KLA Tencor results
file. The defect review dialog allows the user to open a
wafer defect file (.rff/.001) and view the defect list (with
associated images) and file header details.
Requires: Licence STAGEREG 348224-6029
Useful: Licence CENTRE 348224-6005
Depth Mode DEPTH_MODE 348224-6084 Enables higher depth of field at lower resolution.
Different levels of relief-like specimens with height var-
iations can be in focus at the same time.
Drift Correction DRIFT- 348224-6058 Image analysis software to compensate for image drift
CORR by beam shift control.
Requires additional hardware.
Dual Channel DUAL- 348224-6062 Enables the display of two different detector signals in
CHANNEL different SmartSEM® windows.
Dual Image DUAL IMAGE 348224-6047 Dual image - Win 2k uniplinth only.
Dual Magnification DUALMAG 348224-6003 Enables a user defined area on the left hand half of a
split screen display to be zoomed from 1x to 10x.
Images from different detectors can be displayed at
the different magnifications.
Dynamic Focus DYNFOCUS 350076-0364 Enables a dynamic adaptation of the focus to tilted
specimen surfaces during beam passage.
Extended Voltage EXVOLTS 348224-6042 Acceleration voltage range maximum is set to 40 kV

Range (without this licence only max. 20 kV can be set).
Field Mode FIELD_MODE 350700-0743 Ability to select field mode (wide field of view) on EVO
systems
Fisheye FISHEYE 348224-6080 Enables fisheye image of sample holder and interior of
the specimen chamber.
FTP Remote Archiving REMARCH 348224-6038 Enables to send files to a FTP server or network
printer.
Graticule GRATICULE 350076-0379 Allows display of a grid on the screen with a line dis-
tance between 50 and 512.
High Current Mode HIGH- 348224-6048 Special control of the electron optics to increase the
CURRENT specimen current.
Not available for SUPRA™ 25.
Image Maths IMMATH 348224-6013 Allows mathematic manipulation of the content of the
image memory, e.g. by using Kernel functions, by
adding or subtracting images or by detecting grey
levels.
Image stitching licence IMAGESTITCH 351434-6113 SmartStitch, standalone application for producing tiled
images or montages from a set of individual over-
palling images captured via SmartSEM®.

2. Description
Available licences
Input Gamma GAMMALUT 348224-6009 Release of the Input LUT function to individually adjust
the characteristic input line of a detector.
Input Signal Invert INVERT 350076-0367 Enables to invert of the signal using Input-LUT.
Knights Camelot KNIGHTS 351434-6043 Knights Camelot software is a CAD navigation tool for
Integration CAMELOT locating specific features on a semiconductor die. It
works by registering the sample with the design of the
die to allow the CAD image and SEM images to be
synchronised to the same field of view. It is also possi-
ble to overlay the image with parts of the design.
Large Beamshift LARGE-BEAM- 348224-6072 Allows working with an expanded beam shift (+/-
SHIFT 100 µm in X and Y).
Requires particular hardware.
Low Voltage Working LOWVOLTS 348224- 6041 Acceleration voltage range minimum is set to 0.1 kV
(without this licence only 0.5 kV can be set).
OptiProbe OPTIPROBE 348224-6079 Allows automatic setting of the probe current.

Piezo Integration PIEZO- 348224-6075 Allows the integration of a Piezo stage.

INTEGRATION
Pivot Point Calibration PIVOT_POINT_ 354734-6108 Allows user to ise software thad does a very precise
CAL mag calibration for forensic work.
Plasma Cleaning PLASMA 351434-6177 Enables software control of the Plasma Cleaner.
Remote SEM REMOTESEM 348224-6057 Remote operation of the microscope is possible using
the Windows XP Remote Desktop Connection feature.
RS232 Remote Control REMCON 348224-6014 Allows remote operation and interrogation of the SEM/
FESEM by serial communication using RS 232.
Scan Rate Expansion SCANEXP 350076-0358 Makes fifteen different scan speeds available (without
this licence only three are available).
Scan Rotation SCANROT 350076-0359 Allows electronic rotation of the image by changing the
scan direction.
Signal Mixing SIGMIX 350076-0350 Allows continued mixing of two detector signals in the
range between 0 and 100%.
SmartBrowse SMART- 351434-6144 The additional software SmartBrowse allows the user
BROWSE to sort images by various parameters, such as stage
position or detector used.
Smart Stage Mapping SMART- 348224-6081 Calibration routine that optimises the stage accuracy.
STAGE-
MAPPING
SmartImage SMARTIMAGE 348224-6077 Enables the SmartImage image processing dialog

Enhancement (noise reduction and contrast enhancement).
SmartSEM Report REPORT_GEN 351434-6092 Enables an Office 2007 add in ribbon that imports
Generator ERATOR CZTIFF images and can read the tags so users can
create reports. The CZTIFF images can be created by
previous software versions.

2. Description
Available licences
Split SPLIT 350076-0360 Split screen
Spot Mode SPOT 350076-0383 Spot positioning of the electron beam on a given spot
of the specimen.
Stage Coordinate store STAGECO 348224-6006 Allows saving stage coordinates together with the
and recall magnification and the working distances. The stage
can automatically be driven to these positions.
Stage Fine Step FINESTEP 348224-6050 Allows more precise movement of the stage.
Stage Navigator NAVIGATOR 351434-6109 Allows installation of the StageNavigator.
Stage Registration STAGEREG 348224-6029 Defines user specific coordinate systems for the speci-
men stage.
Stage Registration REGISTER - Stage registration (allowing users to define specimen

coordinate systems for navigation.
Stage Scan STAGESCAN 348224-6007 Allows analysis of a sample range in the form of a
series of exactly defined regularly dispersed image
fields.
Stage Survey Mode SURVEY 348224-6040 Magnifications and working distances for two different
working modes can be started automatically.
Static Stereo STATIC- 348224-6076 -

STEREO
Tilt Compensation TILTCOMP 350076-0362 Allows correction of perspective foreshortening occur-

ring when scanning tilted specimens.
User Accounting ACCOUNT 348224-6031 Automatic registration of special parameters during a

working session to enable the instrument administrator
to trace who worked on the SEM/FESEM. For each
user, the number of saved TIFF images, output photos
and prints is saved.
User Align USERALIGN 351434-6022 The user align function keeps track of which alignment
values each user has utilised for different operating
conditions.
When these conditions are next used, the previous
alignment values will be reloaded. The operation of
user align requires no extra involvement of the user,
once the function has been enabled on the SEM condi-
tions page of the user preferences dialog.

2. Description
Principle of operation
2.5. Principle of operation
The SEM/FESEM is operated by the SmartSEM® software: All commands, settings and functions
necessary for the handling of the SEM/FESEM are controlled by the SmartSEM® software using
keyboard and/or mouse.
The motorised stage can be operated by the dual joystick or by the software.
In most cases, the SmartSEM® user interface offers more than one possibility to run a function.
For instance, to switch on the EHT you can use
• the menu bar or
• the status bar or
• the MiniBar or
• the Gun tab in the SEM Controls panel.
This allows the user to operate the SmartSEM® software according to his/her individual pre-
ferences.

2. Description
SmartSEM® user interface
2.6. SmartSEM® user interface
The SmartSEM® software is operated via a graphical user interface that can be used intuitively.
radio button
caption bar icon panel
menu bar toolbar tab checkbox
panel configuration bar

MiniBar
annotation bar data zone
navigation
box arrow button
status bar
image area mouse assignment slider

2. Description
SmartSEM® user interface
Menu bar When left-clicking on a menu, the pull-down menu shows the different submenus.
User toolbar Most icons in the toolbar are assigned twice. The different functions and parameters can be
activated by pressing the left or the middle mouse button. When moving the cursor across the
icon, tool tips show the different assignments.
MiniBar The MiniBar provides quick access to recently used dialogs and to the recipe management.
Status bar The status bar shows the active mouse assignment:
• Left: left mouse button
• Mid: middle mouse button
Moreover, it shows the Coarse/Fine toggle button and allows access to a pop-up menu for quick
control of important SEM parameters.
Annotation bar The annotation bar allows putting additional information on the SEM image. Text, SEM parameter
data, and even bitmaps (like logos etc.) can easily be added to the image. Moreover, it provides
several measurement functions.
Data zone The data zone contains important information on the recording parameters of the current image.
Each user can design the data zone as desired and store it together with the image.
Panel Confi- The panel configuration bar allows accessing to several functions which are listed alphabetically.
guration Bar
Moreover, the following symbols may be displayed in the user interface:
Anchor symbol The anchor symbol is displayed when using func-

tions that divide the image area into different
zones, e.g. the functions Split, Windowing, or Dual
Magnification.
Image modifications are applied only to the zone
marked with the green anchor symbol.
The red and green anchor symbol indicates that

image modifications are applied to both zones
simultaneously.

2. Description
User access levels
Red dot A red dot displayed in the lower right corner of the
image area indicates that the image has been fro-
zen.
Blue dot A blue dot displayed in the lower right corner of

the image area indicates that the image has been
saved.
Red triangle A red triangle displayed in the lower right corner of

the image area indicates that the image has been
saved by using the Image Capture mode.
2.7. User access levels
SmartSEM® distinguishes three user access levels. The user access level defines which para-
meters are displayed for selection purposes (e.g. in the status window selection, annotation para-
meter selection).
• Novice
Displays only those items assigned as novice category. These include most frequently used
parameters.
• Expert
Displays items assigned as novice and expert category. These include parameters useful for
advanced operators.
• Service/Full
Displays all items, also including infrequently uses items and calibrations.
The user profile is the collection of privileges and settings associated with the username.

3. First steps
Switching on the SEM/FESEM
3. First steps
At a glance This chapter contains information about:
• Switching on the SEM/FESEM

• Starting the SmartSEM® user interface
• Finding your way in the SmartSEM® software
• Obtaining the first image
• Using the help functions
• Closing the SmartSEM® software
3.1. Switching on the SEM/FESEM
If the SEM/FESEM is in OFF mode:

a Lift the protective lid of the yellow
STANDBY button (1) that is located at the
front of the plinth.
b Press the yellow STANDBY button (1).
Now, the SEM/FESEM is in STANDBY mode.
1 To switch on the SEM/FESEM, press the

green ON button (2) that is located at the front
of the plinth.

3. First steps
Starting the SmartSEM® user interface
3.2. Starting the SmartSEM® user interface
Prerequisites:
• The SEM/FESEM is switched on.
• The Windows® operating system has been loaded.
1 Double-click the Carl Zeiss SmartSEM icon.
Alternatively, select Start/Programs/Smart-

SEM/SmartSEM User Interface.
The EM Server opens, loading various drivers.

The function of the EM Server is to implement the
internal communication between the SmartSEM®
software and hardware of the SEM/FESEM.
The EM Server Log On dialog appears.

2 Enter your username and password.
3 Confirm by clicking on OK.

3. First steps
Starting the SmartSEM® user interface
The SmartSEM® user interface opens.
The EM Server is minimised to a small element (icon) on the right side of the Windows® task bar.
The SmartSEM® software is ready to operate the SEM/FESEM.

3. First steps
Finding your way in the user interface
3.3. Finding your way in the user interface
3.3.1. Showing or hiding toolbars
Several toolbars such as user toolbar, status bar, and annotation bar are available for easy
access to the SmartSEM® functions.
1 Select View/Toolbars.
Alternatively, type <Ctrl+B>.
The Toolbar Views panel is shown.
2 If you wish to show a toolbar, tick the respective checkbox.

3 To change the tooltip features of the user toolbar, select the respective radio button on the
right hand side of the panel.

3. First steps
3.3.2. Showing or hiding the data zone
The data zone is a special group of annotation objects which are used to display current para-
meters. You can also include a µ-marker to show the base magnification.
1 Select View/Data Zone/Show Data Zone from the menu.

A tick is shown to indicate that the function is activated.
Alternatively, type <Ctrl+D> to toggle the data zone.
3.3.3. Showing a full screen image
To take advantage of the full monitor size to display the microscopic image, show a full screen
image.
1 Select View/Toggle Full Screen Image from the menu.

Alternatively, type <Shift + F3>.
To undo the function, type <Shift + F3>.

3. First steps
3.3.4. Docking panels
It is possible to dock various panels onto the main window. The purpose of the docking panel is
to keep the area of the image completely clear, as the docking panel is outside the main window.
1 To show the docking panel select View/Tool-

bars from the menu.
2 Tick the Docking Panel checkbox.
The docking panel is shown on the right hand side

of the image area.
3 To move the docking panel to the left hand side, pick up the panel by clicking on the title bar
and drag it to the other side of image area.

3. First steps
4 To stick a control panel to the docking panel, click the title bar of the control panel and drag
it to the docking panel.
The panel becomes integrated into the docking panel.
You can stick several control panels to the dock-

ing panel.
5 To minimise a panel, click the arrow

button (1) in the title bar.

3. First steps
6 To hide the docking panel untick the Docking Panel checkbox.
The docking panel is hidden.
3.3.5. Opening the Panel Configuration Bar
1 Select Tools/Goto Panel from the menu.
Alternatively, click the arrow button at the

side of the image area.
The Panel Configuration Bar opens showing an alphabeti-

cal list of functions.
2 To select a function, double-click it.

3. First steps
Obtaining the first image
3.4. Obtaining the first image
The following section summarizes basic sequences to quickly obtain an image using the SE2 de-
tector. To simplify the procedure, the method described mainly uses SEM Controls panel and
status bar functions.
Dependent on your type of SEM/FESEM (Standard vacuum system, VP vacuum system, Cross
Beam® series), the SmartSEM®user interface may differ slightly.
Prerequisite:
• SmartSEM® software has been started and is ready to control the SEM/FESEM.
Parts required No.
Allen wrench, 1.5 mm delivered with the SEM/

FESEM
Stub delivered with the SEM/

FESEM
Tweezers for specimen delivered with the SEM/

FESEM
Specimen holder delivered with the SEM/

FESEM
If necessary: carbon tape, conductive carbon, adhesive metal tape or -

similar
Appropriate specimen (with conducting properties e.g. gold on carbon) -
Lint-free gloves -
At a glance The complete sequence includes:

• Preparing the sample holder
• Loading the specimen chamber
• Locating the specimen
• Switching on the gun
• Switching on the EHT
• Generating an image
• Optimising the image
• Saving the image

3. First steps
3.4.1. Preparing the sample holder
IMPORTANT
Contamination caused by fingerprints can lead to vacuum deterioration or prolonged
pumping times. Always wear lint-free gloves when touching specimen, sample holder or
stage.
1 Attach the specimen to the stub by using con-

ductive carbon, adhesive metal or carbon tape
etc.
Ensure that the specimen area to be analysed
is in proper contact with the stub.
2 Use the tweezers to insert the stub into the

sample holder.
3 Properly fix the stub to the sample holder.

Use the Allen wrench to tighten the location
screw.

3. First steps
3.4.2. Loading the specimen chamber
1 Click the ChamberScope icon in the

toolbar.
A TV view inside the specimen chamber is shown.
CAUTION
Risk of damaging the objective lens and/or your specimen
Ensure not to hit the objective lens while driving the stage. Change to TV mode to observe
the moving stage.
2 Select Tools/Goto Control Panel from the

menu.
The SEM Controls panel opens.

3. First steps
3 Go to the Vacuum tab.

4 To ventilate the specimen chamber, click
Vent.
A message appears asking: ’Are you sure you

want to vent?’.
5 Confirm by clicking on Yes.
The specimen chamber is filled with gaseous

nitrogen.
CAUTION
Suffocation hazard due to lack of oxygen, since the specimen chamber is ventilated with
nitrogen.
After the specimen exchange, keep the chamber door open as short as possible.
Avoid inhaling the air from within the specimen chamber.
6 Take hold of the door handle and slowly open

the chamber door.
IMPORTANT
Contamination caused by fingerprints can lead
to vacuum deterioration or prolonged pumping
times.
Always wear lint-free gloves when touching
specimen, sample holder or stage. Keep the
chamber door open as short as possible.

3. First steps
All sample holders are equipped with a dovetail so

that the position of the sample holder is exactly
defined.
7 Mount the sample holder:

a Ensure that you place the dovetail in the
correct orientation onto the holding device
on the specimen stage.
b Make sure that the flat side of the dovetail
of the sample holder is flush with the
milled edge of the stage.
8 Look into the specimen chamber to ensure

that the specimen cannot hit any components
when it is introduced into the specimen cham-
ber.
CAUTION
Pinch hazard when closing the chamber door
Use the door handle to close the chamber door. Ensure not to get your fingers caught in
the chamber door gap.
9 Carefully close the chamber door.

3. First steps
10 In the SEM Controls panel, click Pump.
The vacuum status messages show the current

vacuum levels achieved.

3. First steps
3.4.3. Locating the specimen
1 In TV mode (ChamberScope), look into the specimen chamber.
CAUTION
Risk of damaging the objective lens and/or your specimen.
Ensure not to hit the objective lens while driving the stage. Change to TV mode to observe
the moving stage.
2 Move the specimen by using the dual joystick (optional) or by calling the Soft Joystick via
Tools/Goto Panel/Soft Joystick.
3 Carefully move the specimen closer to the objective lens.

The distance between objective lens and specimen surface should be less than about
10 mm.

3. First steps
3.4.4. Switching on the gun
1 In the Vacuum tab:

Check that EHT Vac ready=Yes is indicated.
2 In the status bar, click Gun.

3 Select Gun On from the pop-up menu.
The gun is being run up.

3. First steps
3.4.5. Switching on the EHT
’EHT’ stands for acceleration voltage. This voltage has to be applied to the gun in order to make
it emit electrons.
1 Watch the vacuum status messages on the

Vacuum tab of the SEM Controls panel.
When the required vacuum has been reached you

will see the message ’Vac Status = Ready’.
2 Go to the Gun tab.
3 Set the acceleration voltage:

a Double-click in the EHT= field.
b Enter the desired acceleration voltage in

the EHT Target field, e.g. 10 kV.
c Confirm by clicking on OK.

3. First steps
4 Switch on the EHT:

a Click EHT in the status bar.
b Select EHT On from the pop-up menu.
The EHT is running up to 10 kV.
The status bar buttons are merged together, and

the All: button appears.
Now the electron beam is on.

3. First steps
3.4.6. Generating an image
1 Go to the Detectors tab.

2 Select SE2 from the Detectors drop-down
list.
It is recommended that you select the SE2

detector to obtain the first image, as this de-
tector provides a good signal-to-noise ratio
even at large working distances.
3 Go to the Scanning tab.

Select a fast scan speed, e.g.
Scan Speed = 1 from the drop-down list.
The lower the scan speed number, the faster

the scan of the specimen by the electron
beam. Scan Speed = 1 allows you to get an
image quickly.

3. First steps
4 Set a low magnification e.g. Mag = 500x:

a Click the Magnification/Focus icon in the
toolbar.
b Press the left mouse button and drag the

mouse to adjust the magnification of
500 x.
The current magnification is indicated in the

status bar.
5 Set the focus:

a Press the middle mouse button and drag
the mouse to focus.
The current working distance (WD) is indicated in

the status bar.
6 Adjust contrast and brightness.

a Go to the Detectors tab.
b Use the Brightness and Contrast sliders.
7 Select a detail on the specimen surface.
Focus the detail.
8 Adjust contrast and brightness again.

3. First steps
3.4.7. Optimising the image
1 Set Coarse by toggling the Coarse/Fine

button in the status bar.
2 Step by step, set a high magnification,

e.g. Mag 50.000 x.
Focus in between.
When selecting high magnifications it is

recommended that you move the specimen
by using the beamshift function instead of driving
the stage.
3 Use the Beam shift function:

a Go to the Apertures tab.
b Click Beam Shift.
c Use the slider or the red marker to shift the
beam.
4 Click the Reduced Raster icon.

3. First steps
A small scan frame is shown.

The image outside the scan frame is frozen. Size and position of the scan frame can be
changed by dragging and dropping.
5 Focus the image in the reduced raster.
6 Align the aperture:

a In the Apertures tab, tick the Focus
Wobble checkbox.
The Focus Wobble is a function that sweeps the

focus of the objective lens backwards and forwards
through the focus on the specimen plane. If the
aperture is slightly misaligned, a lateral shift can be
observed.
Intensity of wobble can be adjusted by using
the Wobble Amplitude scroll bar.
Wobble speed can be accelerated by ticking
the Wobble Fast checkbox.
b Click Aperture Align.

Use the left and right slider of the Aperture
Align box until there is no movement of the
detail in X and Y direction.
The specimen detail should just be
pulsating without shifting.
c Untick the Focus Wobble checkbox.

3. First steps
7 In the Scanning tab, set Scan Speed = 7.
8 Bring the image into focus.

9 Toggle to Fine in the status bar.
Use Coarse and Fine mode of adjustment
where appropriate.
10 Correct astigmatism:
a Select a detail (e.g. a mark or an edge) on
the specimen surface.
b Click the Reduced Raster icon.
Ensure the selected detail is in the raster.

3. First steps
c In the Apertures tab:

Click Stigmation.
d In the Stigmation box, use the arrow but-

tons or the left and right slider to obtain the
sharpest possible image.
11 Deactivate the reduced raster.

12 In order to reduce image noise select, a
slower scan speed, e.g. scan speed 6 to 8.

3. First steps
3.4.8. Saving the image
1 Stop the scan:

a Go to the Scanning tab.
b In the Noise Reduction section, select

Freeze on = End Frame from the drop-
down menu.
c Click Freeze.
A red dot at the right bottom of the image area

indicates that the image is frozen.
2 Select File/Save Image from the menu.
3 Enter a path and a file name.

4 Confirm by clicking on Save ....tif.

3. First steps
To continue imaging, unfreeze the image by

selecting Image/Unfreeze from the menu.
Alternatively, you can click Unfreeze in the

Scanning tab.
To finish your work session, switch off the EHT:

a In the status bar, click All:.
b Select EHT Off from the pop-up menu.
It is recommended that you leave the gun on

during the working week. This should help to
optimise lifetime of the filament.

3. First steps
Using the help functions
3.5. Using the help functions
The SmartSEM® user interface offers a multitude of help texts containing information on the
operation of the SEM/FESEM, the optimization of the images and the handling of accessory
options.
3.5.1. Calling the SmartSEM® help
1 Press <F1>.
Alternatively, select Help/SmartSEM help from the menu.
The SmartSEM® help start window opens.

If menus are opened in the SmartSEM® user interface, pressing <F1> will open the help text for
the respective menu. This allows explaining the menu while the SEM/FESEM is being operated.
3.5.1.1. Printing help texts

1 Click the printer icon in the help window.
If a printer is installed, the help text is printed.
3.5.1.2. Bringing help texts to the foreground

1 Select Help/Help Always On Top from the menu.
The displayed help texts remain in the foreground.

3. First steps
3.5.2. Calling the context-sensitive help
1 Press <SHIFT+F1>.
Alternatively, select Help/What’s This from
the menu.
The mouse cursor is equipped with a question

mark.
2 Click an area of interest on the screen.
The help text is shown.

3 To disable the context-sensitive help, press
<ESC>.
3.5.3. Searching for a topic
1 Select Help/Search from the menu.

2 Click the Search tab.
3 Search for the desired topic.

3. First steps
3.5.4. Using the step-by-step guides
The step-by-step guides provide quick information on important operation sequences.
3.5.4.1. Getting started

1 Select Help/Getting started from the menu.
2 Click the topic of interest.
3.5.4.2. Frequently used operation sequences

1 Select Help/How To from the menu.
2 Click the topic of interest.

3. First steps
3.5.5. Calling the shortcuts help
Many functions and menus which are often used in the SmartSEM® user interface can also be
opened using the keyboard. A list of shortcuts (key combinations) can be displayed in the Smart-
SEM® help.
1 Press < F9>.
Alternatively, select Help/Keys help from the menu.
Refer to section 6.6.

3. First steps
3.5.6. Showing information about SmartSEM®
3.5.6.1. Version history

The Release Notes summarise important information about the software version history. New
functions, bug fixes and special features of the different versions are explained.
1 Select Help/Release Notes from the menu.
3.5.6.2. About SmartSEM®

1 Select Help/About SmartSEM from the
menu.

3. First steps
Closing the SmartSEM® software
3.6. Closing the SmartSEM® software
3.6.1. Logging off
1 Select File/Log Off from the menu.
A window appears asking for confirmation to close

the session.
The electron-optical parameters are filed in a

macro in the individual user directory.
The EM Server remains active.
3.6.2. Exiting
1 Select File/Exit from the menu.
A window appears asking for confirmation to close

the session.
The electron-optical parameters are filed in a

macro in the individual user directory.

4. Operation
Controlling the vacuum
4. Operation
4.1. Controlling the vacuum
4.1.1. Checking the current vacuum status
Because a good vacuum is essential for the operation of the SEM/FESEM it is recommended
keeping always an eye on the vacuum in specimen chamber and gun head.

menu.
2 Go to the Vacuum tab.
Alternatively:
Select Vacuum/Vacuum Status from the
menu.
Alternatively:
Type <CTRL+SHIFT+V>.
The System Vacuum is the vacuum in the speci-

men chamber.
The Gun Vacuum is the ultra high vacuum in the
gun head area.
The value of the Gun Vacuum should be less than
about 5 x 10-9 mbar.
To indicate another pressure unit (mbar, Pa, Torr) click in the System Vacuum or the Gun
Vacuum field.
VP If you work with a VP instrument, the Vacuum tab

instruments looks slightly different.

4. Operation
Moreover, there is an additional tab: The Gun

Vacuum tab.
1 To show the gun vacuum, go to the Gun
Vacuum tab.

4. Operation
4.1.2. Ventilating the specimen chamber
In order to be able to open the specimen chamber for specimen exchange, the vacuum has to be
broken in a controlled manner. This is done by filling the specimen chamber with gaseous nitro-
gen.
1 In the toolbar, click the Specimen Change

icon.
The EHT is switched off.

The specimen chamber is ventilated.
Alternatively:
1 Go to the Gun tab and select EHT Off
from the drop-down list.
2 In the Vacuum tab, click Vent.

4. Operation
Alternatively:
1 In the status bar, click All:.
2 Select EHT Off from the pop-up menu.
The Vac button appears.
a Click Vac:.
b Select Vent.
Alternatively:
1 In the MiniBar, click Start.
2 Select EHT Off.
3 Select Start/Vent from the MiniBar.

4. Operation
4.1.3. Evacuating the specimen chamber
To continue operation after a specimen exchange, the specimen chamber has to be evacuated
again.
1 In the toolbar, click Specimen Change.

2 Confirm the message ’Press OK To Pump’.
Alternatively:
1 In the Vacuum tab, click Pump.
Alternatively:
1 In the status bar, click Vac:.
2 Select Pump from the pop-up menu.
Alternatively:
1 Select Start/Pump from the MiniBar.

4. Operation
4.1.4. Working with variable pressure (VP instruments only)
Working with variable pressure (VP) allows you to analyse and image non-conducting, strongly
gassing or humid specimens. This is made possible by a special pumping system, which allows
setting partial pressures of 1 to 133 Pa in the specimen chamber, while preserving the ultra high
vacuum in gun area and beam path.
Using VP mode is only possible with a VP type SEM/FESEM.
4.1.4.1. Switching to variable pressure (VP) mode

1 Go to the VP Control tab of the SEM Con-
trolss panel.
2 Select a VP target by using the slider.
Alternatively:
Double-click the VP Target field and enter the
pressure value.
3 Click Go To VP.
IMPORTANT
In VP mode, InLens detector and SE2 detector cannot be used.
Instead, backscattered electron detectors or specially designed VPSE detectors should be
selected.

4. Operation
4.1.4.2. Returning to high vacuum (HV) mode
1 Click Go To HV.
The vacuum in the specimen chamber is

reduced to high vacuum conditions.

4. Operation
Navigating the specimen
4.2. Navigating the specimen
4.2.1. Moving the specimen with the soft joystick
Alternatively to the dual joystick, you can navigate the specimen by using the software function
Soft joystick. This function is helpful when you wish to move a single axis without the risk of mov-
ing another axis as well.
1 Open the Panel Configuration Bar.

2 Double-click Soft Joystick.
The Soft Joystick panel opens.
3 Move the stage by using the respective sliders

or the red marker in the navigation box.
To stop the moving stage:

1 Release the slider.
To stop the moving stage immediately:

1 Type <F12>.
Alternatively:
Click Stage stop in the Stage tab of the SEM
Controlss panel.
When tilting a specimen ensure that the specimen

to be analysed is always the one next to the objec-
tive lens.
IMPORTANT
To prevent damage, a touch alarm is integrated
in the SEM/FESEM: If specimen or sample hold-
er touch chamber walls, detectors or objective
lens, the stage is stopped immediately. An audi-
ble warning and an on-screen message are
given.

4. Operation
4.2.2. Moving the specimen at high magnifications (Beam Shift)
The Beam Shift function is helpful when moving the specimen at magnifications above 100,000
x. At this magnification range it is generally difficult to exactly position an image feature by driving
the stage. Therefore, the image of the specimen can be moved by shifting the electron beam in-
stead of displacing the specimen itself.
1 Select Beam/Beam Shift from the menu.

The Beam Shift panel is shown.
Alternatively:
Select Tools/Goto Control Panel/Apertures.
2 Click Beam Shift.

3 Use the red marker in the navigation box or the sliders to position the specimen.
The left mouse button is assigned to Beam Shift X and Y. The middle mouse button keeps the
current assignment.
The electron beam can be shifted by +/- 7.5 µm in the X and Y directions.
4.2.2.1. Working with an expanded beam shift (licence: LARGE-BEAMSHIFT)

When you use different apertures sizes it might be helpful to move the image of the specimen by
means of the beam shift function instead of moving the specimen itself. For this reason the range
of the beam shift has to be enlarged.
Requires the licence LARGE-BEAMSHIFT.
1 Open the SEM status.

2 Go to the Select tab.
3 Tick the Large Beamshift checkbox.
The electron beam can be shifted by +/- 100 µm in

the X and Y directions.

4. Operation
4.2.3. Improving stage repeatability by activating the function
is employed to take up the necessary mechanical play in the stage motors, so that any absolute
stage position is always approached from the same direction, improving the repeatability of mo-
torised stage movement.
1 Go to the Stage tab of the SEM Controlss panel.

2 Right-click in the Stage tab.
A submenu opens.
3 Select /On.

4. Operation
4.2.4. Compensating for image drift by shifting the beam (licence: DRIFT
CORR)
The drift correction is a program to compensate for the drift of the specimen by using a reference
image and by controlling the beam shift. This function has two main applications:
• Improvement of the drive precision of the stage
When viewing a specific image section and driving the stage to another point, a drift is often
observed when moving back to the specific point.
• Long-term analysis
If an image section is scanned for a longer time, mechanical, thermal and electrical effects
will always cause a drift of the respective image section.
It is essential to find a striking detail of the specimen to be defined as a reference image. This
detail will be sought later on in the current image by using image analytical algorithms.
Requires the licence DRIFT CORR and the installation of the Matrox Imaging Library, which is
protected by a dongle.
1 Select Start/Programs/SmartSEM.
SEM/FESEM: Select Drift Prepare.
XB: Select SEM Drift Correction.
The Drift Correction window opens.

4. Operation
2 Click Display Rectangle.
A movable frame is shown. The image range in-

side the frame defines the reference image for the
drift correction.
3 Change position and size of the frame to
define a striking detail as reference image.
The reference image should present a good
signal-to-noise ratio.
Do not use Frame Avg, Line Avg as noise
reduction methods.
4 In order to cancel any beam shift settings,

click Zero Beam Shift.
5 If you wish to hide the frame, click
Hide Rectangle.
6 Set the following parameters:

a Drift Max. Pix. Error = Drift maximum pix-
el error
Defines the precision of the drift correction. Indicates the largest allowed pixel distance be-
tween the current image and the corrected image. If this pixel distance is exceeded, the drift
correction will not be accepted.
For most applications this parameter should be set to 1 to 4.
b Drift Max. Tries = Drift maximum tries
Defines how often the algorithm will try to compensate a possible image drift by using the
beam shift.
For most applications this parameter should be set to 5 to 15.
c Drift Min. Conf. = Drift minimum confidence
Defines the precision of the correlation between reference image and found image section.
For most applications this parameter should be set to 40% to 60%.

4. Operation
7 Click Create Reference.
A reference is acquired. In the field Sem drift

status ’Ready’ is indicated.
The button Do SEM Drift Corrn becomes
available.
8 Click Do SEM Drift Corrn.
If the drift correction was successful, ’Success’ is

indicated in the field SEM drift status .

4. Operation
4.2.5. Using fisheye mode (licence: FISHEYE)
Fisheye mode allows you to get a survey of the complete specimen chamber by providing a top
view on the sample holder at a low Z.
Requires the licence FISHEYE.

menu.
2 Go to the Aperture tab.
3 Tick the Fisheye Mode checkbox.
IMPORTANT
Since the image is deformed due to the fisheye lens effect, measurements and the exact
specification of the magnification are not possible. Therefore, a question mark is shown
next to the micron marker.

4. Operation
1 To quit Fisheye mode, untick the Fisheye mode checkbox.

2 Under TV control, carefully drive the stage to the required Z.

4. Operation
4.2.6. Using the stage navigation functions
The Stage Navigation has the following characteristics:

• Plan view of the sample holder
• Display of the specimen chamber with chamber door
• Display of the stage hard limits
• Support for all different Carl Zeiss sample holders
• Ability to zoom in to view the sample holder in great detail
Requires the licence COMPU.
IMPORTANT
This function requires the stage to be initialised.
4.2.6.1. Showing the specimen chamber schematics

1 Select Stage/Navigation from the menu.
Alternatively:
Double-click Stage Navigation in the Panel Configuration Bar.
The Stage Navigation window opens.

The top window shows the lateral view of the stage inside the specimen chamber.
The bottom window shows the plan view of the stage.

4. Operation
2 Select your type of sample holder from the Sample Holder drop-down list.
3 You can change the view:

a To zoom in, move the zoom control slider
to the right (1).
b To change the detail, use the lateral sliders
(2).
c To toggle the size of the window, click the
<< button.
4 To move the stage, double-click the sample po-

sition you wish to move under the electron
2
beam.
5 To access the stage navigation settings, click
Settings (3).
1 3

4. Operation
The Stage Nav Settings dialog opens.

4. Operation
4.2.6.2. Using the Sample Holder Gallery

The Sample Holder Gallery lets you inspect the dimensions of all possible sample holders.
Additionally, it allows setting of the dimensions of custom stage holders.
1 Select Stage/Navigation from the menu.

2 Click Settings.
3 Click Show Gallery.
4 Select the installed sample holder from the list of icons on the left.
The Is available checkbox is ticked to indicate that the selected sample holder can be
installed on the system.
5 If you use a custom sample holder:

a Select one of the custom sample holders.
b Enter the individual dimensions of your sample holder.
c Tick the Is available checkbox.

4. Operation
4.2.7. Eucentrically driving a non-eucentric stage (licence: COMPU)
This function allows rotation-eucentric and tilt-eucentric control of a non-eucentric stage by using
software.
Requires the licence COMPU.
Different calibration procedures are required before the compucentric software can be used:
• Calibration of the rotation centre of the stage
(required for rotation-eucentric control and tilt-eucentric control)
• Calibration of the distance between specimen surface and rotation centre of the tilt axis
(additionally required for tilt-eucentric control)
4.2.7.1. Calibrating the stage centre

It is a prerequisite for all compucentric functions that the centre of the stage rotation is accurately
known. This will normally only need to be performed once each time the stage is serviced. How-
ever, to achieve the ultimate accuracy it may be necessary to recalibrate the rotation centre each
time the stage is initialised.
IMPORTANT
The calibration of the rotation centre is independent of the used sample holder and the
used specimen. Therefore, this calibration can be use generally.
It is recommended that you use a single stub holder and a calibration grid or a TEM grid as spe-
cimen. The specimen must be mounted centrally on the stub.
1 Initialise the stage:

Select Stage/Stage Initialise and confirm.
3 Double-click Calibrate Stage Centre.
Alternatively:
a Go to the Stage tab of the SEM Controlss panel.

b Right-click in the background of the Stage tab.
c Select Calibrate Stage Centre.

4. Operation
The Calibrate Stage Centre dialog opens.
The last coordinates of the centre are indicated.
4 Click Next.
The stage is initialised.
After initialisation, a magnification of 30 x is auto-

matically set.
Crosshairs are displayed.
5 Select a striking feature on the specimen sur-

face, that is positioned outside the centre.
6 Move the striking feature to the centre by using
the joystick or the Centre Point function.
7 Click Next.
The stage is driven back to its initial position.
8 Click Next.
The stage rotates by 180°.
During stage rotation observe the striking fea-
ture on the specimen in order to be able to
relocate it after rotation.

4. Operation
9 Again, move the striking feature to the centre by

using joystick or the Centre Point function.
10 Confirm by clicking on Next.
The software has now calculated the new rotation

centre and indicates the values for X and Y.
11 Click Next.
The stage returns to the initial position.
12 Set the next higher magnification (200 x).

13 Repeat the calibration procedure (steps 5 to
11).
14 Repeat the procedure for the magnifications
500 x, 1500 x and 2000 x.
15 After having calibrated the position with Mag =

2000 x, click OK.
This will finish the calibration routine.
The calculated calibration values are used for stage

navigation and eucentric movement.

4. Operation
4.2.7.2. Calibrating the compucentric height

If you want to tilt the specimen eucentrically or if you want to rotate a tilted specimen eucentrically,
the software has to accurately know the distance between rotation centre of the tilt axis and spec-
imen surface.
This is managed by the additional calibration of the compucentric height.
IMPORTANT
As the calibrated distance depends on specimen and sample holder, this routine must be
performed separately for each specimen and sample holder.

2 Double-click Compucentric Height.
3 Follow the steps on the panel:

a Centre a feature and click Read.
b Tilt the stage.
c Centre the feature again and click
Calculate.

4. Operation
4.2.7.3. Activating the compucentric software functions

Prerequisite: The compucentric software has been calibrated properly. Refer to section 4.2.7.1.
and section 4.2.7.2.
IMPORTANT
The more precisely and thoroughly the calibration is done, the more precisely the stage
can be driven by the compucentric software.
IMPORTANT
If only the stage centre has been calibrated, only rotation-eucentric control in the horizon-
tal line (Tilt = 0) will be possible.
1 Select Tools/Goto Control Panel.

2 Go to the Stage tab.
3 In the drop-down menu Compuc. Mode,

select the desired mode:
Off: Disables the compucentric software
Tilt: Enables tilt-eucentric control
Rotate: Enables rotation-eucentric control
Tilt & Rot: Rotation- and tilt-eucentric control
CAUTION
Danger of malfunction of the stage, when using the joystick.
After activating the compucentric software functions, only drive the stage to absolute or
relative coordinates. To do so, use the ’Go To’ fields or the ’Delta’ buttons.

4. Operation
4.2.7.4. Stage Horizontal Alignment

This function allows you to automatically move an image feature in the horizontal line.
The stage centre must be calibrated.
A wizard is used to drive the stage such that a linear feature on the specimen, identified by two
points, is horizontal with the second of the two points visible on screen.

2 Double-click Stage Horizontal Alignment.
The Stage Horizontal Alignment wizard opens.

Crosshairs are displayed.
3 Centre the first reference point. To do so, use

the joystick or the Centre point function.
4 Click Next.
5 Centre the second reference point.

6 Click Next.
7 Click Finish.

4. Operation
4.2.8. Saving and recalling stage coordinates (licence: STAGECO)
This function offers the possibility to save a list of stage positions together with magnification and
working distance. Thus, the user can recall these positions easily.
Requires the licence STAGECO.
4.2.8.1. Saving and editing stage coordinates

1 Select Stage/Store/Recall from the menu.
2 To enter the current stage position, click
on Add.
3 Enter a name and confirm.
The stage position is displayed on the Stage Position List.
4 To edit a stage position, mark the position and click Edit.

5 To delete a stage position, mark the position and click Delete.
4.2.8.2. Recalling stage coordinates

1 To move the stage to a stored position:
a Select the position.
b Click On Goto.
To cancel the last stage move, click Undo Stage Goto.

4. Operation
4.2.9. Centering a spot or an area (licence: CENTRE)
This function offers the following possibilities:

• Point:
Allows marking a spot in the image which is then automatically moved to the centre of the
image area.
• Feature:
Allows selecting a feature or area in the image which is automatically centered and magnified
so that the selected feature fills the complete image area.
Requires the licence CENTRE.
4.2.9.1. Using the Centre Point function

1 Select Stage/Centre Point from the menu.
Alternatively, type <Ctrl + Tab>.
The mouse cursor is displayed as a cross.

2 Place the cross on the interesting feature.
3 Click.
The feature is being moved to the centre of the image area.
4 To quit this function, right-click.
4.2.9.2. Using the Continuous Centre Point function

If selected, the software remains in centre point mode after each point selection allowing repeti-
tive centre point actions.
1 Select Stage/Continuous Centre Point from the menu.
4.2.9.3. Using the Centre feature function

1 Select Stage/Centre Feature from the menu.
Alternatively, type <Ctrl + Shift + Tab>.
The mouse cursor is displayed as a cross.

2 Place the cross on the interesting feature.
3 Drag the mouse to open a frame, which comprises the area of interest.
4 Click.
The feature range is being moved to the centre of the image area and magnified.

4. Operation
4.2.10. Using Stage Map (licence: CENTRE)
This function allows using a frozen image in the left zone (zone 0) as an overview for the selection
of interesting features on the specimen surface.
1 Select a low magnification.

2 Move the stage to the interesting specimen area.
This setting will be used as stage map.
3 Select Scanning/Split in order to change to spot mode.

4 Select Stage/Stage Map.
The left zone (zone 0) is frozen and serves as an overview.
5 Select a feature of interest in the left zone by placing the cross and clicking.
In the right zone (zone 1), the selected feature is displayed. You can modify the image, e.g. mag-
nify as required.

4. Operation
4.2.11. Scanning defined image fields (licence: STAGESCAN)
This function allows you to scan an exactly defined series of regularly distributed image fields.
This is useful when searching for particles or other objects in a large sample range, as it is en-
sured that no part of the interesting area will be omitted.
Four scan patterns and several methods are available to determine the scan range.
Requires the licence STAGESCAN.
1 Select Stage/Stage Scan from the menu.
The Stage Scanning window opens.
2 Define the stage scan fields:

a Click Setup Wizard.
b Follow the instructions given in the wizard.
Jumps to the first position
Moves to the previous position
Moves to the next position
Jumps to the last position
Selects the scan pattern (sequence)

4. Operation
4.2.12. Toggling between survey view and detail view (licence: SURVEY)
This function offers the possibility to save two different settings for magnification and working dis-
tance and to switch between these settings. The settings are called Survey Mode (provides a
survey view) and Resolution Image (provides a detail view).
Requires the licence SURVEY.
4.2.12.1. Entering survey view and detail view settings
Survey view 1 Set the survey view settings:

settings
Set a low magnification and a large working
distance to achieve a wide field of view.
2 Select Stage/Survey/Settings from the

menu.
3 Enter the desired settings in the Survey Mode
field:
a To automatically set the lowest possible
magnification, tick the Lowest Mag radio
button.
b To take the current magnification and WD
settings, click the Get Current buttons.
You can also manually enter the desired values.
4 Select additional functions:

a Tick the Remember Changes checkbox.
When switching to Survey Mode State, espe-

cially for the first time, it may be necessary to
adjust focus.
When Remember changes is ticked, the new
working distance as a result of focusing will re-
place the target WD in the settings.
b To start an automatic focus adjustment

after start of the respective operation
mode, tick the Auto Focus checkbox.
c To execute a macro, tick the Macro
checkbox and select a macro from the
drop-down list.

4. Operation
Detail view 5 Enter the detail view settings:

settings
Set a higher magnification and a smaller WD.
6 Enter the desired settings in the Resolution

Imaging field:
Click the Get Current buttons after Mag and
WD.
7 Select additional functions:
a If you wish to start an automatic focus ad-
justment after the respective operation
mode, tick the Auto Focus checkbox.
b To execute a macro, tick the Macro
checkbox and select a macro from the
drop-down list.
If you wish to execute a macro when quitting

Survey Mode:
a In the Exit Survey Mode field, tick the
Macro checkbox.
b Select a macro from the drop-down list.

4. Operation
4.2.12.2. Activating the Survey Mode function
IMPORTANT
This function requires the stage to be initialised.
1 Tick the Survey Mode checkbox.
Alternatively:
Select Stage/Survey/Survey Mode from the
menu.
2 To quit Survey Mode, untick the Survey Mode

checkbox.
Alternatively:
Select Stage/Survey/Survey Mode in order
to untick the function in the menu.

4. Operation
4.2.13. Defining a user specific coordinate system (licence: STAGEREG)
This function offers the possibility to define a user specific 2D coordinate system based on three
reference points. Within this coordinate system, the stage can move to specific spots on the
specimen, while the stage coordinates can be saved.
Requires the licence STAGEREG.
If there are three spots on the specimen, whose distances to the saved stage coordinates are
defined, these spots can be used as reference points.
It is possible to create up to nine different coordinate systems.
1 Ensure the stage has been initialised.

2 Load a suitable specimen e.g. a chessy.
4 Double-click Stage Registration.
The Stage Registration window opens.
5 Under Stage List, select a new coordinate system.

4. Operation
6 Enter a name.
7 Click Setup Registration.
The Stage Registration window opens.

8 To show crosshairs, tick the Crosshairs
checkbox.
9 Select an alignment mark on the specimen.
10 Enter the coordinates.
11 Move the stage to the selected alignment
mark.
12 Click Next.
13 Repeat steps 7 to 10 for the second registra-

tion point.
14 Repeat steps 7 to 10 for the third registration

point.
15 Click Finish.

4. Operation
Setting SEM conditions
4.3. Setting SEM conditions
4.3.1. Controlling the gun
4.3.1.1. Switching on the gun

menu.
2 Go to the Gun Vacuum tab.
Check that EHT Vac ready=Yes is indicated.
3 In the status bar, click Gun.

4 Select Gun On from the pop-up menu.
The gun is being run up.

4. Operation
4.3.1.2. Switching off the gun

It is recommended leaving the gun on during the working week. This should help optimise life time
of the Schottky field emitter.
Only at longer breaks such as weekends or holidays you should switch off the gun.
1 In the status bar, click All:.

2 Select Shutdown Gun from the pop-up menu.

4. Operation
4.3.2. Controlling the EHT
4.3.2.1. Switching on the EHT

The electrons emitted by the gun have to be accelerated by applying the acceleration voltage
EHT.

Setting the 3 Set the acceleration voltage:
EHT
a Double-click in the EHT= field.
b Enter the desired value (kV).
c Confirm by clicking on OK.
IMPORTANT
The In-lens detector can be used up to an acceleration voltage of 20 kV.
At higher acceleration voltages the efficiency of the In-lens detector will be markedly re-
duced.
IMPORTANT
SUPRA™ 25 only:
To be able to set a value below 0.5 kV, the licence LOWVOLTS is required.
To be able to set a value from 20 kV to 30 kV, the licence EXTVOLTS is required.

4. Operation
Switching on 4 Switch on the EHT:

a In the status bar, click EHT.
b Select EHT On from the pop-up menu.
Alternatively:
Select Beam/EHT On from the menu.
The EHT (acceleration voltage) is run up to the set value.

The status bar buttons are pushed together, and the All: button appears.
4.3.2.2. Switching off the EHT

1 In the status bar, click All.
2 Select EHT Off from the pop-up menu.
Alternatively:
Select Beam/EHT Off from the menu.

4. Operation
4.3.3. Blanking the beam
To protect sensitive specimens from the electron beam, you can blank the beam.
IMPORTANT
This procedure does not refer to the optional Beam Blanker for MERLINTM.
For information on the optional MERLINTM Beam Blanker, refer to the Instruction Manual
Beam Blanker delivered with the Beam Blanker.

2 Go to the Apertures tab.
Alternatively:
Select Beam/Aperture from the menu.
3 Tick the Beam Blanked checkbox.

4. Operation
4.3.4. Modifying the probe current
The probe current (beam brightness) is determined by aperture size and extractor voltage. More-
over, it can be increased by using the high current mode.
Depending on your application, choose one of these three possibilities to modify the probe cur-
rent.
Using the option OptiProbe offers the possibility to automatically set the probe current.
4.3.4.1. Changing the aperture size

2 Go to the Aperture tab.
Alternatively:
3 Click in the Aperture Size field and select an

aperture from the drop-down menu.
Standard aperture is a multihole aperture with a

central 30 µm aperture hole which is suitable for
most applications.
Large apertures (120 µm, 60 µm diameter) are
used for certain applications that require a high
beam brightness, e.g. EDX, or a large depth of field.
Small apertures (20 µm, 10 µm, 7.5 µm diameter)
are suitable for high resolution imaging or current-
sensitive specimens.
4 Continue with aligning the newly set aperture

as described in section 4.3.5.

4. Operation
4.3.4.2. Changing the extractor voltage

The extractor voltage is preset by the factory, respectively by the Carl Zeiss service engineer.
Within certain limits, the operator may carefully alter the extractor voltage in order to optimise the
probe current for particular applications.
1 Select Tools/Goto Control Panel from

the menu.
3 Use the arrow buttons of the Extractor V

Target slider to increase the extractor voltage.
Increasing the extractor voltage may be suitable to

increase the probe current.
CAUTION
Performance and resolution of the SEM/FESEM can be impaired.
Avoid reducing the extractor voltage.
If at all, reduce the extractor voltage only for a short time (1-2 h) and by maximum 500 V.
IMPORTANT
The newly set extractor voltage is only valid for the current work session.
After a restart of the SmartSEM® software, the SEM/FESEM will restore the nominal volt-
age.

4. Operation
4.3.4.3. Using high current mode (licence: HIGH CURRENT)

High current mode increases the active probe current. This is obtained by a stronger activation
of the condenser lens.
Typical applications are images with a large depth of field.
Requires the licence HIGH CURRENT. Not available with SUPRA™ 25.

Alternatively:
3 Tick the High Current checkbox.
To quit high current mode, untick the High

Current checkbox.

4. Operation
4.3.4.4. Continuously modifying the probe current (licence: OPTIPROBE)

OptiProbe allows you to continuously adjust the probe current.
The function automatically selects a suitable aperture and the current mode while the extractor
voltage is adjusted to meet the probe current selected by the user.
Requires the licences OPTIPROBE and HIGH VOLTAGE.

Requires particular hardware as well as the installation of the specimen current amplifier.
Not available with SUPRA™ 25.

menu.
3 Tick the OptiProbe checkbox.
4 Use the I Probe slider to set the desired probe

current.
As soon as the probe current adjustment is
finished, the status display changes from
Busy to Ready.
The indicated probe current I Probe= corre-

sponds to the actual probe current (+/- 15 %).
5 To deactivate the function, untick the OptiProbe checkbox.

Even if OptiProbe is deactivated, I Probe= indicates the actual probe current (+/- 15 %).
IMPORTANT
After cathode replacement or after re-alignment of the electron optical column, OptiProbe
has to be calibrated. Refer to section 5.3.

4. Operation
4.3.5. Aligning the aperture
The alignment of the aperture in the beam path has a decisive effect on resolution and sharpness
of the image.
The aperture alignment should therefore be adjusted or checked anytime the aperture is changed
and after major modifications of the EHT setting.
Whenever the image is shifting while you are focusing, the aperture should be re-aligned.

Alternatively:
3 Tick the Focus Wobble checkbox.
The Focus Wobble is a function that sweeps

the focus of the objective lens backwards and
forwards through the focus on the specimen
surface. If the aperture is slightly misaligned, a
lateral shift can be observed.
4 Set wobble intensity by using the Wobble Am-

plitude slider.
5 If required, select a higher wobble frequency by
ticking the Wobble Fast checkbox.
6 Adjust the aperture in X and Y direction by

means of the slider in the Aperture Align
navigation box.
Alternatively, you can move the red marker by
holding the left mouse button and dragging.
Adjust until the image pulsates, i.e. there is only

a continuous change from a sharp to a blurry
image without shifting.
7 Untick the Focus Wobble checkbox.
8 Refocus the image.

4. Operation
4.3.6. Correcting astigmatism
Astigmatism is an aberration of lenses, that can be corrected by means of the so-called stigmator.
4.3.6.1. Setting the stigmator

3 Click Stigmation.
Adjust the stigmation by using the X and Y
sliders or the arrow buttons in the
Stigmation box.
Alternatively:
1 In the toolbar, click the Stigmation/Alignment
icon.
The mouse assignment is indicated in the status

bar.
2 To adjust stigmation hold the left mouse button
and drag.
4.3.6.2. Using the Auto Stigmation function
1 In the toolbar, middle-click the Auto Focus+Stig

icon.
A fine auto focus correction is performed followed

by an automatic astigmatism algorithm.

4. Operation
4.3.7. Showing SEM parameters (SEM status window)
The SEM status window is helpful to show, edit and set frequently used parameters. The SEM
status window lists the operation parameters selected by the individual user.
1 Select View/SEM Status from the menu.
Alternatively, type <CTRL+ I>.
2 Select the parameters to be displayed:

a Go to the Select tab.
b Click the parameter you wish to be dis-
played.
The parameter is shown in the Display tab.
3 To change the setting of the displayed

parameter:
a Go to the Display tab.
b Double-click the parameter name.

4. Operation
4 To load a saved combination of parameters:

a Go to the File tab.
b Click Load.
c Select the file.
5 To save a selected combination of parameters:

b Click Save As.
c Enter a file name and confirm.
6 To delete the complete list of parameters:

b Click Clear Display.

4. Operation
4.3.8. Recording SEM parameters
The Gun Monitor utility offers the possibility of recording and displaying important parameters of
the SEM/FESEM at defined intervals during operation of the SmartSEM® user interface.
1 Select Start/Programs/SmartSEM Service/Gun Monitor from the Windows desktop.
The Gun Monitor window opens.
2 To start the record, select Monitor/Start.

Alternatively, click the green dot.
Eight different channels are available, six of them are predefined to record extractor voltage, ex-
tractor current, filament current heating, gun vacuum, liner tube voltage, and acceleration voltage.

4. Operation
3 To modify channel assignments:

a Select Monitor/Options.
The Display Options window opens.
b To remove the checkmark, click it.
4 To change the colour:

a Click the colour square.
b Select another colour and confirm.
5 To enter the minimum and maximum values to be displayed in the diagram:

a Click into the Min Value or Max Value field.
b Enter a minimum value or maximum value.

By clicking on Defaults you can cancel all settings and reset them to the basic
settings.

4. Operation
7 To set the recording interval:

a Select Monitor/Interval.
The monitor interval window opens.
b Enter an interval in seconds.
8 To freeze the record, select Monitor/Freeze.
9 To stop the record, select Monitor/Stop.
10 To save the record, select File/Save As.
11 To print the record, select File/Print.

4. Operation
Imaging
4.4. Imaging
4.4.1. Setting detection parameters
4.4.1.1. Selecting a detector

Detectors provide the signals to be displayed on the monitor. A drop-down list shows the detector
types adapted to your SEM/FESEM. Depending on the detector type selected, different informa-
tion is shown in the image.

3 Select the desired detector Signal A.
Signal A is always the active signal displayed on

the monitor.
Alternatively:
Select Detection/Detectors from the menu.
A list of the adapted detectors is shown.

The active detector is ticked.

4. Operation
Imaging
4.4.1.2. Setting the collector voltage of the SE2 detector

In front of the SE2 detector an electrical field is generated that allows you to influence the detec-
tion. This collector voltage can be varied at a range between -250 V and +400 V.
1 Select Tools/Goto Control Panel/Detectors.

2 To set the collector voltage use the Collector
Bias slider.
For standard applications the Collector Bias should

be set to +300 V.
At higher magnification it is recommended varying
the Collector Bias so that the best possible signal is
obtained in the image.
To generate a so-called pseudo-backscattered im-
age set a negative Collector Bias. This will produce
an extreme topography but nearly no surface qual-
ities and material contrasts.

4. Operation
Imaging
4.4.1.3. Adjusting brightness and contrast

Changing the signal to more brightness shifts all grey levels in the image to lighter levels and vice
versa.
Changing the signal to more contrast expands the range of grey levels in the image and vice ver-
sa.

3 To adjust brightness, use the Brightness
slider.
To adjust contrast, use the Contrast slider.
Alternatively:
1 In the toolbar, click the

Brightness + Contrast icon.
The mouse assignment is indicated in the

status bar.
2 To adjust brightness hold the left mouse

button and drag.
To adjust contrast hold the middle mouse
button and drag.

4. Operation
Imaging
4.4.1.4. Using AutoBC
The Auto BC function allows you to automatically adjust brightness or contrast or both brightness
and contrast.

3 Select one of the settings from the drop-down
menu:
Off: Switches the function off
B: Automatic adjustment of brightness
C: Automatic adjustment of contrast
BC: Automatic adjustment of brightness and
contrast

4. Operation
Imaging
4.4.1.5. Mixing two detector signals (licence: SIGMIX)

This function allows mixing the signals of the detectors selected in Signal A= and Signal B=.
Information registered by one single detector (e.g. topographic contrast) can thus be overlapped
with another detector signal to increase the information of the image.
Requires the licence SIGMIX.
1 Select Tools/Goto Control Panel/Detectors.

2 Tick the Mixing checkbox.
3 Use the Signal slider to adjust the percentage
of mixing between 0 and 1 (i.e. 0 to 100%).
For example, adjusting Signal = 0.6000
means that the image is composed of 60 %
signal A and 40 % signal B.
To quit the mixing function, untick the Mixing

checkbox.
To quickly activate/deactivate the mixing function, select Detection/Mixing from the menu.
When active, the function is ticked.

4. Operation
Imaging
4.4.1.6. Displaying two detector signals on the same monitor (Windowing)

The windowing function allows displaying two different detector signals on the monitor without
requiring an optional licence.

2 Double-click Windowing.
The Windowing dialog opens.
3 Tick the Windowing checkbox.
A reduced raster is shown.

There are two zones (Zone 0 = outside, Zone 1 = in-
side the reduced raster).
Image modifications apply to the zone marked with the
anchor symbol.
4 To displace the anchor symbol, hold the left mouse button and drag.
5 To invert the signal of the respective zone, select Invert A = On.
To quit the Windowing mode, untick the Windowing checkbox and close the Windowing dialog.

4. Operation
Imaging
4.4.1.7. Displaying two image areas (licence: SPLIT)

This function subdivides the image area into two zones. Different detectors can be assigned to
each zone. Each zone can be frozen independently from each other.
Requires the licence SPLIT.
1 In the toolbar, click the Split Screen icon.
Alternatively:
Select Scanning/Split from the menu.
The image area is split into two zones.

The anchor symbol marks the zone for detec-
tor selection, setting of brightness and con-
trast, freezing or deleting.

4. Operation
Imaging
2 To displace the anchor symbol hold the left

mouse button and drag.
To apply image modifications to both zones

simultaneously, double-click the anchor sym-
bol.
The colour of the anchor symbol changes.
To quit the split function, click the Split Screen

icon.
Alternatively, select Scanning/Normal from the
menu.
4.4.1.8. Displaying detector signals on two different monitors (licence: DUAL-

CHANNEL)
This function allows displaying the live image on the second monitor and to select different signal
sources monitors. Panels can be moved to the second monitor.
Requires the licence DUAL-CHANNEL.
1 Select Image/Dual Channel from the menu.
The anchor symbol marks the zone for detec-

tor selection, setting of brightness and con-
trast and freezing or deleting.
To displace the anchor symbol, hold the left

mouse button on the anchor while dragging it
to the other monitor.

4. Operation
Imaging
4.4.1.9. Producing composite images from two detectors (licence: COLOUR

MODE)
Colour mode offers the possibility to convert and combine signals from two different detectors and
display a live false colour image without losing important information.
Requires the licence COLOUR MODE.

2 Double-click Colour Mode.
The Colour Mode window opens.
3 Select Colour Mode = 2 LUT from the Colour

Mode drop-down menu.
This enables the checkboxes in column 1

and 2.
4 Adjust contrast and brightness of the two de-

tector signals A and B by using the respective
sliders.
SE image BSE image Compositional image (colour mode)
SE image BSE image Compositional image (colour mode)

4. Operation
Imaging
4.4.1.10. Displaying images with different magnifications (licence: DUALMAG)

This function allows you to zoom an image without freezing the image at basis magnification. Dual
Mag is recommended in order to accentuate a detail in an image and to simultaneously realise a
view of the specimen at low magnification.
Requires the licence DUALMAG.
1 In the toolbar, click the Dual Magnification

icon.
Alternatively:
Select Scanning/Dual Mag from the menu.
Alternatively:
Tick the Dual Mag checkbox under SEM Con-
trolss Panel/Scanning.
The image area is divided into two zones.

The left zone is displayed at the current magnification. At the same time a frame pops up
which defines the range to be displayed in the right zone.

4. Operation
Imaging
2 To modify size and position of the frame, click it with the left mouse button:
a To change the size of the frame, place the mouse cursor on a mark.
Alternatively, double-click the Zoom factor field in the SEM Controlss/Scanning tab
and enter the zoom factor.
The zoom factor determines the magnification ratio between the left and the right zone.
b To displace the frame, place the mouse

cursor between two marks.
The anchor symbol marks the zone for detector

selection, setting of brightness and contrast and
freezing or deleting.
3 To displace the anchor symbol hold the left
mouse button and drag.
4 To apply image modifications to both zones si-

multaneously, double-click the anchor sym-
bol.
The colour of the anchor symbol changes.

4. Operation
Imaging
4.4.1.11. Using a second CCD camera

If a second CCD camera is attached, it is usually installed as ’Auxiliary 1’.
1 Select Detection/TV Inputs from the menu.

2 Select Aux 1.
Alternatively:
1 Select the Detectors tab of the SEM Con-
trolss panel.
2 Select Aux 1 from the Signal A = drop-down
list.
Icon It might be helpful to assign the pre-defined

assignment TOGGLE TV macro to the ChamberScope icon.
This will make the second CCD camera available
by middle-clicking on the ChamberScope icon.
Refer to section 4.9.6.

4. Operation
Imaging
4.4.2. Setting the working distance
The working distance (WD) is the distance between the focused specimen surface and the end
of the objective lens. The WD determines the possible resolution, the signal-to-noise ratio, the
depth of focus and the lowest possible magnification (low power magnification).
1 In the toolbar, click the Magnification/Focus.
2 Hold the middle mouse button and drag the

mouse in order to focus.
The current WD is indicated in the status bar.

4. Operation
Imaging
4.4.3. Setting scan parameters
4.4.3.1. Selecting a scan speed

A focused beam of electrons is scanned across the specimen. The speed of the scan can be
modified which has an influence on the speed of image generation on the one hand and the
extend of image noise on the other hand.
1 Select Scanning/Speeds from the menu.

A drop-down list shows all available scan
speeds.
2 Select a scan speed and confirm with OK.
The higher the scan speed number, the slower the

scan of the specimen by the electron beam and
the less the noise of the image.
Selection of fifteen scan speeds requires the

licence SCANEXP. Without this licence only three
scan speeds are available.
Alternatively:
1 Select Tools/Goto Control Panel/Scanning.
2 To display the drop-down list, click the Scan
Speed = field.
You can use the Scan+ and Scan- buttons to

increase, respectively decrease the scan speed.

4. Operation
Imaging
4.4.3.2. Scanning a small frame (reduced raster)

The reduced raster function allows you to scan only a small frame. This is recommended for align-
ment procedures such as focusing, aligning the stigmator or using the focus wobble.
Moreover, this function is helpful when using an EDX system: Only the information of this selected
range is shown in the EDX spectrum.
The possibility to adjust size and position of the reduced raster requires the licence REDUCED.
1 In the toolbar, click the Reduced Raster.
Alternatively:
Select Scanning/Reduced from the menu.
A frame is displayed in the image area, which

defines the specimen area to be scanned by the
electron beam.
The image outside the frame is frozen.
With licence REDUCED:

1 To modify size and position of the frame, click it:
a To change the size of the frame, place the mouse cursor on a mark (cursor is double
arrow), hold the left mouse button and drag.
b To displace the frame, place the mouse cursor between two marks (cursor is rectangular
symbol), hold the left mouse button and drag.

4. Operation
Imaging
4.4.3.3. Scanning a spot (licence: SPOT)

In spot mode the electron beam is positioned on a particular spot on the specimen surface. This
mode is recommended for the use with an EDX/WDX system or for the measurement of the spec-
imen current.
Requires the licence SPOT.
1 Select Scanning/Spot from the menu.

The submenu Spot is ticked.
Alternatively, select Tools/Goto Control

Panel/Scanning and tick the Spot checkbox.
A cross is displayed on the monitor.

The image is frozen.

4. Operation
Imaging
2 To displace the cross:

a Hold the left mouse button to drag the cross on the screen.
Alternatively:
a Open the SEM Status window: Select View/SEM Status from the menu.
b Display Spot at X and Spot at Y.
c Double-click Spot at X and Spot at Y in order to enter fixed values.
To quit spot mode, deactivate the submenu Spot or untick the Spot checkbox.

4. Operation
Imaging
4.4.3.4. Scanning a line

This function is used to scan along a defined line while the image is frozen. It is recommended
for measuring and adjusting signals, e.g. for optimising brightness and contrast.
CAUTION
Danger of damaging the specimen if the electron beam scans along the same line position
a longer period of time. This can result in a scan mark on the specimen.
When using the Line Scan function for image optimisation place the Line Scan on a spec-
imen area adjacent to the actual area of interest.
1 Select Scanning/Line Scan from the menu.

The submenu Line Scan is ticked.
Alternatively, select Tools/Goto Control

Panel/Scanning and tick the Line Scan
checkbox.

4. Operation
Imaging
A horizontal line is displayed together with a diagram which shows the course of the signal
along this line.
The displayed graph represents the grey value distribution along the line. The grey values are
represented from 0 to 255 on the ordinate. The illumination of the image can thus be adjusted at
the representative spot.
2 To move it to the desired specimen area, click the horizontal line.

3 To change colour and background of the diagram:
a Position the mouse cursor in the diagram.
b Click the right mouse button.
A pop-up menu opens, where you can select the colour of the graph and a grey background.

4. Operation
Imaging
4.4.3.5. Rotating the image (licence: SCANROT)

This function allows you to rotate the image electronically by rotating the scan direction.
Requires the licence SCANROT.
1 Select Scanning/Rotate/Tilt.
The Rotate/Tilt panel is shown.
2 Tick the Scan Rot checkbox.

3 Set the desired tilt angle with the Scan Rota-
tion slider or by double-clicking on the Scan
Rotation field.
The image is rotated.

4. Operation
Imaging
4.4.3.6. Displaying the scan marker

The scan marker is a small bar on the left side of the image area, which indicates the scanned
line on the monitor. This might be helpful when using slow scan speeds because the scan marker
helps to see which line is currently being scanned by the electron beam. The scan marker is not
recorded on the image.
1 Select Tools/User Preferences.
2 In the tree structure, select SEM Conditions.
3 Select Scan Marker Enable Yes.

4 Select Height, Width and Colour of the scan
marker.
IMPORTANT
The scan marker will only be displayed when you use slow scan speeds (5 - 15). At quicker
scan speeds (4 and faster) it will be deactivated automatically.

4. Operation
Imaging
4.4.4. Setting the magnification
4.4.4.1. Selecting the magnification

1 In the toolbar, click Magnification/Focus.
2 Hold the left mouse button and drag the

mouse to adjust the desired magnification.
The current magnification is indicated in the

status bar.
4.4.4.2. Using pre-defined magnifications (Magnification Table)

Up to ten fixed magnifications can be entered in the Magnification Table for quick access during
the imaging procedure. The magnifications have to be pre-defined in the User Preference panel
(refer to section 4.9.4.4.).
To call the pre-set magnifications:
1 Press <F4>.
Anytime F4 is pressed, the next magnification value will be set.
2 To return to the previous magnification value, press <Ctrl + F4>.
3 To finish the use of the Magnification Table, press <Shift + F4>.
The magnification of the SEM/FESEM will be reset to the level that was active before the Magni-
fication Table was used for the first time.

4. Operation
Imaging
4.4.5. Imaging tilted specimen
4.4.5.1. Using Dynamic Focus (licence: DYNFOCUS)

The dynamic focus allows the dynamic adaptation of the focus to tilted specimen surfaces.
Requires the licence DYNFOCUS.
1 Show the reduced raster:

a Reduce the size of the raster.
b Place it in the centre of the image area.
c Adjust the best possible focus in the reduced raster.

Crosshairs may be helpful.

4. Operation
Imaging
2 Displace the reduced raster to the very upper or the lower image margin.
3 Set a slow scan speed (9 or higher).

4 Select Scanning/Dynamic Focus from the
menu.
5 Tick the Dyn. Focus checkbox.
The dynamic focus is enabled now.
6 Use the FCF Setting slider in order to adjust

optimum sharpness in the reduced raster.
Do not modify the normal focus (middle

mouse button).
7 Select Scanning/Normal to acquire the com-

plete image while using a slow scan speed.
8 Store the image.
9 Untick the Dyn. Focus checkbox to quit the
dynamic focus mode.
IMPORTANT
The best application of the dynamic focus is only possible with tilted plane specimens. If
the specimen presents strong differences in height (topography) or different inclinations
of slope, the depth of focus must be optimised as well.

4. Operation
Imaging
4.4.5.2. Using Tilt Correction (licence: TILTCOMP)

This functions allows the correction of the perspective foreshortening caused by the scan of a tilt-
ed specimen.
If a specimen presents a high tilt angle, the electron beam scans a larger part of the specimen in
tilt direction so that the image is distorted.
Requires the licence TILTCOMP.
1 Ensure the specimen surface is tilted in

Y direction respective to the monitor.
2 Select Scanning/Rotate/Tilt from the menu.
3 Tick the Tilt Corrn. checkbox.
4 Adjust the Tilt Angle slider.

Alternatively, double-click in the Tilt Angle
field and enter the angle.

4. Operation
Imaging
IMPORTANT
When you use an extremely tilted specimen, you should adjust the dynamic focus as well.
IMPORTANT
With Cross Beam series instruments:
If you wish to measure the height, note that you have to enter ’90° - tilt angle value’ in the
’Tilt Angle=’ field.

4. Operation
Imaging
4.4.6. Improving the signal-to-noise ratio (noise reduction)
The signal entering the image processor is made up of two components: image and noise. Image
is the signal of interest and correlates with the object being scanned, noise is random in nature.
Therefore, by averaging multiple scans of the same area, the signal will be reinforced, while the
noise will be reduced. This is the basis on which the noise reduction works.
The signal-to-noise ratio is an important factor for image quality. It does not only depend on the
parameters EHT, aperture size and working distance, but also on the dwell time of the electron
beam per image spot.
To reduce the noise level of an image, you can
• increase the dwell time of the electron beam per pixel or
• scan the respective specimen spot several times and integrate the generated signal.
Method Explanation Typical application
Frame Average Averaging of two or more consecutive frames: Frame averaging is used to reduce random
(Continuous Aver- Frames are scanned continuously and the image noise.
aging) is formed as the average of a number of succes-
sive frames. It can be selected with any scan speed but is
generally most useful at the faster speeds
The live signal is proportionally mixed with the where a larger amount of noise reduction can
stored signal so that the image reflects the aver- be obtained without introducing a long cycle
age of the recent frames. The proportion of live time.
to stored can be adjusted with the parameter N
which represents the number of frames to be
averaged.
Frame Integrate Addition of two or more consecutive frames. The Frame integration is used to enhance contrast
image automatically freezes at the end of the and reduce noise.
integration cycle.
It is useful when applied to beam sensitive
The scan speed defines the time to complete a materials, since the image can be obtained
frame and the noise reduction parameter N while the beam remains scanning quickly and
defines the number of frames to integrate. not allowed to dwell too long on any point of the
specimen. In this mode the image is formed as
the average of a number of successive frames.
Not suitable when sample drift occurs.
Line Integrate Each line to be scanned a number of times

before the scan moves on. The average line sig-
nal is stored and displayed.
The noise reduction parameter N defines the
number of times a line is to be averaged before
moving to the next line.
Line Average The image is built up by averaging a number of Use Line average when the result of the noise
lines. Each line is scanned a number of times reduction needs to be seen without waiting for
before the scan moves on. The average line sig- the cycle to complete.
nal is stored and displayed. Suitable for most applications.
The noise reduction parameter N defines the
number of times a line is to be averaged before The image will automatically freeze at the end
moving to the next line. of the frame.

4. Operation
Imaging
Method Explanation Typical application
Pixel Average A single frame is scanned. Suitable for specimens with good electric and
thermal conductivity.
The frame time is controlled by the scan speed
parameter as follows (100 x 2n-1):
Speed 1: 100 ns per pixel
Speed 2 : 200 ns per pixel
Speed 5 : 1.6 µs per pixel
Speed 15 : 1.6384 ms per pixel
Continuous Displays an image within which each pixel is Most useful for stable, conductive specimens
Average measured repeatedly and the average signal where the beam has little or no damaging effect
(Pixel Averaging) displayed. on the specimen.
Frames are scanned continuously and the image

formed as the average of a number of succes-
sive frames.
The pixel time is determined by the dwell time
parameter, that can be selected.
The number of frames is determined by the scan

speed (2n).
Speed 1: Average of 2 frames

4. Operation
Imaging
4.4.6.1. Selecting a noise reduction method
1 Select Tools/Go To Control Panel from the

menu.
2 Go to the Scanning tab.
3 Select a Freeze on mode:
Command: Causes an immediate freeze of the
current zone (the whole image in normal mode)
if you click Freeze.
End Frame: Causes the zone to freeze at the
end of the current frame.
4 Select a Noise Reduction mode.
When selecting Frame Avg:

a Select N=, set a value between 1 and 256.
b Select a Dwell time from the drop-down
list.

4. Operation
Imaging
4.4.7. Improving image illumination by using Look Up Tables (LUT)
4.4.7.1. Editing a live image (Input LUT)

Using Look Up Tables (LUT) is recommended when the illumination of an image while using a
linear characteristic line is very difficult or impossible. In these cases you may try to obtain better
illumination of the image by adding or displacing discrete points of the characteristic line or by
adding a step function. The Input LUT is used to perform a translation on the input signal as de-
fined by the pattern loaded into the LUT. Modifications of the Input LUT effect the live image.
1 Select Edit/Input LUT from the menu.
The EM LUT Editor window opens.
The following functions are available:
Select Mode
Displaces and deletes points of the transfer characteristic.
Displace: Place the mouse cursor on the point and displace it by holding the left mouse
button.
Delete: Place the mouse cursor immediately near the point and press the middle mouse
button.
Add/Remove Points
Adds and deletes points in the transfer characteristics.
Add: Place the mouse cursor in the graphic field and press the left mouse button.
button.
Undo Last Edit

Undoes the last change of the Input LUT.

4. Operation
Imaging
Open LUT
Loads specific Input LUT settings and apply these settings to the current image.
Save LUT As..

Saves specific settings of the Input LUT.
Reset LUT
Returns the Input LUT to the basic condition (linear characteristic)
Invert LUT
Inverts the current transfer characteristic.
Step LUT
Adds a step function as a transfer
characteristic to convert the transfer
characteristic into a regular
sequence of grey values.
The height of each step (amplitude),

the position of the first step (offset)
and the number of steps (period)
can be separately set.
It is also possible to further modify
the curve by adding or displacing dif-
ferent points.
Adjust Step LUT Settings

Calls up the LUT Step Settings win-
dow to set amplitude, period, and
offset of the step function.

4. Operation
Imaging
4.4.7.2. Editing a saved image (Display LUT)

The Display LUT is used to edit a SEM image, e.g. by subsequent colouring, modification of
brightness and contrast, inversion or addition of a gamma function. These settings effect the
saved image as well as the live image.
1 Load a saved image.

2 Select Edit/Display LUT from the menu.
Select Mode
Displaces and deletes points of the transfer characteristic.
Displace: Place the mouse cursor on the point and displace it by holding the left mouse
button.
button.
Add/Remove Points
Adds and deletes points in the transfer characteristics.
Add: Place the mouse cursor in the graphic field and press the left mouse button.
button.
Undo Last Edit

Undoes the last change of the Input LUT.
Open LUT
Loads specific Input LUT settings and applies these settings to the current image.

4. Operation
Imaging
Save LUT As..

Saves specific settings of the Input LUT.
Reset LUT
Returns the Input LUT to the basic condition (linear characteristic)
Invert LUT
Inverts the current transfer characteristic.
Step LUT
Adds a step function as a transfer
characteristic to convert the transfer
characteristic into a regular
sequence of grey values.
The height of each step (amplitude),

the position of the first step (offset)
and the number of steps (period)
can be separately set.
It is also possible to further modify
the curve by adding or displacing dif-
ferent points.
Adjust Step LUT Settings

Calls up the LUT Step Settings
window to set amplitude, period,
and offset of the step function.
Edits brightness and contrast.
The Gamma option allows to define the transfer characteristic as a curve to enlarge lower
and higher grey scales. This function can be used to improve images containing a large
quantity of detailed information in few grey scales.

4. Operation
Imaging
Inserts a grey wedge (continuous distribution of the grey scales from white to black) as
current image to adjust particular output media.
Switches from RGB to grey value LUT.
Sets the level of a point in the transfer characteristic after selection of a point.
Switches from grey value LUT to RGB LUT and selects the transfer characteristic for the
colour red.
Subsequent modifications of this transfer characteristic refer only to the colour red.
colour green.
Subsequent modifications of this transfer characteristic refer only to the colour green.
colour blue.
Subsequent modifications of this transfer characteristic refer only to the colour blue.

4. Operation
Imaging
4.4.8. Processing the image (licence: IMMATH)
The functions in Image Processing offer the possibility of mathematically manipulating the image
content pixel-by-pixel by using the grey value (0=black, 255=white). Different filter functions, ba-
sic mathematic operations and the detection of grey values can be used.
Requires the licence IMMATH.
4.4.8.1. Grey value detection

1 Select Image/Image Processing from the menu.
2 Go to the Threshold tab.
3 Set the type of threshold:
Select Black, White or Grey from the Image
Detect drop-down list.
Black: Each pixel in the image storage with a
value inferior to the black threshold is col-
oured red.
White: Each pixel in the image storage with a
value inferior to the white threshold is col-
oured red.
Grey: Each pixel in the image storage with a
value superior to the black threshold or inferior
to the white threshold is coloured red.
4 Select the threshold for black by using the Black Threshold slider.
5 Select the threshold for white by using the White Threshold slider.
6 To calculate the area fraction of certain grey values coloured red in the image by clicking Up-
date.
IMPORTANT
If stored images contain annotations or measurements, the grey values of these annota-
tions will be included in calculation and presentation.

4. Operation
Imaging
4.4.8.2. Creating a stereo image

The creation of stereo images allows you to get images showing a 3D effect.
Prerequisite is that you take two images of the same specimen at the same magnification but at
a different tilt angle. Depending on magnification and topography of the specimen, the difference
of the tilt angle should be 2° to 15°.
1 Take the first image:

a Display crosshairs.
b To ease navigation, move a striking detail
to the centre of the image.
c Set the desired magnification.
d Rotate the image by 90° by means of the
scan rotation function.
e Freeze the image.
f Save the image without data zone or
annotations.
2 Take the second image under a different

tilt angle:
a Unfreeze the image.
b Disable scan rotation.
c Display crosshairs.
d Tilt the stage step by step.
In most cases the tilt angle between the
two images should differ by 2° to 15°.
e Compensate for the move of the specimen
range by moving the stage in Y-direction.
Always place the striking detail back to
the centre of the crosshairs.
By tilting the specimen, the focus has been

changed as well.
f When reaching the required tilt angle,
reset the focus by driving the stage in
Z direction.

4. Operation
Imaging
g Rotate the image by 90° by means of the

scan rotation function.
h Freeze the image.
i Save the image without data zone or
annotations.
3 Select Image/Image Processing from the

menu.
4 Go to the Image Maths tab.
5 Reload the first image:

a Under Source select Image Store,
under Operation select Copy To,
under Destination select Buffer 1.
b Click Execute.
The image is copied to buffer store 1.

4. Operation
Imaging
6 Reload the second image:

a Under Source select Image Store,
under Operation select Make Stereo Pair,
under Source 2 select Buffer 1,
under Destination select Image Store.
b Click Execute.
Both images are combined with a colour code and

displayed on the monitor.
7 If the images are not exactly congruent, use the

sliders Stereo Merge and Stereo Tilt to adjust
X- and Y-directions.
IMPORTANT
Stereo glasses are required to be able to recognise the 3D effect in the colour image.

4. Operation
Imaging
4.4.8.3. Histogram equalisation

This function allows a non-linear contrast optimization of the image. Ranges with frequent grey
values are enlarged while ranges with rare grey values are compressed. Certain image structures
can thus be accentuated whereas other structures are reduced so that the total impression of the
image is modified.
1 Select Image/Image Processing from

the menu.
2 Go to the Histogram Equalisation tab.
3 To improve the contrast by calculating the
grey scale distribution, click Histogram
Equalise: Store.
The image is frozen.
4 To generate an image transformation by using

a Display-LUT click Histogram Equal-
ise:LUT.
To undo the calculated Display LUT, click
Reset LUT.
Examples for histogram equalisation:

4. Operation
Imaging
4.4.8.4. 2D filtering
The 2D Filters function enables selection of a kernel to be applied to the image in the source im-
age store.

the menu.
2 Go to the 2D Filters tab.
3 Under Source, select the storage to which the
transformation should be applied to.
4 Select a Filter.
Nine pre-defined filters are available:
Filter Process
User Defined Applies user-specific filters, according to definition below
Smooth Smoothes the image
Sharpen Sharpens the image
Sharpen 2 Sharpens the image
Horizontal edge Detects horizontal edges in the image
Vertical edge Detects vertical edges in the image
Edge Detect Performs irregular edge detection by using a combined detection of horizon-
tal and vertical edges in the image
Edge Detect 2 Performs irregular edge detection by using a combined detection of horizon-
tal and vertical edges in the image
Laplacian Detects edges in the image by realising a Laplace transformation using the
four neighbouring pixels.
Laplacian 2 Detects edges in the image by realising a Laplace transformation using the
eight neighbouring pixels.

4. Operation
Imaging
5 Select a Destination.
6 To start the image processing, click Execute.
If you want to cancel the last calculation, click

Undo.
Examples for 2D filtering:
Original image Inverted image
After application of Sharpen filter After application of Edge Detect filter

4. Operation
Imaging
Defining user-
specific filters
1 Under Filter, select User Defined.
2 Click Execute.
If no user-specific filters are defined, a warning

message pops up.
3 Confirm this message by clicking on OK.
The Apply User Defined Filter window opens.

4 Select New.

4. Operation
Imaging
The Edit User Defines Filter window opens.
5 Create a new filter by means of the Filter Ker-

nel Matrix, enter a file name and confirm.

4. Operation
Imaging
4.4.8.5. Realtime filtering

The function Realtime Filtering offers the possibility of mathematically manipulating the image
during recording. This feature is based on the evaluation of the grey value of a pixel, under con-
sideration of the grey value of the neighbouring pixels.

the menu.
2 Go to the Realtime Filtering tab.
3 Select the Filter type.
Filter Process Remarks
Smooth Smoothes the image. Recommended for live images with a high
noise ratio.
Set the degree of smoothing by using
the Smoothing slider.
Differentiate Differentiates the image. Increases the grey value differences of the
Set the degree of smoohting by using individual pixels. Accentuates fine struc-
the Differentiate slider. tures and increases the focus of the
image.
Being prone to interferences, this filter
should not be used for very noisy images.
User Defined Applies a user-specific filter, which can

be set by means of the Filter Kernel
field.

4. Operation
Annotating images
4.5. Annotating images
The annotation toolbar provides several tools to add notes or graphical objects to your image.
For example, you can insert lines, arrows or texts. Moreover, it is possible to measure distances
or the size of a rectangular area, the diameter of a circle or angle etc.
The image can be saved with the annotation overlaid on the image. Measurements can be per-
formed on either saved or live image.
4.5.1. Adding text
1 Select the Annotation Text icon.

Alternatively, type <CTRL+T>.
2 Click the image where you wish to place the
text.
A dialog opens.
3 Enter the text and confirm by clicking on OK.

4. Operation
Annotating images
4.5.1.1. Modifying text properties

1 Click the annotation text box to mark it.
2 Select Properties from the drop down list.
You can change e.g. font, font style, background style, and background colour.
4.5.2. Adding geometrical objects
1 Select the desired annotation icon such as

Annotation Line, Annotation Rectangle or
Annotation Ellipse.
object.

4. Operation
Annotating images
4.5.2.1. Modifying object properties

1 Click the annotation text box to mark it.
2 Select Properties from the drop-down list.
You can e.g. display a direction arrow at a line, change line settings, background style, and
background colour.
4.5.3. Adding EM parameters
1 Click the EM Parameter icon.
The Annotation SEM Parameter panel opens.
2 Select the parameters to be inserted.

3 If you wish that the value will be displayed
without parameter, tick the Omit Parameter
Name checkbox.

4. Operation
Annotating images
4.5.4. Adding a bitmap or metafile
1 Click the Insert User Bitmap icon.

object.
3 Select the bitmap or metafile.
4 Click Open.
4.5.5. Zone magnification
Zone magnification allows you to show the magni-

fication of a selected zone which might be helpful
when the magnifications of different zones are not
the same.
1 Click the Zone Magnification icon.

2 Click the zone of interest.
The magnification of this zone is displayed.

4. Operation
Annotating images
4.5.6. Adding micron markers
A micron marker is a horizontal bar which indicates the size of an object in the image. Above the
bar its length is displayed.
4.5.6.1. Micron marker

The micron marker is self-sizing as the bar has minimum and maximum lengths. If the magnifi-
cation is changed such that these limits would be exceeded the length represented by the bar is
changed to a whole number which would permit the bar to be within limits.
1 Click the Micron Marker icon.

2 Click where you wish to place the micron
marker.
The micron marker annotation can be picked up

and dragged into the required position. Ensure to
place the annotation not over another zone.
4.5.6.2. Fixed micron marker

1 Click the Fixed Micron Marker icon.
2 Click where you wish to place the micron
marker.
3 Enter the desired value.
4 Confirm.
The micron marker represents a fixed dimension,

and may therefore extend off the screen if the
magnification is too large or may shrink to a single
pixel length if the magnification is too low.
Editing the fixed micron marker allows you to
change the size.

4. Operation
Annotating images
4.5.7. Measuring
4.5.7.1. Measuring a size

1 To measure the size of a certain feature,
select the Point To Point Measure icon.
2 Click the image and keep the left mouse but-
ton pressed while drawing a line across the
feature you which to measure.
3 Release the left mouse button.
The measurement is displayed as a text adjacent to the object.
If you do not wish to display any of the parameters:

1 Double-click the line.
A dialog box opens.

2 Remove any items you do not want to be shown.
3 Confirm with OK.

4. Operation
Annotating images
4.5.7.2. Measuring an angle

1 Click the Angular Measurement icon.
2 Click the image where you wish to measure
the angle.
The measuring angle is shown.
3 Click the side of the angle to move its position.
4.5.7.3. Measuring a length or an area

1 Select the desired annotation icon: Linewidth
Measure or Radial Measure.
2 Click the image where you wish to measure
an object.

4. Operation
Annotating images
4.5.7.4. Measuring distances

1 Select the desired annotation icon such as:
• Width Measurement Cursors: fixed width

• Height Measurement Cursors: fixed height
• Moveable Width Cursors: variable width

• Movable Height Cursors: variable height
The cursors are displayed.

2 To move the cursor, click the cursor line and
hold the left mouse button.
4.5.7.5. Applying extended measuring capabilities (licence: MEASA)

The expanded measuring capabilities refer to adjustable width and height measuring cursors and
the rectangle measuring.
This licence offers four cycle measurements instead of only two without this licence. The point-to
point measurement can be called up to ten times (without licence: twice). The adjustable meas-
uring lines also can be called up to ten times (without licence: twice).
Requires the licence MESASA.

4. Operation
Annotating images
4.5.8. Editing Annotations
4.5.8.1. Moving an annotation

1 To move the annotation text to a different
position, use drag & drop.
4.5.8.2. Undoing the last edit

1 Click the Undo last Edit icon.
4.5.8.3. Hiding/Unhiding annotations

You can show or hide annotations.
1 To hide annotations:
a Select View/Hide Annotations from the
menu.
b From the submenu select which kind of
annotation you wish to hide.
2 To show annotations:
a Select View/Hide Annotations from the
menu.
b From the submenu select which kind of
annotation you wish to show.
4.5.8.4. Deleting an individual annotation

1 Click the annotation object or text.
2 Right-click the annotation object or text.
3 Select Delete from the drop-down list.

4. Operation
Annotating images
4.5.8.5. Deleting all annotations

1 Click the Delete All Visible Objects icon.
4.5.8.6. Saving annotations

1 Click the Save Annotation icon.
2 Enter an annotation name.
3 Confirm.
4.5.8.7. Loading annotations

1 Click the Load Annotation icon.
2 Select an annotation.
3 Confirm.

4. Operation
Annotating images
4.5.9. Displaying crosshairs or graticules (licence: GRATICULE)
4.5.9.1. Crosshairs
1 Select View/Crosshairs from the menu.
Crosshairs are displayed in the image area. In the drop-down menu, Crosshairs is ticked.
In order to remove the crosshairs, select View/Crosshairs again.

4. Operation
Annotating images
4.5.9.2. Movable Crosshairs
1 Select View/Movable Crosshairs from the menu.
Crosshairs are displayed in the image area.

In the drop-down menu Movable Crosshairs is ticked.
2 To move the crosshairs, click the square in the centre and drag.
In order to remove the crosshairs, select View/Movable Crosshairs again.

4. Operation
Annotating images
4.5.9.3. Graticules
1 Select View/Graticules from the menu.
Graticules are displayed in the image area. In the drop-down menu, Graticules is ticked.
2 To change the spacing between the graticule

lines, select View/Graticule Spacing.
3 Enter a value and confirm.
In order to remove the graticules, select View/Graticules again.

4. Operation
Working with recipes
4.6. Working with recipes
Recipes are used to save a set of SEM parameters which are ideal for a certain type of specimen.
When this type of specimen needs to be re-analysed in the future, the SEM parameters can be
recalled by opening the saved recipe. Only fine adjustments should then be required.
An Expert user (supervisor privilege) may set the SEM parameters for a range of applications and
save them as a common recipe that is available to all users. This enables Novice users to recall
such recipes.
4.6.1. Saving a user-specific recipe
A recipe is a file defining the specific set of parameters of the SEM/FESEM. A default ingredient
list defines the parameters to be saved in the recipe.
1 Select File/Save Recipe from the menu.
2 Enter a file name and confirm.

It is recommended selecting a file name which
allows you to clearly identify the very type of
specimen.
4.6.2. Saving a common recipe
Common recipes are available to all users. Saving a common recipe requires the supervisor priv-
ilege.
1 Select File/Recipe Management/Save

Common Recipe from the menu.
2 Enter a file name and confirm.

It is recommended selecting a file name which
allows you to clearly identify the very type of
specimen.

4. Operation
4.6.3. Viewing a recipe
In order to check the content of a recipe you can display a list of saved parameters.
1 Select File/View/Edit Recipe from the menu.
A list is displayed.
2 Mark the recipe you wish to view and confirm.
The content of the recipe is displayed.
Double-clicking on a parameter allows you to edit the parameter setting.

4. Operation
4.6.4. Executing a recipe
1 Select File/Execute from the menu.

2 Mark the recipe you wish to run.
3 If you wish to omit a particular parameter on the list, remove the respective tick.
4 Click Execute.
Only one recipe may be run at a time.
4.6.5. Deleting a recipe
1 Select File/Recipe Management/Delete from the menu.

2 Mark the recipe you wish to delete.
3 Confirm.

4. Operation
4.6.6. Creating an ingredient list
The ingredient list defines the contents of the recipe, i.e. the combination of saved parameters.
Parameters can be added and deleted.
1 Select File/Recipe Management/Ingredient File Editor from the menu.
The Recipe Ingredient List Editor opens.
2 Click Load File.

3 Select a recipe file and confirm.
4 Click Insert Parameter.

4. Operation
An alphabetical list of parameters is displayed.
5 Select the parameter you wish to add.

a To simplify the search, enter a key word in the field at the bottom.
b Select the parameter and confirm by clicking on OK.

4. Operation
The parameter is added to the list.
6 To change the order of the parameters, use the Move Up and Move Down buttons.
7 To insert a delay: Click Insert Delay.

8 Enter a time and confirm.
9 Save the ingredient list:
a To save it as a user-specific ingredient list: Click Save.
b To save it as a common ingredient list: Click Save To Common.

4. Operation
4.6.7. Using the MiniBar to work with recipes
Saving user-defined recipes, editing, and executing is also possible via MiniBar.
1 Click the Recipes icon on the Mini Bar.
2 To save the current SEM/FESEM settings as

a user-specific recipe, select Save Recipe.
3 To view, edit or run a recipe, select Recent for

the latest recipes or All Available for all
recipes.
4 To run a recipe, click the recipe name.
5 To view or edit, click the ... button after the re-

spective recipe name.
A preview list is shown, where you can omit indi-

vidual parameters.

4. Operation
Saving and managing images
4.7. Saving and managing images
4.7.1. Saving images
After optimising and freezing the image, it can be saved as a TIF (Tagged Image Format) file.
2 Enter a file name.

3 Select a file name format from the drop-down menu Format.
4 Select the numbering of the image file.
5 Select the store resolution from the drop-down menu Store Resolution.
6 You can also add text in the field User Text.
This text will be displayed when selecting a file in the Load Image dialog.
7 Click Save ’file name’.

4. Operation
4.7.1.1. Selecting TIF image modes and image dimensions

It is possible to save an image in several formats depending on your requirements. In general,
Grey is recommended.

2 Go to the Settings tab.
3 Select the Image mode:

• Grey
(8 bit, 256 grey scales)
Coloured SEM images which may possibly need to be modified later within the SmartSEM®
user interface, should be saved as grey images together with the respective colour pallet.
• 24 Bit Colour
(16 millions of colours)
IMPORTANT
Images saved as colour images (24 Bit Colour) cannot be reloaded to the SmartSEM® user
interface, but they can be implemented to most Windows® user programs.
• 16 Bit Grey
(65536 grey scales)
Exclusively reserved for later image modification by means of commercial programs.
IMPORTANT
When selecting 16 Bit Grey, no annotations, measurements or data zones will be saved.
4 Set the image dimensions.


4. Operation
4.7.1.2. Saving images as BMP or JEPG

It is also possible to save SEM images as BMP or JPEG. When using these formats, the SEM
images are always saved as grey images with the respective pallet. You cannot save the image
in colour.
IMPORTANT
Images in BMP and JPEG format cannot be reloaded to the SmartSEM® user interface.
Besides, it is not possible to save additional information with the image.
1 Place the cursor into the image area.

2 Right-click.
3 Select Send to/BMP file or JPEG file.
A dialog opens.
4 Go to the Settings tab.

4. Operation
5 Define the image dimensions.
6 When saving the image as JPEG:

a Enter a value for JPEG Quality.
The value can be between 5 and 95. The smaller the value, the higher the compression (re-
duced storage place) and the worse the quality of the image when printed.
A default value of 75 is set for JPEG Quality. In most cases, this value represents a good
compromise between compression of the storage place and quality of the image.
IMPORTANT
Depending on the image content of the respective image, quality and information may be
lost even when saving images at high level of JPEG Quality (75-95).
7 Return to the Save tab.


4. Operation
4.7.1.3. Saving images together with the Windows® overlay (Image Capture Mode)
Actually, the image displayed on the monitor consists of the SEM image itself and a Windows®
overlay. The overlay contains status bar, toolbar etc., while the centre (scan range) is set to trans-
parent.
When you take a screenshot by using the <PRINT> key on the keyboard, the saved image shows
only the Windows® overlay, whereas the SEM image range is displayed as a green or orange
section.
Image Capture Mode should be used to avoid this effect.
1 Select Tools/Image Capture Mode from the

menu.
The submenu Image Capture Mode is ticked.

The Capture Now submenu becomes available.
2 To activate the function one single time:

a Select Tools/Capture Now.
The live image is frozen and saved together

with the Windows® overlay.
A red triangle is displayed in the lower right
corner indicating the saved image.
3 To activate the function for continuous appli-

cation:
a Select Tools/Image Update Frequency.
b In the Image Update Frequency panel
tick the Enabled checkbox.
c Enter an interval.
d Confirm.
The live image is frozen and saved together

with the Windows® overlay.
A red triangle is displayed in the lower right
corner indicating the saved image.
To quit Image Capture Mode, select Tools/Image Capture Mode again.

4. Operation
4.7.2. Taking videos (licence: AVI capture)
The function AVI Capture Mode allows taking video sequences in order to show dynamic proc-
esses. The video can be played using the SmartSEM® user interface or another Windows® ap-
plication.
Requires the licence AVI Capture.
4.7.2.1. Setting parameters
1 Select Tools/AVI Options from the menu.
As a standard, the created video is saved as a

Capture.avi file in the user’s current image direc-
tory.
2 To change the file name or to select another
directory, click in the Capture Filename and
enter the data.
3 Set the maximum file size (max. 2047 MB).
4 In order to save annotations or measurements
together with the video, tick the Annotation
Merge checkbox.
5 If specific compression routines have been in-
stalled under the operating system, these rou-
tines can be selected by clicking on
Compression.
6 To set the number of images to be saved,
enter a value at Capture every.
7 Click OK to confirm.
To reset the default values, click Defaults.
4.7.2.2. Starting the record

1 Select Tools/AVI Capture.
The AVI Capture toolbar is shown.
2 To start recording, click the Start AVI

Capture icon.

4. Operation
4.7.3. Loading images
1 Select File/Load Image from the menu.
Alternatively, type <Ctrl + O>.
The Import TIFF dialog opens.
2 Select the directory by clicking on Change Directory.

Confirm by clicking on OK.
3 Select an image by double-clicking on it.
To return to the live image, select Scanning/Normal from the menu.

4. Operation
4.7.4. Using the Image Gallery
The images of a directory can be displayed as an image gallery. The images are shown as thumb-
nails together with the respective file name.
1 Select Image/Image Gallery from the menu.
The gallery is displayed.
2 To select an image, double-click it.

4. Operation
4.7.5. Printing images
1 Select File/Print Image.

Alternatively, type <Ctr + P>.
2 If you wish to print annotations and measurements together with the image, tick the respec-
tive checkbox.
To print colour annotations or measurements, the Colour Merge checkbox must be ticked as
well.
3 In the Size section, select the size of the printed image.
If you tick Zoom, you should also enter a zoom factor and select the position on the sheet
(Top, Middle or Bottom).
4 To select the printer, click Printer.
5 To start the printing process, click Print.

4. Operation
4.7.6. Copying images to the Windows® buffer (licence: CLIP)
The clipboard functions may be used to copy images to the Windows® buffer. As the image is not
saved to a storage device such as hard disk or floppy disk but to the central memory of the com-
puter, it can be used for other Windows® applications with access to the buffer store.
SEM images or sections of images can thus be copied to other programs without prior storage.
On the other hand, SEM images in the clipboard can be added to the stored image.
4.7.6.1. Storing images

1 Select Edit/Clipboard from the menu.
The Clipboard Copy tab opens.
2 Set the storage resolution by using the drop-down menu.

3 Select a reduction factor between 1 (original size) and 8.
4 To save data zone, annotations and measurement together with the image, tick the Annota-
tion checkbox.
5 To save colour annotations or measurements together with the image, tick the Colour Merge
checkbox.
However, the number of grey values (256) of the image is reduced to 20 as this storage space
is required for the annotation.
6 Set the desired dimensions of the image and click Set.

4. Operation
4.7.6.2. Inserting images

1 Go to the Paste tab.
The field File information lists size and type of the image in the buffer.
2 Select the Image Reduction factor.

Depending on the reduction factor, the size of the graticule is displayed on the screen. This
graticule shows position and format of the loaded image.
3 To change the position of the graticule, use the Centre, Origin, and XY buttons.
Selecting YX allows you to freely position the graticule by means of the mouse.
4 To compose one image out of four images:
a Click Origin.
b Tick the Step Frame checkbox.
5 To insert the image, click Paste.

4. Operation
4.7.7. Transmitting data to a FTP server or a network printer (licence: RE-

MARCH)
The FTP Remote Archiving program offers the possibility of transmitting images to a FTP server
or a network printer by using a network (TCP/IP).
Requires the licence REMARCH.
1 Select Start/Programs/SmartSEM/ImageArchiving.
2 In the middle field of the Source tab, select the files to be sent.
To select several files at the same time, hold the CTRL key and click the files.
3 Click the >> button to copy the selected files to the Image for Archive field.
To copy all files at the same time, click Add All.

4. Operation
4 Go to the Destination tab.
5 Use the radio buttons to select the destination of the image (Codonics Network Printer or FTP
Archive).
6 Click Host Settings.
7 Enter the required settings.
8 Confirm.

4. Operation
9 If you wish to sent the data to the network printer, go to the Network Printer tab.
10 Tick the Enable Transfers to Network Printer checkbox.
11 Set the required Printer Options.

12 Confirm the settings by clicking on Apply Print Settings.
13 To start the printing process, click Print.
The print job can be interrupted by clicking on Cancel Current Job.

4. Operation
4.7.8. Using the Large Image Store Wizard
The Large Image Store Wizard guides you through a process with three main steps to obtain im-
ages with high pixel resolution.
IMPORTANT
No annotations can be saved when using the Large Image Store Wizard.
1 From the menu, select Tools/Goto Panel and then Large Image Store Wizard.
Step 1 of 3 is displayed with a list of possible store

resolutions and a preview image.
In the SmartSEM® main window an image with
the resolution of 1024x768 is continuously
scanned and displayed.
The image in the main window equals the field of
view (FOV) that the final image will cover.
2 Optimise the image as described in section

3.4.7. Changing the magnification will also
change the FOV for the final image.

4. Operation
The size of the FOV and the pixel sizes for each
store resolution are shown in the wizard.
The coloured bar to the right helps you to select a
suitable store resolution. Resolutions marked in
red and yellow can also be selected, but these
resolutions will not provide an optimal image
quality.
The store resolution can still be selected accord-
ing to your requirements, as the coloured bar can
only give you a hint on the technical possibilities to
exclude resolutions that are too high for the se-
lected area.
3 To continue, select a store resolution from the

list and then click Next.
Step 2 of 3 is displayed.
An image preview is displayed at the bottom left of the window. A green rectangle shows the area
of interest displayed in the large image. The field of view and the rectangle represent the image
displayed in the SmartSEM® main window. To change the detail displayed in the large image, the
green rectangle can be moved in the in the image preview or the SmartSEM® main window.
4 To check the alignment, move the green rectangle to different areas. If necessary, optimise
the alignment. If you have problems to obtain satisfactory results, restart the procedure by
clicking Previous.

4. Operation
5 Select an End of scan action:

• None: after the scan is complete, it will restart at the beginning
• Freeze: after the scan is complete, the scan will be stopped
• Save as TIFF: after the scan is complete, the image will automatically be saved to the user‘s
image directory with the last used Export TIFF settings.
6 Click Next.
Step 3 of 3 is displayed.
Depending on the selected store resolution, the acquisition might take several minutes. You can
observe the process by moving the green square in the Image preview to a region that is already
displayed. If you need to stop the scan to change any settings, you can go back to step 2 by click-
ing Previous.
The selected End of scan action will be performed.
If you have selected Save as TIFF, a message
appears to confirm that the image has been suc-
cessfully saved.

4. Operation
Managing users
4.8. Managing users
The SmartSEM® software uses the SmartSEM® Administrator for user management. By means
of the SmartSEM® Administrator you can create new users and assign them with certain privileg-
es.
The Administrator creates the various user directories and edits existing folders and user config-
urations. A user directory is a closed data path which saves frequently modified configuration pa-
rameters of the SmartSEM® user interface and system software files for the various users.
If each user has their own directory for configuration parameters, the software can be configured
in such a way that toolbar, menus, data zones, etc. meet the specific requirements of each user.
Thus there is no need to reconfigure the user interface each time SmartSEM® is started.
4.8.1. Managing user profiles
4.8.1.1. Starting the SmartSEM® Administrator

1 Select Start/Programs/SmartSEM/SmartSEMAdmin.
The Administrator Log on window is shown.
2 Log on as follows:
Logging on for On initial installation of the SmartSEM® software:

the first time
a The person responsible for the SEM/FESEM should log on as SYSTEM with a blank
password.
The user list is shown.

4. Operation
Managing users
b Change the password to a suitable string:

Mark System in the user list. Select the menu Users/Edit.
c Click Change Password.
Change the password. It will take effect on the next log on.
d Confirm by clicking on OK twice.
IMPORTANT
Record the System password in a safe place. If you lose the password a chargeable
service visit will be required.
Logging on On regular log on:

regularly
a Enter username and password.
b Confirm by clicking on OK.
IMPORTANT
Logging on requires Supervisor privileges.
The SmartSEM Administrator window opens showing the user list.

4. Operation
Managing users
4.8.1.2. Creating a new user profile

1 Click New.
The New User window opens.
IMPORTANT
New user profiles are based on user templates or on existing users. This reduces the
workload when allocating rights for new users, while still being able to refine the profiles
later on.
2 To create a new user based on a user template or on an existing user, tick one of the radio
buttons.
3 Select a profile or an existing user from the
drop down list.
4 Click OK.

4. Operation
Managing users
The Creating new User Profile window opens.
5 Enter a User Name.

The user name must consist of at least three but not more than 20 characters.
6 Select a User Directory:

a Click the ... button to browse the folders.
b Select a user directory and confirm.
In the user directory, all user specific parameters and configurations such as appearance of
toolbar, data zone, and coordinates are stored and can be loaded again.

4. Operation
Managing users
7 Select an Image Directory:

a Click the ... button to browse the folders.
b Select an image directory and confirm.
In the image directory, all images of the user will be saved.
8 Set the User Level Permissions.

Any Level gives access to all available para-meters.
Full, Expert and Novice only enable access to a certain number of privileges and permissions.
Select the User Privileges.
If ticked, the user is allowed to modify

parameters as explained in the following
table:

4. Operation
Managing users
Checkbox Privilege
Calibration Enables the user to perform instrument calibration operations.
Change Image Directory Enables the user to change the location, where all images will be saved.
Change Toolbar Enables the user to change the toolbar.
Change User Directory Enables the user to change the location, where all user specific
parameters and configurations are saved.
Extractor Enables the user to change the extractor voltage.
Gun Align Enables the user to modify the alignment of the electron beam.
Gun Off Enables the user to switch off the FE filament
Stage Initialise Enables the user to initialise the motorised stage.
Supervisor Enables the user to

- start the Administrator, create and edit users
- set User Max EHT
- modify the filament current
- set-up, edit and delete global stage coordinates
- save common macros and toolbars
- save common recipes
- activate Partial Vent on Standby, Z Move on vent, Protect Z,
Go to HV@Shutdown, EHT Off & Log Off and Leave Gun ON at Shut-
down.
- use the bakeout function
- start the FIB filament heating.
Vent Enables the user to ventilate the specimen chamber.
IMPORTANT
Assign SUPERVISOR privileges only to a restricted number of authorised users.
The SUPERVISOR privilege permits the user to start the Administrator and to edit or create
user directories.
IMPORTANT
The default password for a new user is the user name.
Continue with assigning a personal password as described in the next section.

4. Operation
Managing users
4.8.1.3. Assigning or changing a password

1 Mark the user whose password is to be
assigned/changed.
2 Click Edit.
3 Click Change Password.
The Change password for.. window opens.

4 Enter the password.
It must consist of at least three but not more
than 20 characters.
4.8.1.4. Modifying a user profile

1 Mark the user whose user profile is to be
changed.
2 Click Edit.
3 Change the Preferences as desired.

4 Confirm.

4. Operation
Managing users
4.8.1.5. Deleting a user profile

1 Mark the user whose user profile is to be
deleted.
2 Click Delete.
3 Confirm.
4.8.1.6. Closing the SmartSEM® Administrator

1 Click the cross to close the Administrator software.

4. Operation
Managing users
4.8.2. Managing user accounts (licence: ACCOUNT)
The utility SmartSEM User Accounting allows recording of important information during individual
working sessions on the SEM/FESEM. The information is stored in a separate database file.
The SmartSEM User Accounting is part of the SmartSEM® program suite.
Requires the licence ACCOUNT.
IMPORTANT
Only Supervisor level users and higher are supposed to manage user accounts and use
the SmartSEM Administrator.
4.8.2.1. Starting the SmartSEM User Accounting

1 Select Start/Programs/SmartSEM/SmartSEM User Accounting.
The SmartSEM Accounting Log On window is shown.
2 Enter user name and password.

The User Accounting window opens.

4. Operation
Managing users
4.8.2.2. Using the help functions

1 Click Help.
2 Select Help Contents from the drop-down menu.
The SmartSEM Accounting Help opens.

4. Operation
Managing users

4. Operation
Managing users
4.8.2.3. Creating a new database file

1 Click Create.
An empty file (’Account.accdb’) is created in the directory C:\Program Files\Carl Zeiss Microscopy
Ltd\SmartSEM\system.
If a file has already been created, a warning message will pop up.
4.8.2.4. Activating/deactivating user accounting

1 To start recording, click Activate/Activate.
2 To stop recording, click Active/Deactivate.

4. Operation
Managing users
4.8.2.5. Deleting session records

This function offers the possibility to delete data in the database as from a specific date.
1 Click Delete.
1 Under Delete Records To enter the date.

A pop-up message appears.

3 Confirm.

4. Operation
Managing users
4.8.2.6. Grouping users

In order to group users together by the same institute or cost centre you can assign a user to a
so-called owner.
1 Click Owners.
2 Click Add.
The Creating new Owner window is shown.
3 Complete the fields.

The fields Name and Company are com-
pulsory.

4. Operation
Managing users
To assign a user to an existing owner:

1 Mark the owner in the list.
2 Mark an entry in the field Unasssigned
Accounts.
3 Click the arrow button.
4 Close the window by clicking on the cross.
To delete an owner:
1 Mark the owner.
2 Click Delete.
3 Confirm.

4. Operation
Managing users
4.8.2.7. Compressing the database

When the data within the database is modified the file will include unused sections inflating the
size of the database file on disk. To remove unused sections and remove errors:
1 Click Compact.
A back-up copy (account.bak) will be created in the directory

C:\Program Files\Carl Zeiss Microscopy Ltd\SmartSEM\system.
The database file will be compacted.
If errors occur during compaction, reset the original state by deleting the file ’Account.accdb’ and
renameing the file ’account.bak’ to ’Account.accdb’.

4. Operation
Customising the SmartSEM® software
4.9. Customising the SmartSEM® software
4.9.1. Customising joystick and control panel settings
You can change the settings for joystick speed, stigmator sensitivity and the sensitivity of the con-
trol panel encoders such as the Focus encoder.

2 Double-click User Settings.
The User Settings panel opens.
3 Use the respective slider to adjust joystick

speed, stigmator sensitivity and panel sensi-
tivity.
4.9.2. Setting mouse adjustment preferences
This option allows you to use the right mouse button for parameter adjustment when selecting
’3 Button wheel mouse’.
You may also show or hide the mouse adjustment image.
1 Select Tools/Configure Mouse Adjust from

the menu.
The Mouse Adjustment Preferences dialog

opens.
2 Make the desired settings.

4. Operation
4.9.3. Disabling the splash screen on startup
1 Go to the EM Server window.

2 Select Options from the menu.
A drop-down menu opens.
3 Click Disable Splash Screen On Setup.

The function is ticked in order to indicate that it is activated.

4. Operation
4.9.4. Personalising the user interface (User Preferences)
The user preferences offer the possibility to define user-specific pre-settings in the SmartSEM®
user interface.
4.9.4.1. Selecting the language

2 Under User/Language select English, French or German.
At present, switching to German or French is only possible within certain limits.
Help texts are available in English only.

4. Operation
4.9.4.2. Selecting the indicated pressure unit

2 Under User/Pressure Units select Torr, mbar or Pascal.
4.9.4.3. Selecting the User Access Level

The setting in User Access Level refers to parameters and commands to be selected e.g. in the
SEM Status window.
2 Under User/Access Level select Novice, Expert or Service.
Novice: Enables frequently used parameters and commands

Expert: Enables parameters and commands which may be helpful for an advanced user
Service: Activates all available parameters and commands

4. Operation
4.9.4.4. Entering pre-defined magnifications

Up to ten fixed magnifications can be entered in the Magnification table for quick access the dur-
ing imaging procedure.

2 In the tree structure, click Magnification Table.
3 Click into the Value field of Magnification 1 Value.

4 Enter the desired magnification.
5 Enter the desired magnification values for the other entries.
To use the Magnification Table while obtaining an image:

a Press <F4>.
Anytime <F4> is pressed, the next magnification value will be set.
b To return to the previous magnification value, press <Ctrl + F4>.
c To finish the use of the Magnification Table, press <Shift + F4>.
The magnification of the SEM/FESEM will be reset to the level that was active before the
Magnification Table was first used.

4. Operation
4.9.4.5. Tracking the user alignments (licence: USERALIGN)

The user align function tracks the alignment values each user has utilised for different operating
conditions. When these conditions are used the next time, the previous alignment values will be
reloaded.
Values are stored in an indexed table, where the index is generated from a combination of the
parameters making up the operating conditions.
1 To activate the function, select Tools/User Preferences.

2 In the tree structure, select User/User Align.
3 Select Enable User Align Yes.
Resetting The indexed table is automatically reset every

the table time the cathode is changed.
In addition, each user can reset his/her table indi-
vidually:
2 Double-click User Settings.
3 Click Reset User Align.

4. Operation
4.9.5. Customising the data zone
The data zone displays a special group of annotation objects which are used to show current
parameters, such as SEM parameters, username, time or date.
4.9.5.1. Unlocking the data zone

By default, the data zone is locked, so that the parameters stay within the data zone. Before you
can make any modifications, you have to unlock the data zone.
1 Click the Select Annotation Object(s)

icon in the annotation bar.
2 Click anywhere in the data zone to mark it.
3 Right-click the data zone.

4 Select Properties/Unlock this Panel from the
pop-up menu.

4. Operation
4.9.5.2. Inserting a parameter

1 Unlock the data zone.
2 Select the EM parameter icon in the annota-
tion bar.
3 Click in the data zone, where you wish to in-
sert the new parameter.
4 Select the parameter from the drop-down list.
6 Drag the new parameter to the required posi-
tion.
7 To change font, size or colour:
a Right-click the parameter.
b Select Properties/Font.
c Make your selection and confirm.
4.9.5.3. Inserting a logo

Logos or other images to be inserted have to be in bitmap (bmp) or metafile (wmf, emf) format.

2 On the Insert User Bitmap or Metafile icon in
the annotation bar.
3 Click the data zone.
4 Select a bitmap or metafile and confirm.
5 Arrange size and position of the inserted logo.
4.9.5.4. Displaying a value without parameter name

2 Click the parameter you wish to edit.
3 Right-click the parameter.
4 Select Properties/SEM Parameter.
5 Tick the Omit Parameter Name checkbox.

4. Operation
4.9.5.5. Modifying data zone features

You can change background colour, background mode (solid or transparent), select section lines,
style of frame, as well as fonts, colour and size of fonts.
2 Click anywhere in the data zone.
3 Right-click.
4 Select Properties
a To modify fonts, font style, font colour, and size: Select Set Panel Font.
b To change background mode: Select Solid Background Mode/Transparent Back-
ground Mode.
c To change colour of background: Select Background Colour.
4.9.5.6. Deleting a parameter

2 Click the parameter to be deleted.
3 Type <Del>.
Alternatively, right-click and select Delete.
4.9.5.7. Saving the customised data zone

1 Click the data zone to mark it.
2 Right-click in the data zone. Select Properties/Lock this Panel.
3 Right-click and select Save as Data Zone.
4 Enter a file name and save.
4.9.5.8. Loading a saved data zone

1 Select View/Data Zone/Load User Data Zone from the menu.
2 Select a file and confirm.

4. Operation
4.9.6. Customising the toolbar
The toolbar is fully customisable and can be altered to fit the needs of each individual user.
IMPORTANT
If ’Use Common Toolbar’ has been assigned to a user in the user profile, the functions
Move Up, Move Down, Save, Load, Remove, Add Button, Add Separator are NOT available.
1 Select Edit/Toolbar from the menu.

The Configure Toolbar window opens.
The toolbar editor is divided into several columns.

• The column Image shows the icon.
Each icon can have a double assignment activated by means of the left or the middle mouse
button.
• The column Button shows the assignment. You can toggle between left and middle mouse
assignment.
• The column Type shows the type of function (Special, Command, Macro, Dialog, Parameter-
Toggle, No Function) to be executed, when clicking on the toolbar icon.
• The column Name shows the name of the function.
• The column Tooltip Text shows the text to be displayed when moving the mouse cursor over
the icon.
• The column Button Text shows the text to be displayed below the icon.
To show the button text, click Options and tick the Enable the text below buttons checkbox.
• The column Menu shows the definition of a submenu, that can be assigned to each icon
regardless of the assigned functions.

4. Operation
4.9.6.1. Changing the order of the icons

1 Select an icon in the Configure Toolbar window.
2 Click Move Up, respectively on Move Down.
3 To insert a space between two toolbar icons, click Add Separator.
4.9.6.2. Deleting an icon

1 Select an icon in the Configure Toolbar window.
2 Click Remove.
4.9.6.3. Adding a new icon

1 Select the row in the Configure Toolbar window where you wish to insert the new icon.
2 Click Add Button.
3 Insert an icon:
a Double-click the No Icon symbol.
b Select an icon and confirm.
4 Assign a function:
a Double-click in the Type column.
b Select a function from the drop-down list:
Commands: Lists different commands
such as ’EHT on’.
Dialogs: Lists the commands to call up
menus and windows.
Macros: Lists all macros of the standard
macro library as well as individual macros
which have been implemented to this
library.
Parameters: Lists different commands to
read or set important parameters of the
SEM/FESEM.
Special Functions: Lists the Restore Sys-
tem Conditions and Save System Condi-
tions routines.
Toggle: Lists digital parameters which can
be used as a switch.
c Confirm.

4. Operation
5 Select Mid in the Button column.

6 Assign a function to the middle mouse button as described in step 4.
7 For both assignments, double-click the Tooltip Text field and enter a help text.
4.9.6.4. Assigning a menu to an icon

1 Double-click in the Menu field of the row you wish to edit.
The Edit Button Menu window opens.

2 Click Add.
3 Double-click No Function in the Function

Name column.

4. Operation
The Select Function window opens.

4 Select a type of function from the drop-down
list.
5 Select one of the functions shown.
6 Confirm.
The new menu is shown in the list.
7 Confirm.
The toolbar editor shows a small icon in the Menu column.

By double-clicking on this icon, you can directly open the Edit Button Menu window.

4. Operation
4.9.6.5. Saving the toolbar

Edited toolbars have to be saved with their own names.
1 Click Save.
2 Select Save As.
If you wish to make the toolbar available to all users, select Save As Common Toolbar.
3 Enter a name.
4 Confirm.

4. Operation
4.9.7. Customising the magnification display
4.9.7.1. Calibrating a user-specific magnification

In the factory, certified magnification standards are used for the calibration of magnification. How-
ever, it is possible to carry out a user-specific calibration of the magnification. This will allow the
comparison with other instruments or the use of specific application settings.
1 Load a calibration standard as specimen.

2 Select the User preferences Expert or Service.
3 Set acceleration voltage, working distance, and aperture size typically used for your applica-
tion.
4 Adjust the best possible focus and stigmation.
6 Double-click Magnification Calibration.
7 Select Cal User Magnification from the
upper drop-down list.
Two vertical lines are displayed on the screen.
8 Click the vertical lines and use them to mark an exactly defined distance on the image.
Refer to the documents delivered with the calibration standard.

4. Operation
9 Click into the Mag Cal Actual Width field.

10 Enter the value (µm) of the distance between
the two vertical lines.
11 Confirm by clicking on OK twice.

12 Close the Magnification Calibration window.
13 Place the cursor into the image area and

right-click.
14 Select User Calibration Enable.
Now, the calculation and setting of the magnifica-

tion is based on the user-specific calibration.
This is symbolised by an asterisk next to the
micron marker in the data zone.
To disable the user-specific calibration:

a Place the cursor into the image area.
b Right-click.
c Select User Calibration Enable so that the tick is being removed.

4. Operation
4.9.7.2. Calibrating an output device

The magnification is the ratio between the edge length of the image displayed on an output device
and the edge length of the scanned range on the sample. This means that it depends on the se-
lected output device.
If a defined range of the specimen is scanned and imaged on the monitor, the magnification will
correspond to the value X1. If the same specimen range is scanned and imaged in a Polaroid, the
magnification will correspond to the value X2. The value X2 is 3-4 time inferior to the value X1 (de-
pending on the monitor size), a Polaroid being 3-4 times smaller than the image range on the
screen.
When exchanging or installing an output media on a SEM/FESEM, a re-calibration is necessary

if the size of the presentation or print image has been changed.
1 Select the User preferences Expert or Service.

3 Double-click Magnification Calibration.
4 Select Cal Output Device from the
upper drop-down list.
Two vertical lines are displayed on the screen.

5 Click the vertical lines and use them to mark
an exactly defined distance on the image.
6 Click into the Output Dev cal actual field.
7 Enter the value (mm) of the distance between

the two vertical lines.
8 Confirm by clicking on OK twice.
9 Close the Magnification Calibration window.

4. Operation
4.9.8. Showing the installed licences
The licences installed on your SEM/FESEM can be shown from the SmartSEM® Administrator.
1 Open the SmartSEM® Administrator.

2 Click Licences.
A window with all installed software licences is displayed.

The checkboxes in the Standard column indicate the standard licences.
The checkboxes in the Enabled column indicate which licences are active.
You can sort the list according to part numbers, sales codes or descriptions. To do so, click into
the respective column title.

4. Operation
Remotely controlling the SEM/FESEM
4.10. Remotely controlling the SEM/FESEM
4.10.1. Using RS232 (licence: REMCON)
The program RemCon32 offers the possibility of remotely controlling the SEM/FESEM by using
the serial interface (RS232). Thus, it is possible to read or control specific parameters of the SEM/
FESEM. This option is especially useful if an EDX/WDX system is attached to the SEM/FESEM
as it enables communication between both systems by means of the serial interface.
1 Start the SmartSEM® user interface.

2 Select Start/Programs/SmartSEM/RemCon32.
3 Enter your username and password.
The RemCon32 window opens.
4 Select Comms/Settings from the menu.

5 Enter the port settings.
6 If you wish that the port automatically starts
after starting RemCon32, while the window is
reduced, tick the Open port and minimise
checkbox.

4. Operation
Remotely controlling the SEM/FESEM
8 To display the transmitted commands and replies, select Comms/Echo On.

9 For test purposes it might be helpful to use RemCon 32 in local mode:
a Select Comms/Local Mode from the menu.
b Enter commands and queries manually.
If correct communication is possible, the respective reply is displayed in the window and
the command is executed in the SmartSEM® user interface.
4.10.2. Using Windows XP Remote Desktop Connection (licence: Remote

SEM)
Remote operation of the SEM/FESEM is possible using the Windows XP Remote Desktop Con-
nection feature.
See the Window help on Using Remote Desktop Connection or contact your network administra-
tor for information on configuring Windows XP Remote Desktop Connection to operate over your
network.
To see the live microscope image over a remote connection, Image Capture Mode must be
turned on.
Image Capture Update Frequency should be set to the minimum value of 100 ms, which is only
available if the Remote SEM licence is present.
Remote SEM requires a minimum of 10 Mbps network bandwidth for useable operation, but a
100 Mbps LAN connection is recommended for true real time remote operation. If bandwidth is
limited, fast scan rates should be avoided and reduced raster should be used when possible to
minimise network traffic.

4. Operation
Communication with additional software
4.11. Communication with additional software
4.11.1. Communicating with Camelot software (licence: KNIGHTS CAMEL-

OT)
Knights Camelot software is a CAD navigation tool for locating specific features on a semicon-
ductor die. It works by registering the specimen with the design of the die to allow the CAD image
and SEM images to be synchronized to the same field of view. It is also possible to overlay the
image with parts of the design.
Requires the licence KNIGHTS CAMELOT.
1 Select Tools/Camelot Interface from the

menu bar.
The Camelot Properties panel opens.
2 Click Start Listening.
The indicated state changes from Waiting to
Listening.

4. Operation
Communication with additional software
4.11.2. Reading wafer defect files (licence: DEFECT REVIEW)
Defect review is used to find defects on a wafer or mask based on the results from KLA Tencor
results file.
Requires DEFECT REVIEW licence as well as STAGEREG and CENTRE licences.
Requires the KLA Tencor Resultsfile Specification V1.7
1 Select Tools/Go To Panel from the menu bar.

2 Double-click Defect Review.
3 Click Load and select a defect file (*rff).

4. Operation
Backing up / restoring data
4.12. Backing up / restoring data
When upgrading to a new PC or when reinstalling Windows on the PC, SmartSEM® configuration
and calibration data is lost. SmartBackup allows you to keep the data without having to recalibrate
the workstation.
4.12.1. Creating a backup
1 Close the EM Server.

2 Select Start/Programs/SmartSEM Service/SmartBackup Tool.
The SmartBackup window opens.
3 To select a backup directory, click Browse.

5 Click Save.

4. Operation
6 To backup the data to the selected directory, click Backup.
7 A message shows that the backup was

sucessful.
8 Confirm with OK.

4. Operation
4.12.2. Restoring data
Once a backup has been made, it can be restored to regain the configuration and calibration data
on a new PC or new Windows installation.
1 Close the EM Server.
2 Select Start/Programs/SmartSEM Service/SmartBackup Tool.
The SmartBackup window opens.
3 Go to the SEM Restore tab.

4 To select a previously saved backup, click Browse.
5 Select the backup file.

6 Click Open.

4. Operation
A message shows that the system is compatible.

7 Confirm with OK.
8 Click Restore.
A message shows that the restore process has

completed successfully.
9 Confirm with OK.

4. Operation
Working with optional accessories
4.13. Working with optional accessories
4.13.1. Using the Laser Finder
The Laser Finder is an accessory option that is designed to ease finding the area of interest on
the specimen surface. It consists of a chamber mounted laser, which is only illuminated in TV
mode. The laser spot is visible in the image of the CCD camera. It is used to make specimen
navigation easier.
For details on operation refer to the Instruction Manual Laser Finder.
4.13.2. Using the Quiet Mode
The automatically controlled Quiet Mode is optionally available.

It allows switching off the pre-vacuum pump after specimen exchange when the vacuum thresh-
old is achieved. This will provide a more comfortable noise level for operator and SEM/FESEM
while reducing power consumption of the pre-vacuum pump.
1 Go to the Vacuum tab of the SEM Controlss

panel.
2 Tick the Vac Quiet Mode checkbox.
The Quiet Mode is activated: The pre-vacuum

pump will be switched off when the vacuum
threshold is achieved.
To deactivate Quiet Mode, untick the checkbox.

4. Operation
4.13.3. Measuring the specimen current
The specimen current is the current flowing through the specimen. It corresponds to the total
number of electrons that hit the specimen.
A specimen current monitor can be attached to the SEM/FESEM as an optional accessory.
The Faraday cup consists of a strongly absorbing material with a cavity covered by an electron-
microscopic aperture.
1 Load a Faraday cup into the specimen chamber.

2 Pump the specimen chamber.
3 Switch on the electron beam.
4 Set a magnification that allows transmission of the complete electron beam into the cavity
through the aperture orifice.
6 Double-click Specimen Current Monitor.
7 Tick the SCM On checkbox.
The measurement is started. The measured val-

ue is displayed in the field Specimen I =.
The ground connection of the sample holder is

interrupted to interpose a pico-ampere meter. If
there is no risk that secondary electrons or
backscattered electrons leave the Faraday cup
the displayed current is the same as the incident
beam current.
8 In order to switch to Spot mode, tick the Spot

checkbox.
CAUTION
For all SEM/FESEM, except MERLIN:
Risk of damaging objective lens or specimen due to collision
During specimen current measurement the touch alarm is deactivated. Ensure to untick
the SCM On checkbox after finishing the specimen current measurement.

4. Operation
4.13.4. Using the Plasma Cleaner
The Plasma Cleaner is an optional accessory that allows you to decontaminate the specimen
chamber and any loaded specimens.
The Plasma Cleaner generates reactive gas-phase radicals in a plasma. This plasma is fully con-
tained in the Plasma Cleaner unit. The radicals migrate into the specimen chamber and chemi-
cally react with unwanted hydrocarbons.
After a plasma cleaning cycle, the specimen surface provides optimal imaging conditions even at
very low imaging voltages.
CAUTION
Sensitive specimen materials might suffer damage from plasma cleaning.
We recommend to test this on specimens of the same material before cleaning any impor-
tant specimens.
4.13.4.1. Activating the Plasma Cleaner
CAUTION
Unstable pressure or unwanted reactions with inserted gas can damage specimen or vac-
uum system.
The chamber pressure needs to be stable during plasma cleaning. If the gas injection sys-
tem or the charge compensation function are active, the gas insertion will affect the
pressure range and can create unwanted reactions with the inserted gas. Do not use GIS
or CC when using the Plasma Cleaner.
1 Check that the gate valve of the airlock is closed. Do not use the airlock while using the Plas-
ma Cleaner.
2 Switch off the EHT.
CAUTION
The pressure range applied during plasma cleaning can damage the electron source.
To protect the electron source from the harmful pressure range, close the column cham-
ber valve.
3 Close the column chamber valve:

a Go to the Vacuum tab.
b Click Column Chamber valve = and set it to Closed.

4. Operation
4 From the menu, select Tools/Goto Panel and then Plasma Cleaning.
The Plasma Cleaning window is displayed.

5 Check that the Plasma Cleaner controller
hardware is switched on and the Connected
LED is active in the software.
6 Select a recipe from the Recipe drop-down

list.
There are five preset recipes for different pur-
poses that can not be edited. Additionally, you
can create custom recipes (see next section).
7 To start the plasma cleaning, click Start

cleaning.
The plasma cleaning process starts.

4. Operation
To avoid damage, various parameters are changed automatically in the following sequence:
• The turbo pump is slowed down by 10 nitrogen impulses
• The specimen chamber is vented for 40 seconds
• The turbo pump is switched off
• Only the pre-vacuum pump remains active
The current status is displayed under Plasma

Cleaning Sequence.
If the selected recipe involves nitrogen purges, the

number of purge cycles (1) is displayed next to the
flow chart. The arrow shows which steps will be
repeated.
8 Wait until the Finished LED activates.

This indicates that the plasma cleaning proc-
ess is complete.
The chamber will be pumped.

9 Wait until ‘Vac Status = Ready‘ is displayed.
Gun and EHT can then be switched back on
and you can return to regular SEM/FESEM
operation.
IMPORTANT
You can view a log file that contains all relevant events by clicking ‘View Log...‘
This log file can be used for troubleshooting and to determine when the next plasma clean-
ing process should be sheduled.

4. Operation
4.13.4.2. Creating custom recipes

The five preset cleaning recipes should be enough for most applications.
In addition to the five preset recipes, you can create recipes for custom cleaning cycles.
1 Click Edit Recipes...
The Cleaning Recipes list is displayed with the five preset recipes. These recipes are fixed. This
means they can not be edited or deleted. Therefore, Edit... and Delete... are greyed out.
If you want to know whether or not a recipe can be edited, check the respective entry in the Type
column.
2 To create a new recipe, click Add...
The Cleaning Recipe window opens.

3 Enter a name for the cleaning recipe.
4 Select the desired values according to your
specific application.
5 If nitrogen purge cycles are necessary, tick
the Purge enabled checkbox. This will add
additional values that can be edited.
6 Once the settings are complete, click OK.
The recipe is now added to the list of available recipes. In the Type column the new recipe will
be displayed as User, which tells you that the recipe can be edited or deleted.

4. Operation
4.13.4.3. Setting up a schedule

If you want to schedule the next plasma cleaning, you can set up a date and time for an automat-
ed decontamination cycle.
1 To select a date for your cleaning schedule,
click the calendar icon (1).
2 Once you have selected the date, enter a time
(2) and activate the Schedule cleaning cycle
at: checkbox (3). 2
3 1
The cleaning cycle schedule is now active. 30 seconds before the scheduled cleaning cycle a
countdown will be displayed to inform you that a cleaning cycle is about to start.
You have the following options:
• To abort the countdown and start the cleaning cycle right away, click Start Now.
• To abort the countdown and cancel the scheduled cleaning cycle, click Cancel.
• To start the cleaning cycle as scheduled, no action needs to be taken.
4.13.4.4. Returning to regular SEM/FESEM operation

1 To be able to return to regular SEM/FESEM operation,
- click Stop cleaning to abort a cleaning cycle
- close the window if no cleaning cycle is running.
The chamber will be pumped.

2 Wait until ‘Vac Status = Ready‘ is displayed.
Gun and EHT can then be switched back on and you can return to regular SEM/FESEM
operation.

5. Troubleshooting
5. Troubleshooting
Error When an error message occurs, a message window will pop up. This indicates a serious condition
messages which must immediately be drawn to the operator's attention.
Most error messages are self-explaining.
The following table summarises important error symptoms and how to remedy.
Keyword Symptom Possible reason Recommended action
Stage Stage does not move. Stage needs to be initialised. Initialise the stage.
Stage does not move accu-
rately.
A stored stage position can-

not be approached.
Absolute stage movement is

required.
Stage/Joystick Under TV control, the direc- TV joystick angle does not fit for Change the joystick TV angle.
tion of dual joystick move- the selected CCD camera. Refer to section 5.2.
ment and direction of stage
movement seem to be differ-
ent.
Stage/Joystick Stage cannot be moved by Joystick Disable checkbox is Untick the checkbox in the
using the joystick ticked Stage tab of the SEM Controls
panel
OptiProbe After cathode replacement, after Calibrate OptiProbe.

re-alignment of the electron Refer to section 5.3.
optic column
Touch alarm Touch alarm message is Specimen or sample holder has Reset touch alarm.
shown. touched objective or wall of the Refer to section 5.4.
specimen chamber.
Temperature, Error message Flow of cooling water is not OK. Check water flow and tempera-
water flow ’Stage Board too hot’ (or sim- ture.
ilar) is shown. Refer to section 5.5.
EHT EHT cannot be switched on. Column chamber valve is Select Airlock panel from the
closed. Panel Configuration Bar. Click
Open Column Chamber Valve.
MERLINTM The workstation has crashed. CAN communication has failed. Check the CAN communication
workstation freeze as described in section 5.7.

5. Troubleshooting
Initialising the stage
5.1. Initialising the stage
The stage needs to be initialised before any absolute stage movement can be executed.
Executing this function requires the Stage Initialise privilege in the user profile.
Prerequisite: Specimen chamber has to be evacuated.
1 Select Stage/Stage initialise from the menu.

IMPORTANT
If initialisation of the stage does not solve the
stage problem, contact your Carl Zeiss service
engineer.
5.1.1. Defining the post initialisation position of the stage
You can configure the position to which the stage drives after the initialisation procedure. Other-
wise the stage will drive to the centre position.
Changing this setting requires the Supervisor privilege.

2 Click Column/Stage.
3 In the Stage Post Initialisation Position field, enter the desired position.
Alternatively:
a Move the stage to the required position.
b Click Set to current Posn.
4 To activate the function, tick the Post Init. Posn Valid checkbox.

5. Troubleshooting
Changing the joystick TV angle
5.2. Changing the joystick TV angle
In TV mode (chamberscope) it might occur that dual joystick (optional) and stage seem to move
to opposite directions. This is because the selected CCD camera is installed in a certain angle
relatively to the stage. Thus, the camera shows a side-inverted view.
To remedy, change the joystick TV angle setting in the software. Changing this setting requires
the Supervisor privilege.
IMPORTANT
If you are working with two CCD cameras: The joystick TV angle can only be set for one
CCD camera. When selecting the other CCD camera, you have to change the setting.

2 Click Column/Stage.
3 Double-click the Joystick TV Angle field.
180°
4 Enter an angle depending on the installation
location of the CCD camera.
90°
When the CCD camera is installed:
at the back: Enter 180°.
at the front: Enter 0°.
chamber door
at the side: Enter 90°.
0°

5. Troubleshooting
Calibrating OptiProbe
5.3. Calibrating OptiProbe
After cathode replacement or after re-alignment of the electron optic column, OptiProbe has to
be calibrated.
A calibration wizard facilitates the calibration procedure.
Parts required Part no.
Faraday cup, 348342-8055-000

orifice diameter at least 200 µm
1 Load a Faraday cup into the specimen

chamber.
2 Set WD 5 mm and select spot mode.
Focus the spot into the orifice of the
Faraday cup.
3 Select Start/Programs/SmartSEM/Opti-
Probe calibration.
The OptiProbe Cal dialog opens.
4 Click OK.
The OptiProbe Cal window opens.

5. Troubleshooting
Calibrating OptiProbe
5 To start the calibration, click Start.
The User Action window is shown.
6 Click OK.
An automatic calibration routine is performed,
which takes about fifteen minutes.
7 When the calibration procedure is finished, a

message appears.
8 To finish the dialog, click Yes.
Now OptiProbe is ready to be used.

5. Troubleshooting
Resetting touch alarm
5.4. Resetting touch alarm
To prevent damage, a touch alarm is integrated in the SEM/FESEM: If specimen or sample holder
touch chamber walls, detectors or objective lens, the stage is stopped immediately. An audible
warning and an on-screen message are given.
1 Accept the warning by clicking on OK.

2 Move the stage in the reverse direction.
5.5. Checking water flow and temperature

2 Double-click Water Flow/Temperature.
The Water Flow/Temperature panel opens.
3 Check the entries.
Note that the current values for EO Temp and

EO Temp Limit are only shown in case of
an error.
Resetting To reset overheat:

overheat
a Remedy the reason for overheating.
b Click Reset Overheat.
c Close and restart SmartSEM®.

5. Troubleshooting
Checking water flow and temperature (MERLINTM only)
5.6. Checking water flow and temperature (MERLINTM only)

2 Double-click Water Flow/Temperature.
The Water Flow/Temperature panel opens.
If a value is critical, it is displayed in red.

5. Troubleshooting
Checking the CAN communication (MERLINTM only)
5.7. Checking the CAN communication (MERLINTM only)
If the workstation does not react to your commands anymore:

2 Double-click CAN Communication.
The CAN Communication window opens.
If any of the values is indicated as Yes,

a make sure that all cable connections
between workstation and PC are plugged in
correctly.
If this does not help,

a reset the workstation as described in the
workstation manual.
IMPORTANT
If the problem persists,
contact your Carl Zeiss service engineer.

6. Summary of software functions
Menus
The different software functions can be called via:

• Menu bar
• Panel Configuration Bar
• Toolbars
- Toolbar
- Annotation bar
• Shortcuts
6.1. Menus
The different panels and dialogs necessary to operate the SEM/FESEM can be called by using
the menu bar and its submenus.
6.1.1. Menu File
The menu File offers the possibility

to manage recipes (i.e. a ’snapshot’ of a sample-
specific set of SEM/FESEM parameters),
• to load, save and print images,
• to use annotations, and
• to close SmartSEM®.

Menus
6.1.1.1. Execute Recipe

Opens the Select and Execute Recipe window.
• Select Recipe section

Allows selection of a recipe.
• Preview section
Checkboxes to activate/deactivate a para-
meter.
• Help
Calls the help function.
• Cancel
Aborts the selection.
• Execute
Runs the selected recipe.
6.1.1.2. Save Recipe

Opens the Save Recipe dialog.
• OK
Confirms the selection.
• Cancel
• VV
Allows you to select a recipe ingredient list.

Menus
6.1.1.3. View/Edit Recipe

Opens the Select Recipe dialog.
• Select recipe section

Allows you to select a recipe.
• OK
• Cancel
• Help
6.1.1.4. Recipe Management

Opens a submenu with three selections.
Delete Recipe
• Select file to delete section
Allows you to select a recipe.
• OK
• Cancel
• Help

Menus
Save Common Recipe

• OK
• Cancel
Aborts the selection
• VV
Allows you to select a recipe ingredient list.
Ingredient File Editor

• Help
• Delete File
Deletes the selected file.
• Load File
Loads the selected file.
• Insert Parameter
Adds a parameter.
• Insert Delay
Adds a delay.
• Move Up
Changes the position of the item in the list.
• Move Down
Changes the position of the item in the list.
• Delete Item
Removes an item from the list.
• Save
Saves the list so that it can be used together
with a user-specific recipe.
• Save to Common
Saves the list so that it can be used together
with a common recipe.
• Close
Closes the Ingredient File Editor.

Menus
6.1.1.5. Load Image

Opens the Import TIFF window.
Alternatively, type <Ctrl + O>.
6.1.1.6. Save Image

Opens the Export TIFF window.
Alternatively, type <Ctrl + E>.
• Change Directory
Selects the directory.
• Save xxx.tif
Saves the file.
• Annotation
Has to be ticked, when annotations
or measurements should be saved with the
image.
• Colour merge
Has to be ticked, when colour annotations
or measurements should be saved with the
image.
6.1.1.7. Print Image

Opens the Print Setup window.
Alternatively, type <Ctrl + P>.
Refer to section 6.1.1.8.

Menus
6.1.1.8. Print Setup

• Annotations and Measurements
Prints annotations and measurements to-
gether with the image.
• Colour Merge
Has to be ticked, when colour annotations or
measurements should be printed.
• Size
Selects the size of the image (Fit to Page/
Zoom)
• Position
Selects the position on the sheet (Top/Middle/
Bottom).
• Printer
Opens the printer selection dialog.
• Print
Prints the image.
• Close
Closes the dialog.
• Cancel
• Help
6.1.1.9. Load Annotation

Offers the possibility to load a previously saved
annotation.
6.1.1.10. Save Annotation

Offers the possibility to save an annotation or a
set of annotations.

Menus
6.1.1.11. Log Off

Shuts down the SmartSEM® user interface and all
other SmartSEM® applications such as the
RemCon32 program.
• Yes
Confirms the action.
• No
Aborts the action.
6.1.1.12. Exit
Shuts down the SmartSEM® user interface.
• Yes
• No
Aborts the action.

Menus
6.1.2. Menu Edit
The menu Edit offers the possibility

• to edit current or saved images, e.g. by modi-
fying brightness and contrast, inserting meas-
urements or annotations, copying images by
using the buffer store,
• to edit the user-specific current toolbar,
• to work with annotations,
• and to copy and paste items.
6.1.2.1. Input LUT

Opens the EM LUT Editor window.
The LUT editor is an applet that allows you to
modify the Input LUT
Requires the licence GAMMALUT.
6.1.2.2. Display LUT

Opens the EM LUT Editor window.
The LUT editor is an applet that allows you to
modify the Display LUT
Requires the licence GAMMALUT.

Menus
6.1.2.3. Toolbar
Opens the Configure Toolbar window.
• OK
• Cancel
Aborts the action.
• Move Up
Changes the position of the selected toolbar icon.
• Move Down
Changes the position of the selected toolbar icon.
• Save
Save As: Saves the toolbar with a user-specific name.
Save As Common Toolbar: Saves the toolbar that can be recalled by other users.
• Load
Loads a previously saved toolbar.
• Remove
Deletes the selected toolbar icon.
• Add Button
Inserts a new toolbar icon.
• Add Separator
Inserts a space between the toolbar icons.
• Options
Opens the Global Toolbar Options panel.
• Help

Menus
6.1.2.4. Annotation
Shows annotations.
Alternatively, type <Ctrl + A>.
6.1.2.5. Insert Annotation Text

Opens the Annotation Caption window.
Alternatively, type <Ctrl + T>.
• Insert Into Caption
Time Now
Inserts the current time.
Date Now
Inserts the current date.
User Name
Inserts the name of the current user.
• WordWrap Enabled
If ticked, text is made up.
• OK
• Undo
Cancels the selection.
• Insert New
Adds another annotation.
• Cancel
6.1.2.6. Insert Point to Point Marker

Adds a point to point marker.
Alternatively, type <Ctrl + M>.

Menus
6.1.2.7. Copy
Copies an item.
Alternatively, type <Ctrl + C>.
6.1.2.8. Paste
Inserts an item.
Alternatively, type <Ctrl + V>.
6.1.2.9. Clipboard
Allows you to copy and paste images by using the buffer store.
Requires the licence CLIP.
• Store resolution
Selects the storage resolution.
• Copy
Copies the image to the buffer.
• Reduction
Allows you to reduce the size of the stored image. Selection possible between 1 (original size)
and 8.
• Annotation
If ticked, data zone, annotations and measurements are copied together with the image.
• Colour Merge
Has to be ticked, if colour annotations or measurements should be copied.
• Whole
If ticked, the whole screen area, which will be overlayed blue, will be copied as the image.
• Dimensions
Sets the image dimensions.
• Set
Adopts the dimension settings.

Menus
Selects the storage resolution.
• Centre
Displaces the position of the shown graticule.
• Origin
• YX
• Paste
Inserts the image.
• Image Reduction
Sets the image reduction factor.

Menus
6.1.3. Menu View
The menu View offers features mainly referring to

the design of the SmartSEM® user interface.
Moreover, it is possible to enable or disable a cer-
tain group of measurements and annotations.
In the SEM Status window, the user can establish
a list of different parameters which can be dis-
played and interactively changed in this window.
6.1.3.1. Toolbars
Opens the Toolbar Views window.
Alternatively, type <CTRL+B>.
• By deactivating the checkboxes the respective feature is hidden.
• One of the radio buttons below User Toolbar Tool Tips has to be selected.
Show immediately/Show: A short explanation (tool tip) is displayed whenever the mouse button
is placed on one of the user toolbar icons.
Hide: The tool tip information is not shown.

Menus
6.1.3.2. Data Zone

Allows you to select the data zone to be shown.
• Toggle Data Zone <Ctrl + D>

Shows/hides the data zone.
• Display Default Data Zone
Shows a standard data zone.
• Hide Data Zone(s)
If ticked, the data zones are not shown.
• Unhide Data Zone(s)
If ticked, the data zones are shown.
• Load Data Zone
Allows loading a data zone.
6.1.3.3. Toggle Visible Dialogs

Shows/hides visible dialogs.
Alternatively, type <F3>.
6.1.3.4. Toggle Full Screen Image

Hides all bars and panels (complete Windows® interface) to show a full screen image.
Alternatively, type <SHIFT + F3>.
To show bars and panels again press <SHIFT + F3>.
6.1.3.5. Movable Crosshairs

• Displays movable crosshairs
If this function is activated, a tick is shown in the pull-down menu.

Menus
6.1.3.6. Crosshairs
• Displays crosshairs
6.1.3.7. Graticule
• Shows a grid on the image.
6.1.3.8. Graticule Spacing

Allows you to select the space between the
graticule lines.
• OK
• Cancel
6.1.3.9. SEM Status

This submenu opens the SmartSEM Status
window which allows showing, editing and setting
of frequently used SEM parameters.
• Display
Shows the selected parameters.
• Select
Allows you to select the parameters to be
shown.
• File
Allows you to load, save or delete a combina-
tion of parameters.
6.1.3.10. Thumbnails
Shows thumbnails.

Menus
6.1.4. Menu Beam
The menu Beam allows you to control the electron

beam parameters.
6.1.4.1. EHT On/EHT Off

Switches the acceleration voltage EHT on or off.
6.1.4.2. Gun Setup

Opens the Gun Service panel.
This submenu is reserved for the service engineer in order to set specific gun para-meters.
Each Schottky emitter has its individual values for filament heating current and extractor voltage.
The respective values are set by the Carl Zeiss service staff after the cathode has been changed.
CAUTION
Modifications of the filament heating current affect emitter life and resolution.
Therefore, any modification should be discussed with the local service engineer in
advance.
6.1.4.3. Emission
Changes to emission image mode.
Mainly used by service engineers.

Menus
6.1.4.4. Accelerating Voltage

Opens the EHT Target panel.
• OK
Confirms the setting.
• Cancel
Aborts the setting.
6.1.4.5. Apertures
Brings the Apertures tab to the fore of the SEM Controls panel.
6.1.4.6. Beam Shift

Opens the Beam Shift panel.
• Mag/Focus
Activates the magnification/focus function.
• BeamShift
Activates the Beam Shift function.

Menus
6.1.5. Menu Detection
Offers the possibility to select detection settings.
6.1.5.1. Detectors
Allows you to select a detector.
The selected detector is ticked.
6.1.5.2. Mixing
Allows you to mix the signals of two different detectors.
If active, this submenu is ticked.
Requires the licence SIGMIX.
6.1.5.3. Further submenus depending on installed detectors

Allow controlling the detectors installed.

Menus
6.1.6. Menu Image
The menu Image allows you to freeze the image,

to perform noise reduction, process images,
and to manage images.
6.1.6.1. Noise Reduction

Opens the noise reduction functions.
• Freeze on =
Selects the moment of freezing the image.
• Noise Reduction
Selects the noise reduction method.
• Freeze/Unfreeze
Freezes/unfreezes the live image.
6.1.6.2. Freeze/Unfreeze
Freezes respectively unfreezes the live image.

Menus
6.1.6.3. Image Processing

Opens the Image Processing panel with several tabs.
Requires the licence IMMATH.
Threshold tab
• Black threshold
Sets the threshold for black.
• White Threshold
Sets the threshold for black.
• Image Detect
Selects the type of threshold.
• Reset LUT
Resets the Look-up-table.
• Update
Calculates the area fraction.
Image Maths tab
• Source
Selects the source.
• Source 2
Selects source 2.
• Operation
Selects the operation.
• Execute
Executes the selected operation.
• Undo
Aborts the settings.

Menus
Histogram Equalisation tab
• Histogram Equalise Store

Calculates the grey scale distribution.
• Histogram Equalise LUT
Uses Display LUT for image transformation.
• Reset LUT
Undoes the calculated Display LUT.
2D Filters tab
• Source
Selects the storage to which the transforma-
tion will be applied to.
• Filter
Selects a filter from the drop-down list.
• Destination
Defines the buffer.
• Execute
Starts the image processing.
• Undo
Pre-defined kernel
filter matrices:

Menus
Realtime Filtering tab
• Filter type
Selects the type of filter, e.g. Smooth and Dif-
ferentiate.
• Smoothing
Sets the degree of smoothing.
• Differentiate
Sets the degree of differentiation.
6.1.6.4. Dual Channel

Allows you to display the live image on a second monitor.
Requires the licence DUAL-CHANNEL.
6.1.6.5. Copy To
Selects the buffer the image is to be copied to.
6.1.6.6. Copy From

Selects the buffer the image is to be loaded from.
6.1.6.7. Delete all buffers

Deletes all buffers.
6.1.6.8. Find Image

Activates an automatic procedure to find an image.
6.1.6.9. Image Gallery

Shows the images of a directory as thumbnails.
6.1.6.10. Realtime FFT

Shows a Fourier transformation of the current image. Aid for image optimisation.

Menus
6.1.7. Menu Scanning
The menu Scanning allows to control scanning

parameters.
6.1.7.1. Speeds
Offers the possibilty to select the scan speed.
Selection of fifteen scan speeds requires the

licence SCANEXP.
• OK
• Cancel
6.1.7.2. Normal
Returns from special scanning modes such as
Reduced, Spot, Line, Split, or Dual Mag to the nor-
mal scanning mode.

Menus
6.1.7.3. Reduced
Scans only a small frame (reduced raster), which
is suitable for alignment procedures.
6.1.7.4. Split
Activates the split screen function: The image
area is subdivided into two zones. Different detec-
tors can be assigned to each zone.
Requires the licence SPLIT.
6.1.7.5. Quad
Activates the quad split screen function: The im-
age area is subdivided into four zones. Different
detectors can be assigned to each zone.
Requires the licence QUAD.
6.1.7.6. Dual Mag

Allows zooming an image without freezing the im-
age at basis magnification.
Requires the licence DUALMAG.
6.1.7.7. Spot
Positions the electron beam on a particular spot
on the specimen surface.
6.1.7.8. Line Scan

Allows scanning a defined line while the image is
frozen.

Menus
6.1.7.9. Rotate/Tilt
Opens the Rotate/Tilt panel.
• Scan Rot
If ticked, the scan rotation is active.
• Scan Rotation
Allows setting of the scan rotation angle.
• Tilt Corrn.
If ticked, the tilt correction is active.
• Tilt Angle
Allows adjustment of the tilt angle.
6.1.7.10. Dynamic Focus
Allows you to dynamically adapt the focus of tilted

specimen surfaces.
Requires the licence DYNFOCUS.
• Dyn. Focus
If ticked, the dynamic focus is active.
• FCF Setting
Sets the degree of the dynamic focus
(FCF=Frame Corrected Focus).
6.1.7.11. Store Resolution

Allows you to select the storage resolution from a
drop-down menu.

Menus
6.1.8. Menu Stage
The menu Stage allows you to control several

stage functions.
6.1.8.1. Stage Initialise

Initialises the stage.
Requires the Stage Initialise privilege.
6.1.8.2. Store/Recall
Opens the Stage Points List (refer to section 6.2.35.).
6.1.8.3. Continuous Centre Point

If selected, the software remains in centre point mode after each point selection allowing repeti-
tive centre point actions.
To quit Centre Point mode, right-click.
6.1.8.4. Centre Point

Allows marking a spot in the image which is then automatically moved to the centre of the image
area.
6.1.8.5. Centre Feature

Allows selecting a feature or range in the image which is automatically centered and magnified
so that the selected image feature fills the complete image area.

Menus
6.1.8.6. Stage Scan

Allows you to scan an exactly defined series
of regularly distributed image fields.
• Setup Wizard
Opens the wizard.
6.1.8.7. Stage Map

This function allows using a frozen image in zone 0 as an overview for the selection of interesting
features on the specimen surface.
6.1.8.8. Survey
Opens the submenu.
Requires the licence SURVEY.

Menus
6.1.8.9. Navigation
• Toggle view
Changes the view.
• Stage stop
Stops the stage immediately.
• Z move on Vent
If ticked, the stage is driven to the lowest Z when the specimen chamber is ventilated.
• Track Z
If ticked, the focus will be automatically re-adjusted after every change if the Z coordinate
• Protected Z
If ticked, the current Z coordinate is compared with the new coordinate when calling saved
stage coordinates.
If the new Z position is higher than the current one, the stage drives to the X/YT/R coordinate
first, then to the new Z position.
If the new Z position is lower than the current one, Z is moved first, then the other axes.
• Settings
Opens the Stage Navigation setting dialog.
• More stage functionality
Opens a drop-down list.

Menus
6.1.9. Menu Vacuum
The menu Vacuum allows the control of the most

important parameters of the vacuum system.
6.1.9.1. Vacuum Status

Opens the Vacuum tab of the SEM Controls panel.
Alternatively, type <CTR+SHIFT+V>.
Standard vacuum system

• System Vacuum
Indicates the vacuum in the specimen cham-
ber.
• Gun Vacuum
Indicates the vacuum in gun head and liner
tube.
• Vent inhibit
None
Beam Present: EHT is on
• Vac Status
Indicates status of vacuum release.
Ready: Specimen chamber is evacuated and
ready to switch on EHT/Gun.
At Air: Specimen chamber is ventilated.
• Column Chamber Valve
Indicates the position (open/closed) of the
column chamber valve which separates
cathode head and specimen chamber.
• EHT Vac ready
Indicates status for high voltage release
• Pump / Vent:
Evacuates/Ventilates the specimen chamber.
Vent is available when the electron beam is
switched off.
Pump is available after changing the specimen.
• Partial Vent on Standby
If ticked, the specimen chamber will be ventilated partially when the SEM/FESEM is switched
to STANDBY mode.
Tick the checkbox if the vacuum is OK and the SEM/FESEM will not be operated for a longer
time (e.g. weekend). This can help to prevent oil vapours from penetrating into the specimen
chamber during STANDBY mode.
IMPORTANT
If the SEM/FESEM is vented or partially vented, it is NOT possible to start the bakeout.

Menus
VP vacuum system
• System Vacuum
Indicates the vacuum in the specimen cham-
ber.
• Vent inhibit
None
Beam Present: EHT is on
• Vac Status
Indicates status of vacuum release.
Ready: Specimen chamber is evacuated and
ready to switch on EHT/Gun.
At Air: Specimen chamber is ventilated.
• EHT Vac ready
Indicates status for high voltage release
• Pump / Vent:
Evacuates/Ventilates the specimen chamber.
Vent is available when the electron beam is
switched off.
Pump is available after changing the speci-
men.
• Partial Vent on Standby
If ticked, the specimen chamber will be venti-
lated partially when the SEM/FESEM is
switched to STANDBY mode.
Tick the checkbox, if the vacuum is OK and
the SEM/FESEM will not be operated for a
longer time (e.g. weekend). This can help to
prevent oil vapours from penetrating into the
specimen chamber during STANDBY mode.
IMPORTANT
If the SEM/FESEM is vented or partially vent-
ed, it is NOT possible to start the bakeout.
• Go to HV @ Shutdown
If ticked, the SEM/FESEM is automatically
switched to HV mode, when switching the
SEM/FESEM to STANDBY.
• Chamber
Indicates the actual pressure in the
specimen chamber in VP mode
• VP Target
Slider used to adjust the desired pressure in
the specimen chamber
• Go To HV / Go To VP
Changes to High vacuum mode/Variable
pressure mode.

Menus
6.1.9.2. VP Control (VP instruments only)

The submenu VP Control opens the VP Control panel.
• Chamber
Indicates the actual pressure in the
specimen chamber in VP mode.
• VP Target
Slider used to adjust the pressure in the spec-
imen chamber.
• Go To HV / Go To VP
Changes to High vacuum mode/Variable
pressure mode.
• Collector Bias
Sets the collector bias of the VPSE detector.

Menus
6.1.10. Menu Tools
The menu Tools offers the possibility to work with

macros, to customise the software and to start
recording a video.
6.1.10.1. Run A Macro

Opens the Selected a Macro to be Executed
dialog.
6.1.10.2. Macro Editor

Opens the macro editor.

Menus
6.1.10.3. Goto Control Panel

Opens the SEM Controls panel, which has six (standard vacuum system) or seven
(VP vacuum system) tabs.
Apertures tab
• Aperture Size.
Indicates the selected aperture sizes.
Drop-down list allows selection of another
aperture
• Focus Wobble
If ticked, the focus wobble is active in a reduced
raster. Used to optimise the image
• Wobble Fast
Accelerated wobble speed
• Wobble Amplitude
Allows changing the extent of the wobble move-
ment if the Focus Wobble checkbox is ticked.
• Beam Blanked
If ticked, the electron beam is removed from the
beam path, the specimen is not scanned any
more. This function blanks / unblanks the beam
with the scanning coils in the column.
The optional Beam Blanker is not controlled by
this checkbox.
• Emission
Changes to emission mode, which is mainly re-
served to Carl Zeiss service staff.
• Navigation box
Navigation box for adjustment of the
parameters shown on the buttons on the left.
• Mag/Focus
Allows setting of the magnification
• Aperture Align
Allows setting of the aperture alignment
• Gun Align
Allows setting of the gun alignment
• Stigmation
Allows setting of the stigmator
• Beam Shift
Allows setting of the beam shift.
• Fisheye Mode
If ticked, Fisheye Mode is active.
Requires licence FISHEYE.
• High Current
If ticked, high current mode is active.
Requires licence HIGH CURRENT.

Menus
Detectors tab
• Collector Bias
Sets the collector voltage.
• Signal A
Selects the active signal to be displayed on the
monitor
• Signal B
Selects the signal to be mixed with A
• Mixing
If ticked, the signals A and B are mixed
(requires the licence SIGMIX)
• Signal
Indicates the percentage of signal A while
mixing
• AutoBC
Sets the AutoBC function
Off: Switched the function off
B: Automatic adjustment of brightness
C: Automatic adjustment of contrast
BA: Automatic adjustment of brightness and
contrast
• Brightness
Adjusts brightness
• Contrast
Adjusts contrast
• Input LUT
Trans: Regular image display
Gamma: Allows user to adjust gamma with the
Gamma slider
Inverse: Inverts the image display
User: Opens the EM LUT Editor window
(section 6.1.2.1.)
• Gamma
Adjusts gamma

Menus
Gun tab
• EHT
Indicates actual acceleration voltage
• Extractor V
Indicates the current value of the extractor
voltage
• Ext I Monitor
Indicates the current value of the extractor
current
• Fil I
Indicates the current value of the filament heat-
ing current
• Beam state
Indicates the beam state
Drop-down list allows to switch EHT on/off and
to switch the gun on/off
• Leave Gun On at Shutdown
If ticked, the gun stays on when closing the
SmartSEM® software and changing to
STANDBY mode.
• EHT Off@ Log Off
If ticked, the EHT is automatically shut down
when the SmartSEM® software is closed by
using Log Off or Exit from the menu
• FIL I Target
Allows user to set the filament heating current
• Extractor V Target
Requires Service setting under Tools/User Preferences/User Access Level
• EHT Target
Allows user to set the
acceleration voltage
Each Schottky emitter has its individual values for filament heating current and extractor
voltage. The respective values are set by the Carl Zeiss service staff after the cathode has
been changed.
• OptiProbe
Allows automatic setting of the probe current.
With additional hardware only.

Menus
Scanning tab
• Operating Mode
Selects the operating mode
Normal
Split: Subdivides the image area into two zones
(requires the licence SPLIT)
Reduced: Scan a small frame (reduced raster)
Emission: Changes to emission mode
Select the stored resolution
• Line Scan
If ticked, a line is scanned permanently
• Spot
If ticked, spot mode is active (requires the li-
cence SPOT)
• Dual Mag
If ticked, the dual mag function is active (re-
quires the licence DUALMAG)
• Scan Speed
Sets the velocity of the scan
• Cycle Time
Indicates the cycle time depending on the
selected scan speed
• Zoom factor
Sets the zoom factor
• Freeze on
Defines when the image is frozen.
• Noise Reduction
Selects the noise reduction method
• Scan+/Scan-
Increases/decreases the scan speed
• Freeze/Unfreeze
Freezes/Unfreezes the scan

Menus
Stage tab
• Stage At
Indicates position of the stage axis
• Go To
Coordinates to be approached
• Stage Is
Current state of the stage
Busy: stage is moving
Idle: stage is standing still
• Z move on Vent
If ticked, the stage is driven to the lowest Z
when the specimen chamber is ventilated.
• Track Z
If ticked, the focus will be automatically re-ad-
justed after every change of the Z coordinate.
• Protected Z
If ticked, the current Z coordinate is compared
with the new coordinate when calling saved
stage coordinates.
If the new Z position is higher than the current
one, the stage drives to the X/Y/T/R coordinate
first, then to the new Z position.
If the new Z position is lower than the current
one, Z is moved first, then the other axes.
• Stage XY + Z
Affects the Stage Scan function.
If ticked, Z is moved in relation to the Z start co-
ordinate if the stage moves in tilt direction.
• Joystick Disable
If ticked, the dual joystick is disabled.
• Undo Go To
Cancels the last movement.
• Stage Stop
Stops the stage immediately.

Menus
Column tab (MERLINTM only)
• Column mode
Selects the column mode.
Crossover Free
Crossover
Depth of Field
Fish-eye
• EHT Target
Sets the EHT target.
• I Probe
Sets the I probe.
• Wobble Amplitude
Allows changing the extent of the wobble
movement if the Focus Wobble checkbox is
ticked.
• Focus Wobble
If ticked, the focus wobble is active in a
reduced raster. Used to optimise the image.
• Wobble Fast
Accelerated wobble speed.
• Beam Blanked
If ticked, the electron beam is removed from
the beam path, the specimen is not scanned
any more. This function blanks / unblanks the
beam with the scanning coils in the column.
The optional Beam Blanker is not controlled
by this checkbox.
• Offset Correction
Performs an offset correction.
• Navigation box
Navigation box for adjustment of the
parameters shown on the buttons on the left.
• Mag/Focus
Allows setting of the magnification
• Aperture Align
Allows setting of the aperture alignment
• Gun Align
Allows setting of the gun alignment
• Stigmation
Allows setting of the stigmator
• Beam Shift
Allows setting of the beam shift.

Menus
Vacuum tab
Gun Vacuum tab (VP instruments only)

6.1.10.4. Goto Panel

Opens the Panel Configuration Bar.
6.1.10.5. Camelot Interface

Allows the communication with the Camelot software.
Connect tab
• Port Number
Select the port number.
• Start Listening
Toggles between Start Listening and Stop Lis-
tening.
6.1.10.6. Image Capture Mode

Enables the image capture mode.
6.1.10.7. Capture Now

Saves the frozen image together with the Windows® overlay.
6.1.10.8. Image Capture Frequency

Sets the image update frequency.

Menus
6.1.10.9. User Preferences

Opens the user preferences dialog.
6.1.10.10. Configure Mouse Adjust
• OK
Confirms the settings.
• Cancel
• 3 Button wheel/standard
Selects the type of mouse
• Show the mouse adjustment...
If ticked, the mouse image is shown.
6.1.10.11. Administrator
Changes to the SmartSEM® Administrator.

Menus
6.1.10.12. AVI Capture

Allows you to take a video sequence (AVI file).
Starts record
AVI toolbar before start
Plays the saved video sequence
Opens the AVI File Capture

Options panel
AVI toolbar during record
Stops record
Pauses record
AVI toolbar during play
Fast forward during AVI play
Rewinds during AVI play
6.1.10.13. AVI Options

• Capture Filename
Sets the file name.
• Max file size
Sets the maximum size of the file.
• Annotation merge
If ticked, the annotations will be recorded in
the AVI file.
• Compression
Selects the reduction factor.
• Defaults
• OK
• Cancel

Menus
6.1.11. Menu Help
The menu Help leads to a multitude of help texts

and functions.
6.1.11.1. What’s This

Activates the context-sensitive help.
The mouse cursor is equipped with a questions mark and can be moved to a point of interest on
the screen.
Left-clicking indicates the appropriate help text.
6.1.11.2. Search
Opens the search function.
6.1.11.3. Release Notes

Shows a list of documents that contain information on software version history, such as new
functions, bug fixes and special features.

Menus
6.1.11.4. SmartSEM Help

Leads to a range of help topics.
Comprises the tabs Contents, Index, Search, and Favorites. Favorites can be added by clicking
on the Add button.
6.1.11.5. Getting Started

Opens a step-by-step guide for the first steps of operation.
6.1.11.6. How To
Opens a a step-by-step guide for frequently used operation sequences.
6.1.11.7. Keys help

Shows a list of the shortcuts (key combinations) for the operation of SmartSEM®.
6.1.11.8. About SmartSEM

Shows identification data of the installed SmartSEM® version.
6.1.11.9. Help Always On Top

Brings help texts to the fore.

Panels on the Panel Configuration Bar
6.2. Panels on the Panel Configuration Bar
To access the Panel Configuration bar, select Tools/Goto Panel from the menu.
Alternatively, click the arrow button at the right side of the image area.
A list of panel opens.
• ...
Opens the Docking Panel Options dialog.
• Toggle
Shows/hides the docking panel.
• Help
• >
Hides the Panel Configuration Bar.
To select a panel, double-click the panel name.

6.2.1. Airlock (optional)
Airlocks are used to reduce the possible contami-

nation of the specimen chamber.
• Column Chamber valve =

Indicates the status of the column chamber
valve, which separates gun area and specimen
chamber
• Open Column Chamber valve/Close Column
Chamber valve
Opens/Closes the column chamber valve if
EHT is switched off
• Pump/Vent
Starts pumping/venting procedure the airlock
• Hold Vacuum
Pumps of the specimen chamber are switched
off, but the airlock is not vented. Thus, the vac-
uum in the transfer room is preserved.
• Airlock Ready=
Indicates status of the airlock
• Specimen Change/Resume Exchange
Activates pre-defined macros to automate
airlock procedure

6.2.2. Bakeout
Requires the Supervisor privilege.
CAUTION
To prevent parts of the SEM/FESEM from being damaged, refer to the detailed instructions
in the instruction manual of the SEM/FESEM before starting the bakeout procedure.
• Bakeout
Selects the bakeout duration.
Quick: 2 h heating / 1 h cooling
Overnight: 8 h heating / 2 h cooling
Weekend: 40 h heating / 3 h cooling
User: To be defined by the operator.
• Bakeout State =
Indicates the current state.
Idle/Heating/Cooling
• Bakeout Heat=
Indicates the heating period set.
• Bakeout Cool
Indicates the cooling period set.
• Bakeout Start
Starts the bakeout procedure.
• Bakeout Cancel
Aborts the bakeout procedure.

6.2.3. Bakeout (MERLINTM only)
Requires the Supervisor privilege.
CAUTION
in the instruction manual of the SEM/FESEM before starting the bakeout procedure.
• Bakeout
Selects the bakeout duration.
Quick: 2 h heating / 1 h cooling
Overnight: 8 h heating / 2 h cooling
Weekend: 40 h heating / 3 h cooling
User: To be defined by the operator.
• Bakeout State =
Indicates the current state.
Idle/Heating/Cooling
• Target /°C
Displays the target temperature.
• Actual /°C
Displays the current temperature.
• Heat /hours
Displays the selected heating duration in
hours.
• Cool /hours
Displays the selected cooling duration in
hours.
• Total /hours
Displays the total bakeout duration including
heating and cooling.
• Bakeout Start
Starts the bakeout procedure.
• Bakeout Cancel
Aborts the bakeout procedure.

6.2.4. Beam Shift
• Mag/Focus
Changes to magnification and focus setting.
• Beam Shift
Activates the beam shift function.
Assigns beam shift X and Y to the left mouse
button.
• Beam Shift navigation box

Changes the position of the specimen by
shifting the beam.
6.2.5. BSD Control (optional)
Allows control of detectors with four diode quad-

rants such as AsB™ detector and 4QBSD.
• Quadrants
Symbolise the four quadrants
Normal (+)
Inverted (-)
Disabled
• BSD Gain
Selects the gain range.
• BSD:COMPO
Activates compositional mode (all quadrants
are in normal mode)
• BSD:TOPO
Activates topography mode.
• Apply
Applies the changes
• BSD: Set TOPO
Changes the settings for TOPO.
• BSD Auto range
If ticked, the auto range function is activated.

6.2.6. CAN Communication (MERLINTM only)
Displays the status of the Controller Area Network (CAN) communication for EHT, vacuum and
stage.
This dialog is only used to display the communica-
tion states of the subsystems for diagnostic
purposes.
• EHT Comms Fail

Indicates if the CAN communication with EHT
unit has failed.
• Vac comms fail
Indicates if the CAN communication with the
Vac Board has failed.
• Stage comms fail
Indicates if the CAN communication with the
Stage Board has failed.
6.2.7. CZ Detector Calibration (optional)
Requires setting Service under Tools/User Preferences/User Access Level.

6.2.8. Calibrate Stage Centre
• Centre: Pos X
Indicates the last value for X.
• Centre: Pos Y
Indicates the last value for Y.
• OK
• Cancel
• Next
Leads to the next step of the calibration pro-
cedure
6.2.9. Calibrate Stigmation
This dialog should only be used by authorised Carl Zeiss service staff.
6.2.10. Colour Mode (licence: Colour Mode)
• Brightness A
Sets brightness of signal A
• Contrast A
Sets contrast of signal A
• Colour Mode
Select colour mode
• Brightness B
Sets brightness of signal B
• Contrast B
Sets contrast of signal B

6.2.11. Column Calibration
Requires Service setting under Tools/User Preferences/User Access Level
Follow the instructions in the panel.

6.2.12. Compucentric Height (licence COMPU)
This dialog allows you to measure the compucen-

tric height. (Refer to the SmartSEM® help for a de-
tailed description)

6.2.13. Defect Review (licence DEFECT REVIEW)
• Load
Loads a defect file (*rff).
• Properties
Shows properties of the selected defect file.
• Wafer map
Shows a two dimensional view of the wafer.

6.2.14. Define User Output Device Magnification
• Define Text ID
Shows the name
• Define Image Width
Indicates the width
6.2.15. Detector Signal Out Configuration (MERLINTM only)
This dialog is used to configure external detector outputs on the system. There are two detector
outputs on each detector board fitted. Each may be configured as Signal A, Signal B or a speci-
fied detector name e.g. Inlens. A separate configuration can be selected for internal scan and
each of the 4 external scan inputs. A detector signal can only be assigned to one video out.
• Scan Source
Allows you to select the scan source.
Internal
Ext 0
Ext 1
Ext 2
Ext 3
• Video Out 0-5
Allows you to select the signal depending on
the selection in the other Video Out drop down
lists.

6.2.16. Drift Correction
• Reference Image
- Display Rectangle
Displays a movable frame. The image range
inside the frame defines the reference image
for the drift correction.
- Hide Rectangle
Hides the movable frame.
- Create Reference
Acquires a reference based on the current
settings.
• SEM drift status =:
- No reference
Reference has not yet been set.
- Busy
Busy creating reference.
- Ready
Reference has been created.
Do SEM Drift Corrn can be clicked.
• Do SEM Drift Corrn
Starts the SEM drift correction.
• Settings
- Drift Max. Pix.Error =
This determines how close consecutive drift
correction attempts should be to each other if
they are to be considered as the same.
- Drift Min Conf =
As the drift correction algorithm uses a statistical image matching algorithm there is an ele-
ment of uncertainty over whether the drift values it returns are correct. The certainty level de-
termines the minimum certainty that the drift values are correct required to use those values
to adjust the drift. Generally this should be a bit lower than the values returned during the test
drift correction on the Take reference image page. A minimum of 25% is allowed. Values of
50% are quite reasonable and although you can enter up to 100% it is unlikely that an image
would match with that strength of correlation. Note: The percentages are measures of corre-
lation, not of probability; for example a certainty of 50% does not mean that for every 10
matches returned with this value 5 are wrong, in fact it is quite likely that they are all correct.
- Drift Max Tries =
When the drift correction algorithm is being used it takes the current image more than once
and sees if the drift values returned are the same within certain limits on consecutive attempts
this helps prevent mistakes. Max attempts sets how many times it should try to get a match
before it decides that the drift correction is not working. If you set this to 0 then no drift cor-
rection will be used. If more than Max Attempts are required to find a matching image then
the system assumes that the drift correction is not working and ignores it until the next drift
interval.
- Default Settings
Restores the default settings.
- Periodic Drift Correction Period(s)
Allows you to schedule a periodic drift correction. A drift correction will be carried out every-
time the set timespan in seconds has expired. This can only be used after a reference has
been created.

• Beam Shift
- X/Y
Displays the current beam shift in X/Y.
- Zero Beam Shift
Sets the X/Y beam shift to zero.
- Go to Reference
Moves the specimen stage to the reference
point.
• Options
- Use Stage
If activated, only the stage is used for drift cor-
rection.
- Field Search
If activated, the reference point is searched in
a larger field outside the rectangle.
Recommended in case of stronger drift .
- Auto Brightness
If activated, the Auto Brightness is activated to
optimise image recognition.

6.2.17. Ext Scan Control
• Ext On
Switches external scan control on
• Ext Off
Switches external scan control off
• Ext. Scan Select
Allows you to set the Ext Scan value

6.2.18. Image Navigation
Allows you to load an image from a variety of sources and then set-up a stage registration be-
tween the image and the stage. This will enable to navigate the stage by clicking on the image.
There are two ways to register an image: manually (Manual Registration) or automatically (Auto
Registration).
CAUTION
Danger of damaging stage or stubscope
When using the stubscope, the stage will often be at high Z values.
Tick the ’Protected Z’ checkbox and set an appropriate value for Safe Z whenever moving
between electron axis and stubscope axis.
• External Image
Loads an externally generated image from a file.
• Setup
Starts the Stage Registration wizard.
• Clear registration
Cancels the registration.
• Load
Loads an image.
• Save
Saves an image.
• Current SEM Image
Loads the current SEM image.

6.2.19. Large Image Store Wizard
The Large Image Store Wizard guides you through a process with three main steps to obtain im-
ages with high pixel resolution.
• Field of view:
Displays the currently selected field of view in
µm.
• Store resolution:
Allows you to select a store resolution and the
corresponding pixel size.
• Image preview:
Displays a preview of the currently selected
ROI.
• Next (active if resolution has been selected):
Continues with the next step.
• Previous (active in steps 2 and 3):
selects the previous step.
• Cancel wizard:
Closes the Large Image Store Wizard.

6.2.20. Laser Finder (optional)
The Laser Finder is an accessory option designed to ease finding the area of interest on the spec-
imen surface.
CAUTION
in the Instruction Manual Laser Finder before using the Laser Finder.
• Laser Finder
If ticked, the Laser beam is active.
• Laser Illumination
Changes brightness of laser spot.
• CCD Illum.
Changes brightness of infrared light for CCD
TV camera detection.
6.2.21. Long Distance Measurement
This allows you to measure the physical distance

between two points on the specimen, which can-
not be seen in a single field of view so cannot be
measured using annotation.
(Refer to the SmartSEM® help for a detailed de-
scription).

6.2.22. Magnification Calibration
Requires Service or Expert setting under Tools/User Preferences/User Access Level.
• Calibration mode
Selects the calibration mode
Cal Mode Off
Cal Stig Balance
Cal Output Dev
Cal User Magnification
6.2.23. Nano Motor Control
This window refers to the optionally available Piezo Substage for AURIGA®.
For detailed information on the Piezo Substage, refer to the Instruction Manual Piezo Substage.
• Piezo at X
Displays the current position of the Piezo
stage in X direction.
• Piezo at Y
Displays the current position of the Piezo
stage in Y direction.
• X/Y high/low limit hit
If a X/Y high/low limit is reached, a message
box is displayed in red.
Otherwise the box is hidden.
• Nanomotor Step
This function allows you to select the step size
from a drop down menu.
Coarse
Medium
Fine
The arrow buttons can be used to move the stage in single steps of the defined size, or to
continuously move the Piezo stage when pressing down one of the arrow buttons.
To be able to move the Piezo stage with the arrow buttons, the Piezo Manual checkbox has
to be ticked.
• Piezo Exchange Defined
Indicates whether a specimen exchange position is defined for the Piezo stage or not.
An exchange position can be set by clicking on Set Exchange Position.

• Piezo Goto X / Y
Allows you to enter predefined coordinates in a separate window.
When clicking on OK, the Piezo stage will move to the entered coordinates.
• Piezo State
Indicates the current state of the Piezo stage
Idle: stage is standing still
Moving: stage is moving
Uninitialised: stage has not been initialised yet
• Piezo Manual
Activates/deactivates the arrow buttons.
• Die Navigation
• Fold in / out icon
Folds in / out the lower part of the window.
• Set Exchange Position
Allows you to set a specimen exchange position for the Piezo stage.
• Piezo Initialise
Initialises the Piezo stage
6.2.24. Peltier Stage
• Peltier
Indicates if a Peltier cool stage is fitted and the
Peltier Fitted checkbox in the SmartSEM®
Administrator is ticked.
• Peltier Temp
Indicates the current Peltier temperature if a
Peltier cool stage is fitted and the Peltier Fitted
checkbox in the SmartSEM® Administrator is
ticked.
• Peltier Target
Indicates the Peltier target temperature.

6.2.25. Plasma Cleaning
6.2.25.1. Main window

Recipe
• Recipe drop-down list
Opens a selection of available recipes.
• Edit Recipes...
Opens the Cleaning Recipes list.
• Recipe values
Shows the following values of the currently
selected recipe:
- Plasma ignition pressure
- Plasma pressure
- Plasma time
- Plasma power
- Plasma total time
• Schedule cleaning cycle at:
If activated, a cleaning cycle will be carried out
at the currently selected time and date with
the active recipe.
• Date and time field
Allows you to select a time and date for a
scheduled plasma cleaning cycle.
• Status message area
Shows status and error messages.
• Vac Status
Displays the currently present vacuum status.
• Plasma State
Displays the currently present plasma status.
• Plasma cleaner connected
Shows if a Plasma Cleaner is connected.
• Cleaning status
Shows if a plasma cleaning cycle is running.

Plasma Cleaner
• Connected
If active, the Plasma Cleaner controller hard-
ware is switched on and connected.
• Enabled
If active, a plasma cleaning process is run-
ning. This LED is also present on the Plasma
Cleaner controller hardware (ENABLE/DISA-
BLE).
• RF On
If active, a plasma cleaning cycle is running
and the radio frequency is on, which is neces-
sary for the plasma to start. This LED is also
present on the Plasma Cleaner controller
hardware (RF ON).
• Plasma On
If active, a plasma cleaning cycle is running
and the plasma has ignited. This LED is also
present on the Plasma Cleaner controller
hardware (PLASMA ON).
• Fault
If active, the Plasma Cleaner is in error state.
• Plasma Cleaning Sequence
Displays the steps of the currently running
plasma cleaning cycle and their completion
status.
• View Log...
Opens the Log file.
Start cleaning
Starts a plasma cleaning cycle using the current
settings.
Stop cleaning
Stops the currently running plasma cleaning cycle
and pumps the chamber.

6.2.25.2. Cleaning Recipes list
• Type
Displays the type of recipe:
- Fixed: Not editable and not deletable
- User: Editable and deletable
• Recipe Name
Displays the name of the recipe.
• Ignition Pressure (mbar)
Displays the plasma ignition pressure.
• Plasma Pressure (mbar)
Displays the plasma operating pressure.
• Plasma Power (Watts)
Displays the plasma operating power. Up to 20 Watts can be selected.
• Plasma Time (hh:mm)
Displays the plasma time.
For recipes without nitrogen purge, Plasma Time equals Total Time.
• Purge Pressure (mbar)
Displays the nitrogen purge pressure.
• Purge Time (hh:mm)
Displays the timespan for each nitrogen purge.
• Cycles
Shows the number of cycles. One cycle consists of plasma cleaning and a nitrogen purge.
This value is only present if the recipe includes one or more nitrogen purges.
• Total Time (hh:mm)
Displays the total time required to run the recipe. It is determined by the values Plasma Time,
Purge Time and Cycles.
• Add...
Opens a dialog that allows you to create a new recipe.
• Edit...
Opens a dialog that allwos you to edit the currently selected recipe. This is only available for
‘User‘ type recipes.
• Delete...
Opens a dialog that allows you to delete the currently selected recipe. This is only available
for ‘User‘ type recipes.
• Close...
Closes the Cleaning Recipes list.

6.2.26. Rotate/Tilt
• Scan Rot
If ticked, the scan rotation is active.
• Scan Rotation
Allows setting of the scan rotation angle.
• Tilt Corrn.
If ticked, the tilt correction is active.
• Tilt Angle
Allows adjustment of the tilt angle.
6.2.27. SEM Controls
6.2.28. Soft Joystick
The Soft Joystick window opens.

• Stage vector navigation box
Moves the X- and Y-axes.
• Stage vector Z
Moves the Z-axis.
• Stage vector T
Move the T-axis.
• Stage vector R
Rotates the stage.
• Stage vector M
Moves the M-axis.

6.2.29. Specimen Current Monitor
The Specimen Current Monitor dialog opens.

• SCM On
If ticked, the specimen current monitor is
switched on.
• Spot
If ticked, spot mode is active, i.e. the electron
beam is positioned on a particular spot on the
specimen surface.

6.2.30. Stage Encoder Calibration
Requires setting Service under Tools/User Preferences/User Access Level.
6.2.31. Stage Horizontal Alignment
Follow the instructions.
6.2.32. Stage Limits
Allows entering the stage limits.

6.2.33. Stage Nav Settings
• Show Gallery
Shows the Sample Holder Gallery
• Calibrate Stage Centre
Calibrates the centre of the stage.
• Calibrate
Calibrates the height of the stage.

6.2.34. Stage Navigation
6.2.35. Stage Points List
• Save/Load
- Load
This function loads the coordinate list from a
previously saved file. The current list of position
data is deleted.
- Save
Saves the active list to the user directory.
The extension is *.XYZ.
• On Goto
Opens a drop-down list with these entries:
- Set Magnification
If activaded, the magnification of a list entry will
be applied when the respective entry is select-
ed. If deactivated, the magnification will remain
at the current setting.
- Set Working Distance
If activated, the working distance will of a list
entry will be applied when the respectivy entry
is selected. If deactivated, the magnification will
remain at the current setting.
- Move XY Only
If activated, the stage will only move in X and Y
when a list entry is selected.
• Add
Opens the Label Request dialog that allows
you to add a new stage position with a custom
label.
• Del
Allows you to delete a stage position from the list. Only available if a list entry has been se-
lected.
• Edit
Allows you to edit a stage position on the list. Only available if a list entry has been selected.
• Undo Stage Goto
Cancels the stage movement.
• Stage stop
Stops the movement.
• Goto
- First
Moves the stage to the position defined by the first entry in the Stage Points List.
- Next
Moves the stage the position defined by the next entry in the Stage Points List.
- Prev
Moves the stage to the position defined by the previous entry in the Stage Points List.
- Selected
Moves the stage to the position defined by the highlighted entry in the Stage Points List.

6.2.36. Stage Registration (licence STAGEREG)
Allows you to define a user specific 2D coordinate system.
6.2.37. Stage Scanning (licence STAGESCAN)
Allows you to scan an exactly defined series of regularly distributed image fields.
• Setup Wizard
Starts the wizard

6.2.38. Stage Survey (licence SURVEY)
Survey Mode provides the facility to enter a defined state Survey Mode State. Typically a long
working distance and low magnification to achieve a wide field of view in which the specimen may
be reviewed for features of interest. (Refer to the SmartSEM® help for a detailed description)
.
6.2.39. User Settings
• Joystick speed
Changes the speed of the joystick
• Stig Sensitivity
Changes the sensitivity of the stigmator
• Panel Sensitivity
Changes the sensitivity of the control panel
encoders such as Focus
• Reset User Align
Resets the user-specific user alignment table
• OK
Confirms the settings

6.2.40. VP Control (VP instruments only)
• VP Target
Sets the desired pressure.
• Go To HV/Go To VP
Toggles between high vacuum mode (HV)
and variable pressure mode (VP).
• Collector Bias
Sets the collector bias of the VPSE detector.

6.2.41. Water Flow/Temperature
• Stage Too Hot

Indicates the temperature status.
• EO Too Hot
• Water OK
Indicates the water status.
• EO Temp
Only in case of an error: Indicates the current
temperature of the EO Board.
• EO Temp Limit
Only in case of an error: Indicates the limit
temperature of the EO Board.
• SEM Overheat
Indicates the status.
• Reset Overheat
Quits the error message.
• Close
Closes the Water Flow/Temperature dialog.

6.2.42. Water Flow/Temperature (MERLINTMonly)
• Stage Too Hot

EO
This section covers all water supply of the EO
board, which is divided in the EO dynamic and the
EO static.
• EO dynamic flow
Indicates the status of the EO dynamic water
flow.
• EO dynamic temperature
Indicates the status of the EO dynamic water
temperature.
• EO static water flow
Indicates the status of the EO static board
water flow.
• EO static water temperature
Indicates the status of the EO static water
temperature.
Water Flow
This section covers overall water flow and
temperatures
• Water OK
Indicates the water flow status.
• Water flow temperature
Indicates the water flow temperature.
• Water return temperature
Indicates the water return temperature.
Water Temperature Status

This section summarises all water thresholds.
• Water in high critical
Indicates if the water in high critical value has
been reached.
• Water in low critical
Indicates if the water in low critical value has
been reached.
• Water out high critical
Indicates if the water out high critical value
has been reached.
• Water out low critical
Indicates if the water out low critical value has
been reached.
• Close
Closes the Water Flow/Temperature dialog.

6.2.43. Windowing
Windowing allows you to display two different de-

tector signals on the monitor.
• Windowing
If ticked, the windowing function is active.
• Zone =
Selects the active zone.
Zone 0: outside the reduced raster
Zone 1: inside the reduced raster
• SignalA =
Selects the detector signal
• Invert A = On/Off
Activates/deactivates the inversion of the sig-
nal of the respective zone

Assignments of toolbar icons (default toolbar)
6.3. Assignments of toolbar icons (default toolbar)
Icon Tool tip text Left mouse button Middle mouse button
Restore Conditions/ Loads the state stored last when Activates the window loading a
Load State the program was ended. stored state (Load State).
Accelerating Voltage/ Opens the EHT target window to Calls the Gun tab in the SEM
Gun Control set the acceleration voltage Controls window
Specimen Change/ Ventilates the specimen cham- Calls the Gun Vacuum tab in
Vacuum Control ber. the SEM Controls window.
Pumps the specimen chamber.
VP Control/VP Target Calls the VP Control panel. Assigned with the VP Target
Pix Avg 1/ Cont Avg 2 Pixel averaging at scan speed 2 Continuous frame averaging at
scan speed 2
Pix Avg3/Cont Avg4 Pixel averaging at scan speed 3 Continuous frame averaging at
scan speed 4
Pix Avg6/Cont Avg? Pixel averaging at scan speed 6 Continuous frame averaging at
scan speedspeed 6
Pix Avg 9/Frame Int 5 Pixel averaging at scan speed 9 Frame averaging at scan speed
5 (image is frozen after scan)
Frame Int/Frame Int 8 Frame averaging at scan speed Frame averaging at scan speed
7 (image is frozen after scan) 8 (image is frozen after scan)
Faster/Slower Sets a higher scan speed. Sets a lower scan speed.
Freeze:Unfreeze/ Freezes/unfreezes the image. Calls Scanning tab in the SEM

Scanning Controls window
Normal/Scanning Normal screen mode (Scan Calls Scanning tab in the SEM
range displayed over the com- Controls window
plete monitor). Wobbler is
switched off. Mouse button
assignment: magnification/focus

Assignments of toolbar icons (default toolbar)
Icon Tool tip text Left mouse button Middle mouse button
Reduced Raster/ Switches between reduced scan Calls Aperture tab in the SEM
Apertures and normal screen mode. Controls Panel.
Split Screen/ Switches between split screen Calls Detectors tab in the SEM
Detectors and normal screen mode. Controls Panel.
Dual Magnification/ Switches between dual magnifi- Calls Detectors tab in the SEM
Detectors cation and normal screen mode. Controls Panel.
ChamberScope/ Activates the CCD TV camera. Calls Detectors tab in the SEM
Detector Control Mouse button assignment: Controls Panel.
brightness/contrast
Stigmation/ Activates the reduced raster. Calls wobbler and activation of

Alignment Mouse button assignment: StigX, reduced scanning.
StigY/ Focus
Point To Point/ Inserts a point to point measure- Calls text editor.

Annotation Text ment.
Brightness + Con- When AutoBC is deactivated in Switches from AutoBC= ON

trast/ the detector window, the mouse (mouse button assignment
Toggle ABCC button assignment is switched to GAIN/ OFFSET) to AutoBC=
brightness/contrast. When the OFF (mouse button assignment
AutoBC function is activated, the brightness/contrast) and back.
mouse button assignment is
switched to GAIN/OFFSET
Toggle INLENS:SE2/ Switches between In-lens and Calls Detectors tab in the SEM
Detector Control SE2 detector Controls Panel.
Magnification + Mouse button assignment: mag- Calls Auto Focus and Auto Stig-
Focus/ nification/focus mator algorithm.
Auto Focus + Stig
Save TIFF/ Saving an image as TIFF file with Calls Export TIFF window.
TIFF Export Dialog the agreed settings
Print Image/ Prints the image on the default Calls Print Setup window
Printer Dialog printer.

MiniBar icons
6.4. MiniBar icons
Icon Tool tip text Function
Start.. Allows quick access to Pump/Vent as well as EHT

On/EHT Off and Gun ON/Off function.
Recent Panels.. Allows quick access to recently used functions.
Recipes.. Allows quick access to stored recipes

Annotation icons
6.5. Annotation icons
Select Annotation Object(s) Allows you to select individual annotations.
EM Mouse Control Enables the control of EM parameters via mouse.
Undo Last Edit Cancels the last step.
Load Annotation Loads a user annotation.
Save Annotation Saves the annotations as user annotation.
Delete All Visible Objects Deletes all visible annotations.
Export Area Selection Defines the export area.
Annotation Text Adds a text the user can enter.
EM Parameter Adds parameters, the user has selected from a list dis-
played.
Insert User Bitmap of Metafile Adds an image, e.g. a logo.
Annotation Line Adds a line.
Annotation Rectangle Adds a rectangle.

Annotation icons
Annotation Ellipse Adds an ellipse or a circle.
Sticky Panel Adds a rectangle to the overlay plane onto which anno-
tation objects can be "stuck". The rectangle can be
transparent or filled with a pattern.
Zone Magnification Allows you to show the magnification of a selected

zone which might be helpful when the magnifications of
different zones are not the same.
Micron Marker Adds a horizontal bar which indicates the size of an

object in the image. Above the bar its length is dis-
played.
Fixed Micron Marker Adds a horizontal bar which indicates the size of an
object in the image. The bar represents a fixed dimen-
sion.
Point to Point Measure Allows you to measure the size of a certain feature.
Angular Measurement Allows you to measure an angle between two objects.
Linewidth Measure The linewidth measurement facility is a rectangle which

may be adjusted in height, width, and angle.
Radial Measure The radial measurement facility is a circle which may

be adjusted in diameter.
Width Measurement Cursors Comprises a related pair of vertical lines. Each line may
be adjusted in position.
Height Measurement Cursors Comprises a related pair of horizontal lines. Each line
may be adjusted in position.
Moveable Width Cursor Comprises a vertical measurement bar with variable

length and position.

Annotation icons
Moveable Height Cursor Comprises a horizontal measurement bar with variable

length and position.
Stored Vector Profile Shows a vector profile.
Stored Data Histogram Shows a data histogram.
Insert TIFF Data Inserts tiff.

Shortcuts
6.6. Shortcuts
Many functions and menus which are often used in the SmartSEM® user interface can also be
opened using the keyboard.
The function keys F5, F6, F7, F8 and F11 as well as SHIFT + F5, F6, F7, F8 and F11 can be
assigned with different functions via the macro editor.
The different keys and key combinations in the SmartSEM® software are briefly explained in the
table below.
Key/Key combination Function
<F1> Calls the general help texts.
<Shift + F1> Calls the context-sensitive help.
<F2> Hides/shows the toolbar.
<Shift + F2> Corrects the lens hysteresis.
<F3> Hides/shows open a window in the SmartSEM® user inter-

face.
<Shift + F3> Hides/shows toolbars, menu bar, status bar etc.
<F4> Activates the Magnification Table and switches to the next

fixed magnification.
or resets the Centre Feature magnification (when pressing
F4 after using the Centre Feature function, the old magnifi-
cation is reset.)
<Shift + F4> Ends the use of the Magnification Table.
<F5> Reserved for user defined macros.

<F6>
<F7>
<F8>
<F11>
<Shift + F5> Reserved for user defined macros.

<Shift + F6>
<Shift + F7>
<Shift + F8>
<Shift + F11>
<F9> Calls the help function for shortcut keys.
<F10> Sets the cursor into the menu bar.
<F12> Stops the specimen stage immediately.

<Shift + F12>
<TAB> Toggles between coarse and fine mode.
<CTRL + TAB> Performs the Centre Point function.
<CTRL + SHIFT + TAB> Performs the Centre Feature function.
<HOME> Resets Beam Shift to zero.
Table 6.1: Important keys and key combinations

Shortcuts
Key/Key combination Function
<SCROLL LOCK> Toggles between Freeze and Unfreeze.
<PAUSE> Causes currently executing macro to continue

Stops a running macro
<CTRL + A> Calls the Annotation panel.
<CTRL + B> Calls the Toolbar View panel.
<CTRL + C> Copies.
<CTRL + E> Calls the Export TIFF dialog for saving the image.
<CTRL + F> Starts Auto Focus fine.
<CTRL +G> Switches SEM Controls panel On.
<CTRL + I> Calls the SmartSEM Status Panel.
<CTRL + M> Adds a point -to-point marker.
<CTRL + O> Loads an image.
<CTRL + P> Calls the Pint Setup dialog.
<CTRL + S> Starts the Auto stigmation procedure.
<CTRL + T> Inserts annotation text.
<CTRL + V> Pastes.
<CTRL + F4> During the use of the Magnification Table: Returns to the
previously used magnification.
<CTRL + SHIFT + F> Starts Auto Focus (coarse).
Table 6.1: Important keys and key combinations

7. Abbreviations
7. Abbreviations
2D Two dimensional
4QBSD Four quadrant backscattered electron detector
ABCC Automatic brightness and contrast control
Auto BC Auto brightness and contrast
AVI Audio video interleaved
BC Brightness and contrast
BMP Bitmap
CC Charge compensation
DB Database
EDX Energy dispersive spectroscopy
EHT Electronic high tension
EM Electron microscope
EsB Energy selective Backscattered electrons
FCF Frame Corrected Focus = Dynamic Focus
FESEM Field emission scanning electron microscope
FOV Field of view
FTP File transfer protocol
GIS Gas injection system (optional accessory)
HV High vacuum
I Current
ID Identification
JPEG Joint Photographic Experts Group
LB Left mouse button
LUT Look-up table
MB Middle mouse button
SCM Specimen current monitor
SE Secondary electron
SEM Scanning electron microscope
TIF Tagged image format
V Voltage
VP Variable pressure
WD Working distance
XB Cross Beam®

7. Abbreviations

8. Glossary
8. Glossary
Administrator The SmartSEM® Administrator is part of the SmartSEM® program suite,

which allows user management e.g. creating users and assigning them
with certain privileges. The SmartSEM® Administrator is protected by an
administrator password.
Annotation Software function that allows adding notes or graphical objects to the
image.
Crosshairs A graphical object for assessing the relative position of objects in the
image.
Dongle A device that is needed in order to use protected software.
EM Server A server that implements the internal communication between control

software and microscope hardware.
Eucentric Type of stage, the rotation axes of which intersect in the same point.
The specimen surface is located in the eucentric point, where the tilt axis
meets the beam axis. This guarantees that the focus is maintained when
the specimen is tilted at a certain working distance.
Expert One of the SmartSEM® user levels, good for a person with special knowl-
edge and training in operating a FESEM.
Graticules A grid displayed over the image.
High current Mode which increases the active probe current obtained by a stronger
activation of the condenser lens.
Ingredient list A list that defines the contents of a recipe, i.e. the combination of saved
parameters.
Licence Licences are used to enable specific functionality in the SmartSEM® soft-
ware.
LUT Look Up Table which can be used to improve the image illumination.
Magnification Table Function of SmartSEM® that allows you to enter fixed magnifications for
quick access during the imaging procedure.
MiniBar Part of the SmartSEM® user interface which allows quick access to
recently used dialogs and to the recipe management.
Novice One of the SmartSEM® user levels, good for a person who is new and
has little experience in operating a FESEM.
OptiProbe Optional function which allows you to continuously adjust the probe cur-
rent.
Recipes Function of SmartSEM® that allows you to save a set of SEM parameters
which are ideal for a certain type of specimen.
Service/Full The highest SmartSEM® user level.
Splash screen Animated start screen of SmartSEM® .
Supervisor Privilege that permits to start the Administrator and - among others - ena-
bles to edit or create user directories and to start the bakeout function.

8. Glossary
User Preferences Section that allows you to define user-specific pre-setting of the Smart-
SEM® user interface e.g. language or pressure units.
Zone Part of the image area when displaying different detector signals or
image areas.

9. Index
9. Index
A D
Acceleration voltage 95 Data zone 25, 212, 260
Accounting 198 DEFECT REVIEW 227
Administrator 190 Detector Signal Out Configuration 300
Airlock 291 Detectors 109
Anchor symbol 25, 114 Dongles 15
Annotation bar 25 Dot, blue 26
Annotation icons 326 Dot, red 26
Annotations 153 Drift Correction 301
Any Level 194 Drift Max Tries = 301
Aperture 102 Drift Max. Pix.Error = 301
Aperture size 98 Drift Min Conf = 301
Astigmatism 103 Dynamic Focus 131
Auto Stigmation 103
AutoBC 112 E
AVI 178 EDX 124
EHT 95
B Error messages 239
Backlash 68 Evacuating 63
Backup 228 Expert 26, 194, 209
Bakeout 292 Ext Scan Control 303
Beam shift 67, 263 Extractor voltage 99
Beam shift, large 67
Blanking the beam 97 F
BMP 175 Fisheye mode 72
Brightness 111 Focus wobble 48, 102
Frame Average 135
C Frame Integrate 135
Calibrating magnification 220 FTP server 184
Camelot software 226 Full 194
CAN Communication 295
CCD camera 120, 241 G
Centre feature function 85 Graticule spacing 261
Centre point function 85 Graticules 163, 165, 261
ChamberScope 120 Gun 93, 94
Cleaning Recipes 311 Gun Monitor 106
Clipboard 257 Gun Vacuum 59, 60
Collector Bias 110
Collector voltage 110 H
Colour mode 117 Help 53
Column Chamber Valve 275, 291 High current mode 100
Compucentric 78 HV mode 65
Continous Average 136
Continuous Centre Point 85 I
Contrast 111 Icons 216
Control panel 206 Image area 115
Coordinate system 91 Image Capture Mode 177
Copying images 182 Image drift 69
Crosshairs 163, 261 Image Gallery 180
Crosshairs, movable 164, 260 Image Navigation 304
Image stitching 20
Image Stitching Application 17

9. Index
Ingredient list 169 Pixel Average 136

Initialise stage 195, 239, 240 Plasma Cleaner 234
Intended use 11 Plasma Cleaning 309
Pressure unit 209
J Printing images 181
JEPG 175 Privileges 194
Joystick 206, 241 Probe current 98, 101
Joystick TV angle 239, 241 Protected Z 274, 283
K Q
Knights Camelot 226 Question mark near micron marker 72
Quiet Mode 232
L
Language 208 R
Large Image Store Wizard 187, 305 Recipe 248
Laser Finder 232, 305 Recipe, common 166
Licence 15, 19, 223 Recipe, user-specific 166
Line 126 Recipes 166
Line Average 135 Reduced raster 123
Line Integrate 135 RS232 224
Line Scan 126
Loading images 179 S
Logo 213 Safety 11, 12
Long Distance Measurement 306 Sample Holder 75
Look Up Tables 138 Sample Holder Gallery 77
LUT 138, 147 Saving images 173, 177
Scan mark 126
M Scan marker 129
Macros 278 Scan speed 122
Magnification 118, 130, 220 Scanning 269
Magnification Table 130, 210 SCANROT 128
Magnifications, pre-defined 130, 210 SEM parameters 104, 106
Measuring 158 SEM Status 261
Menu bar 25 SEM status window 104
Menus 247 Service 209
Micron marker 72, 157 Service/Full 26
MiniBar 25, 172, 325 Signal-to-noise ratio 135
Mixing 113 SmartSEM® Administrator 190
Mouse 206 SmartStitch 17, 18
Mouse buttons 323 Soft joystick 66
Specimen chamber 74
N Specimen current 233
Nano Motor Control 307 Specimen exchange 61
Noise reduction 135, 137 Splash screen 207
Novice 26, 194, 209 Spot 124
Stage centre 78
O Stage coordinates 84
OptiProbe 101, 239, 242 Stage initialise 195, 240
Overheat 244 Stage Map 86
Owners 203 Stage navigation 74
Stage, non-eucentric 78
P Status bar 25
Panel Configuration Bar 25, 34, 290 Stereo image 144
Partial Vent on Standby 275 Stigmator 103, 206
Password 191, 195 Supervisor 191, 195
Peltier Stage 308 Survey Mode 88, 90

9. Index
System requirements 15
System Vacuum 59
T
Taking videos 178, 287
Temperature 244, 245
Terms 14
TIF 173
Tilt Correction 133
Toolbar 25, 215, 255, 259
Toolbar icons 323
Touch alarm 66, 239, 244
Triangle, red 26, 177
Troubleshooting 239
Typography 13
U
User 190
User access levels 26, 209
User accounting 198
User interface (UIF) 24, 208
User Level Permissions 194
User preferences 208
User profile 192, 196
User toolbar 25
Users 198
V
Vac Quiet Mode 232
Vacuum 59
Variable pressure 64
Ventilating 61
VP instruments 59, 64
VP mode 64
W
Wafer defect files 227
Water flow 244, 245, 246
WDX 124
Windowing 114
Windows XP Remote 225
Wobble 48, 102
Working distance 121
working session 198
Z
Z 195
Z move on Vent 195, 274, 283

Carl-Zeiss-Promenade 10
07745 Jena
Germany
Carl Zeiss Microscopy Ltd.

509 Coldhams Lane
Cambridge
Cambridgeshire
CB1 3JS
UK
Carl Zeiss Microscopy, LLC

One Zeiss Drive
Thornwood, NY 10594
USA
Plus a worldwide network of distributors
www.zeiss.com/microscopy
Due to a policy of continuousdevelopment, we

reserve the right to change specifications without notice.
© Carl Zeiss Microscopy GmbH
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Software Manual

Carl Zeiss Microscopy GmbH

Carl Zeiss Microscopy GmbH

Document name: Software Manual SmartSEM® V05.06

© by Carl Zeiss Microscopy GmbH

3. First steps ................................................................................................... 27

Instruction Manual SmartSEM® V05.06 en01 V

3.5.3. Searching for a topic ............................................................................................. 54

VI Instruction Manual SmartSEM® V05.06 en01

Instruction Manual SmartSEM® V05.06 en01 VII

4.11. Communication with additional software .................................................226

5. Troubleshooting ....................................................................................... 239

6. Summary of software functions .............................................................. 247

VIII Instruction Manual SmartSEM® V05.06 en01

6.2.8. Calibrate Stage Centre ........................................................................................ 296

Instruction Manual SmartSEM® V05.06 en01 IX

7. Abbreviations ............................................................................................ 331

8. Glossary .................................................................................................... 333

9. Index .......................................................................................................... 335

X Instruction Manual SmartSEM® V05.06 en01

1.1. For your safety

1.1.1. Intended use

1.2. About this manual

This software manual contains the following chapters:

Instruction Manual SmartSEM® V05.06 en01 11 of 338

1.2.1. Safety instructions in this manual

Moreover, you will find the following type of hints:

12 of 338 Instruction Manual SmartSEM® V05.06 en01

1.2.2. Typographical conventions

Push <ENTER>. Push the ENTER key on the keyboard.

Set FIB Fil V Target to zero.

Click... Press the left mouse button.

Right-click... Press the right mouse button.

Double-click.... Press the left mouse button twice.

Instruction Manual SmartSEM® V05.06 en01 13 of 338

1.2.3. Definition of terms

The following terms are used in this software manual:

SEM Scanning electron microscope, referred to as SEM.

FESEM Field emission scanning electron microscope, referred to as FESEM.

Operator A trained person, who is assigned to operate the SEM/FESEM.

SmartSEM®Administrator Program for user management

14 of 338 Instruction Manual SmartSEM® V05.06 en01

2.1. System requirements

2.1.1. Operating system

SmartSEM® V05.06 requires the operating system Windows® XP or Windows® 7.

To operate the software, a SmartSEM® dongle has to be installed.

The SmartSEM® software is pre-installed on your SEM/FESEM by the factory.

Instruction Manual SmartSEM® V05.06 en01 15 of 338

2.3. SmartSEM® program suite

Program/Utility Function Remarks

ChamberScope Allows to show the chamberscope Option, requires particular

OptiProbe Calibration Calibration of OptiProbe after cathode

ReadMe Important information on the current

RemCon32 Serial interface for remote operation Requires REMCON licence.

SampleHolderGallery Module to inspect the dimensions of

Slideshow speed Adjustment of slideshow speed

SmartSEM Administrator User management and instrument

SmartSEM User Interface Graphical user interface of

SmartSEM User Allows recording of important informa-