Manual SpecsLabProdigy PDF

SpecsLab Prodigy
Data Acquisition and Experiment Control Software Package

User Manual 4.12.0r49869 | March 31, 2015

SPECS Surface Nano Analysis GmbH
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Tel: +49 30 46 78 24-0
Fax: +49 30 46 42 08-3
Email: support@specs.com
Web: http://www.specs.com

SPECS User Manual
SpecsLab Prodigy—Data Acquisition and Experiment Control Software Package
SpecsLab Prodigy Version 4.12.0r49869

March 31, 2015

©2015. All rights reserved. No part of this manual may be reproduced without the prior per-
mission of SPECS GmbH. Other product and company names mentioned in this document may
be the trademarks or registered trademarks of their respective owners and are used for iden-
tification purposes only.
Table of Contents
Chapter 1 – Introduction
1.1 Installation 1
1.2 Starting SpecsLab Prodigy 1
1.3 Information 2
Chapter 2 – Interface Overview

2.1 Menu Bar 3
2.2 Managing Views 3
2.3 Opening a Second Window 4
2.4 Scrollbar Navigation Markers 5
Chapter 3 – Experiment Editor I: Basic Use

3.1 Measuring a Spectrum 7
3.1.1 Adding a Source 7
3.1.2 Adding an Analyzer and Other Devices 8
3.1.3 Creating a Spectrum Group 9
3.1.4 Setting Up a Spectrum 11
3.1.5 Starting a Measurement 13
3.1.6 Saving Data 14
3.2 Scheduling Tasks 15
3.2.1 Building Schedules 16
3.2.2 Reusing the Schedule 16
3.2.3 Saving a Schedule 17
3.3 Templates 17
3.3.1 Creating Templates 17
3.3.2 Adding Templates to Experiments 18
3.3.3 Managing Templates 19
3.4 Expert Mode 19
Chapter 4 – Experiment Editor II: Schedule Options

4.1 Electron Spectroscopy 22
4.2 Spectrum Group 22
4.2.1 Spectrum Definition 23
4.2.2 Analyzer Configuration 23
SpecsLab Prodigy 4.12.0r49869 March 31, 2015 iii

4.2.3 Context Menu 24
4.2.4 Menus 25
4.2.5 Tools 26
4.3 Devices 26
4.4 Pausing to Prompt User Action 27
4.5 Adding Sleep Intervals 28
4.6 Using Groups 29
4.7 Dimension Profiling 31
4.7.1 Setting Up Devices 32
4.7.2 Defining the Profile 33
4.7.3 Adding a Second Dimension 34
4.7.4 Running the Profile 35
4.8 Depth Profiling 36
4.8.1 Defining the Sputter Cycles 36
4.8.2 Adding an Ion Source for Sputtering 37
4.8.3 Completing the Sputter Cycle 38
4.8.4 Running the Depth Profile 39
4.9 Auto Adjustment of Flood Gun 40
4.9.1 Configuring Auto Flood Gun 40
4.9.2 Running Auto Flood Gun 42
4.9.3 Results of Auto Flood Gun Procedure 44
4.10 Auto Sample Height Adjustment 45
4.10.1 Configuring the Auto Sample Height Adjustment 46
4.10.2 Running Automatic Sample Height Adjustment 48
4.10.3 Viewing Results of Auto Sample Height 49
Chapter 5 – Experiment Editor III: Reference Information

5.1 Scan Modes 51
5.1.1 Fixed Analyzer Transmission 51
5.1.2 Fixed Retarding Ratio 52
5.1.3 Fixed Energies 54
5.1.4 Snapshot 55
5.1.5 Detector Voltage Scan 56
5.1.6 Constant Final State 57
5.1.7 Constant Initial State 59
5.2 Exporting Data 61
5.2.1 VAMAS Files 62
5.2.2 XY Format 64
5.3 Instrument Status 65
5.3.1 Status Indicators 65
5.3.2 Dealing with Errors 66
Chapter 6 – Plot View I: Features

6.1 Data Browser 71
6.1.1 Displaying Spectrum Components 72
6.1.2 Setting Color and Appearance of Data 73
6.1.3 Showing and Hiding Spectra 73
6.1.4 Adding New Spectra 74
6.1.5 Additional Data Display Settings 75
6.2 Toolbar Controls 75
6.2.1 Setting the Cursor Position 76
6.2.2 Selecting an Area 76
6.2.3 Displaying the Grid in the Plot View 77
6.2.4 Zooming and Autoscaling in the Data Window 77
iv March 31, 2015 SpecsLab Prodigy 4.12.0r49869

6.2.5 Displaying the Z Axis 78
6.2.6 Copying an Image to the Clipboard 78
6.2.7 Printing the Plot View 79
6.3 Periodic Table 80
6.3.1 Identifying Peaks using the Periodic Table 81
6.3.2 Selecting Peaks 82
6.4 Changing the Axis Labels 83
Chapter 7 – Plot View II: Data Operations

7.1 Defining Data Operations before Measurement 85
7.2 Performing Operations on Regions of Interest 87
7.3 Normalizing Spectrums 89
7.4 Annotation Syntax 89
7.5 Peak Operations 91
7.5.1 Peak Area 91
7.5.2 Peak Fit 93
7.5.3 Peak FWHM 97
7.6 Peak Identification 100
7.6.1 Peak Location 102
7.7 Fitting Operations 105
7.7.1 Background 105
7.7.2 Fermi Edge 108
7.8 Smoothing Operations 111
7.8.1 Despiking 111
7.8.2 Noise Settings 113
7.8.3 Savitzky Golay Smooth 115
7.8.4 Smoothing Spline 118
7.9 Miscellaneous Operations 120
7.9.1 Arithmetic Mean 121
7.9.2 Dead Time Correction 122
7.9.3 Least Squares Gradient 124
7.9.4 Linear Operations 126
7.9.5 Spin Asymmetry for VLEED 129
Chapter 7 – Chemical Databases

7.10 Viewing Pre-Installed Databases 133
7.11 Creating and Editing User Databases 134
Chapter 8 – Image View

8.1 Opening Data in the Image View 136
8.2 Image Pane 138
8.3 Horizontal and Vertical Profiles 138
8.4 Histogram 139
8.5 Cursor and Zoom Controls 140
8.5.1 Setting Cursor Positions 141
8.5.2 Selecting a Region of Interest (ROI) 141
8.5.3 Zooming in the 2D Viewer 141
8.5.4 Toggling between Pixels and Physical Units 142
8.5.5 Displaying the Grid in the 2D Viewer 142
8.6 Performing Operations in the Image View 142
Chapter 9 – Live View

9.1 Opening the Live View 145
9.2 Features and Options in the Live View 146
SpecsLab Prodigy 4.12.0r49869 March 31, 2015 v

9.3 Active Area and Channels 148
9.4 Removing Hot Pixels 150
Chapter 10 – Live Parameter View

10.1 Selecting Parameters 154
10.2 Viewing Live Parameters 155
Chapter 11 – Live Data View

11.1 Selecting Parameters 158
11.2 Viewing Live Data 160
11.3 Saving Live Data 161
11.4 Clearing the Live Data View 162
Chapter 12 – Data History View

12.1 Opening Data History 164
12.2 Viewing Data History 164
12.3 Saving Data History 165
Chapter 13 – Detector Calibration

13.1 Calibration Procedures 167
13.1.1 Calibrating Fixed Analyzer Transmission Groups 169
13.1.2 Calibrating Snapshot Fixed Analyzer Transmission Groups 171
13.1.3 Replacing a Calibration 174
13.2 Managing Dataset Files 174
13.2.1 Saving Calibrations 174
13.2.2 Loading Calibrations 175
Chapter 14 – Transmission Function

14.1 Viewing the Transmission Function 178
14.2 Selecting a Transmission Function 179
14.3 Replacing the Transmission Function 180
Chapter 15 – Device Controls

15.1 Arranging Devices 183
15.2 Device Control Toolbar 184
15.3 Unknown Devices 185
Index
vi March 31, 2015 SpecsLab Prodigy 4.12.0r49869

1
Chapter 1 – Introduction
Welcome to the user manual for the SPECS SpecsLab Prodigy. This is a software package for
controlling SPECS equipment, acquiring data and performing basic analysis.

SpecsLab Prodigy has a modular design and is therefore extremely extensible. Some details
concerning your instrumentation will therefore not be available. Information that is typically not
included in this manual includes:
Instrument-specific details. Please refer to the instrument manual for instructions on how
to control the instrument using SpecsLab Prodigy. Such information is included in the
Online Help.
Advanced configuration operations that cannot be performed in the GUI.
Support of third-party equipment such as synchrotron beamlines.
Programming details, such as integrating SpecsLab Prodigy into other software archi-
tectures.

However, because of the licensing system that determines which features are available in the
software, this manual describes features that you may not be able to access. If you read about
a feature that you cannot find in the software, but you would nevertheless like to use, please
contact SPECS for licensing information.

Further documentation is available in the doc folder of your SpecsLab Prodigy installation dir-
ectory. If you need further assistance, please contact SPECS support.

This manual was prepared using SpecsLab Prodigy version 4.12.0r49869.
1.1 Installation
SpecsLab Prodigy is pre-installed on delivery. It is configured for your equipment and requires
no further changes.

The Quick Guide contains details about installing the software as well as configuring licenses
and equipment.
1.2 Starting SpecsLab Prodigy

To start SpecsLab Prodigy
1. Switch on the HSA 3500plus. This power supply is controlled by SpecsLab Prodigy to
provide all necessary voltages for the analyzer.
2. Select Start/ SPECS/ Prodigy. SpecsLab Prodigy will start.

SpecsLab Prodigy4.12.0r49869 | March 31, 2015

When it starts, the initial window of SpecsLab Prodigy is divided into three panes, as shown in
2
the screenshot below. You can select items from the Views menu for further functionality. This
manual is divided according to the available views. Major areas, such as the Experiment Editor,
have more than one chapter to cover all their features and workflows.

1.3 Information
SpecsLab Prodigy is a modular program. This manual covers the core functionality as well as a
few specific applications involving other equipment. In addition to the analyzer, SpecsLab
Prodigy can control a variety of other equipment. You should therefore consult the SPECS user
manuals for other manuals for details of how to control specific instruments using SpecsLab
Prodigy.

The Quick Guide contains installation and configuration instructions as well as the basic pro-
cedures for acquiring and analyzing data.

The Online Help contains the information in this manual as well as instrument specific instruc-
tions.

Selecting Start/ SPECS/ Documentation opens a folder containing a set of documents related
to SpecsLab Prodigy.

For further advice and assistance, please also contact SPECS support:
Tel. +49 30 46 78 24-0
email: support@specs.com

3
Chapter 2 – Interface Overview
SpecsLab Prodigy uses an intuitive graphical user interface for controlling instruments, design-
ing experiments and viewing data. The following sections describe some of the basic interface
tools for managing the appearance of the program:
Features on the menu bar.
Managing views.
Opening a second window.
Scrollbar markings to help you find features in various views.
2.1 Menu Bar

The menu bar at the top of the window contains three items:
Layout—Allows you to save and select pre-saved view layouts.
Views—Contains entries for opening different views. These views are described elsewhere:
Device Controls: See "Device Controls" on page 183.
Experiment Editor: See "Experiment Editor I: Basic Use" on page 7, "Experiment
Editor II: Schedule Options" on page 21 and "Experiment Editor III: Reference
Information" on page 51.
Image View: See "Image View" on page 135.
Plot View: See "Plot View I: Features" on page 71 and "Plot View II: Data Oper-
ations" on page 85.
Setup—For opening a second window, using Expert Mode and exiting SpecsLab Prodigy.

The menu bar also contains a "panic button" icon which switches off all connected instru-
ments. When instruments are connected, their icons are displayed here, with their operational
status indicated by their color. As with many other features in SpecsLab Prodigy, hovering the
mouse over the features produces a tooltip with more information.
2.2 Managing Views

SpecsLab Prodigy offers a number of methods for arranging the different views. These are
described in the sections below.

Moving views
To move a view and dock it in a new position:
1. Click and hold the mouse pointer on the icon in the control bar of the view you want to
move.
2. Drag the view to a new position. The other views will slide to make room for the view.
3. Release the view in its new position.

4
Tabbing views
Views can occupy the same area in the window. Tabs at the top of the view allow you to switch
between the views:
1. Click and hold the mouse on the control bar of the view you want to move.
2. Drag the view onto a second view. The whole view will be highlighted.
3. Release the view. The old view will appear as a tab at the top of the view.

Closing, maximizing and minimizing views
Clicking the icon at the top right of each view will close the view. You will be prompted to
confirm before the window is closed, because all settings in the view are lost on closing.

The icon can expand the view to the full size of the window. In this case, it is replaced with
the icon, which will return the view to its original size.

Saving and loading view layouts
You can save the current view layout for future sessions:
1. Select Layout/ Save Current Layout. A dialog will open.
2. Enter a new name to save the layout, or select an existing layout from the drop-down list to
overwrite the selected layout.

3. Click OK to save the layout.

You can easily restore the layout to a previous setting:
Click Layout in the menu bar and select the name of a layout.
2.3 Opening a Second Window

You can open a second window in SpecsLab Prodigy. This is ideal if you have a second monitor.
A typical example is to have the experimental setup in one window with the data display in the
second.

To open a second window:

1. Select Setup/ Second Window from the menu bar.
5
2. Drag a view from the original window into the second.
2.4 Scrollbar Navigation Markers

For more complex experiments, the schedule can be very long; there may also be a large num-
ber of results in the data browser. To help you navigate, the scrollbars have additional marks
that act as anchors:
The dark blue line shows the position of the current selection in the schedule. Clicking the
mark takes you directly to the selection.
The light blue lines show similar objects to the selection. For example, if a spectrum group
is selected, other spectrum groups are marked in light blue. Again, clicking these marks
takes you to the corresponding part of the schedule.

The currently active part of the schedule is colored green. The currently acquired spectrum in
the data browser is also shown in green. A green bar appears in the schedule so you can easily
find which part of the experiment is running.


6

7
Chapter 3 – Experiment Editor I: Basic Use
One of the most important uses of SpecsLab Prodigy is to acquire data in spectroscopy exper-
iments. This chapter guides you through the basic procedure for data acquisition. SpecsLab
Prodigy has an intuitive design—once you understand the basic operation, you should be able
to adapt it to your workflow and requirements.

The information in this chapter is essential for all users. It covers the following aspects:
Measuring a spectrum.
Scheduling tasks in the experiment.
Creating and using templates.
Using expert and standard modes.

A description of all options in the Experiment Editor is presented in "Experiment Editor II:
Schedule Options" on page 21. Background information that is likely to be of interest to the
majority of users is provided in "Experiment Editor III: Reference Information" on page 51.
3.1 Measuring a Spectrum

The Experiment Editor is used to define and run experiments. On opening, it contains a set of
recently performed experiments. If you select one of these links, the experiment, including all
parameters and data, is loaded. This allows you to review your results or modify the exper-
iment and take a new set of results.

To create a new experiment
1. Under Create Experiment from Scratch, click XPS. The Experiment Editor will show the
details for an XPS experiment. Instead of XPS, you can also select options for UPS, AES and
ISS experiments. The difference is the sources that are available for the experiment. The
2. Edit the experiment file name as necessary. The default is Experiment, followed by a date
and time stamp.
3. Enter some text in the Description field. This is recorded with the data. It is valid for the
entire experiment. Typical information would be details of the surface, adsorbate, etc.
3.1.1 Adding a Source

You need to define the properties of the excitation source. For the purposes of this description,
we will use a "dummy" X-ray source. Other SPECS sources, as well as instruments such as
beamline monochromators, can be controlled directly from SpecsLab Prodigy.

To add a dummy X-ray source to the experiment:

1. Click XR50 Dummy: Operate. A new XR50 Dummy entry box will appear in the Experiment
8
Editor.

Note
If there is only one source available, it is automatically added to the experiment.

2. Select the desired excitation energy from the Anode drop-down list. This information is
used to calculated binding energies. It is also stored with the data with other experimental
information.
3. If desired, check the Notify to set up device box. Before data acquisition starts, a dialog
will pop up instructing you to switch on the X-ray source with the correct parameters.
4. For further source parameters, click the button.

5. Enter desired values for the source power and high voltage as necessary.
3.1.2 Adding an Analyzer and Other Devices

An analyzer is essential for all measurements. If you only have one analyzer, this is auto-
matically included in the experiment. If you have additional analyzers and detectors, you can
choose which one to use for the experiment.

In addition to the analyzer, you may be able to select other devices for use in the experiment.
You can then set the operating parameters to be used in the experiment. Typical devices
include:
Flood gun, to be activated during a measurement.

Manipulator, to move the sample to the measurement position.
9

To add an analyzer:
Click the desired analyzer in the list of devices in the Experiment Editor. The analyzer will
be activated when you start the experiment.

In addition to the analyzer, you may be able to select other devices for use in the experiment.
You can then set the operating parameters to be used in the experiment. Typical devices
include a flood gun, manipulator or sample heater.

Some modules are dependent on a device being defined at this point. If you have the Profiling
and/ or Ramping modules, you need to add the device in order to be able to access the para-
meters in the module.

External devices may also be available. These allow you to record a parameter while the exper-
iment is running. A typical example is to measure the sample current for normalizing the sig-
nal. The data from the external device can be viewed in the data browser; this also offers the
facility to use the data for normalizing the signal.

Note
After the end of the experiment, the all devices are put into a safe status. The exact details of
this final status are device dependent.
3.1.3 Creating a Spectrum Group

Spectrum Groups contain one or more spectra. Each spectrum is recorded using the same ana-
lyzer settings, but with different energy settings and lens modes. Within a single experimental
run, you can therefore measure a number of regions in the energy range.

To create a new Spectrum Group:
1. Click the icon next to Add to Electron Spectroscopy. A new Spectrum Group will be
added. If a menu appears, select Spectrum Group.
2. Click the name ("Spectrum Group") and enter a name for the group.
3. Click the Scan Mode drop-down list. There will be a delay while the software connects to
the HSA power supply.

4. Select Fixed Analyzer Transmission from the Scan Mode drop-down list. For a descrip-
10
tion of the other scan modes (which may also change the other setup parameters), please
refer to "Scan Modes" on page 51.
5. Select 1.5 kV from the Lens Voltage drop-down list. For the most accurate meas-
urements, you should select the lowest available voltage for the energy range you want to
measure. The HSA power supply manual contains more information about the available
energy ranges.
6. Select a calibration file suitable for your detector from the MCD Calibration drop-down
list. This corrects energy shifts between different measurement channels.
7. Select Consecutive from the Processing Order drop-down list. There are two options:
Consecutive—all spectra in the group will be measured consecutively.
Cyclic—depends on the number of scans defined. All energy regions are measured
once consecutively. SpecsLab Prodigy then the returns to the start of the group and
goes through the group, as defined for each individual spectrum. This cycles until all
scans are performed.
8. Select a transmission function from the Transmission drop-down. Transmission func-
tions are dependent on the slit settings.
9. Set Auto Compact to Off. Auto compacting allows you to reduce file size by discarding the
information in separate channels (for multichannel detectors) or summing the data from a
number of scans.
10. Set the Entrance Slit and Exit Slit entries according to the slits selected on the analyzer.
11. Set the Iris according to the setting on the analyzer.

The main settings for the Spectrum Group are now complete. You are ready to define a spec-
trum. By clicking the icon in the Spectrum Group, you can hide the settings you have just
defined and concentrate on the details of the spectrum.

11
3.1.4 Setting Up a Spectrum
Individual spectra are defined in the table below the experiment settings. The entries in the
table depend on the scan mode selected.

The spectrum parameters are described in detail for all modes in "Scan Modes" on page 51.

The Lens Mode opens a list that contains all available lens modes for your analyzer. This is
specific to your analyzer—the modes are described in the analyzer manual.

You can select kinetic energy or binding energy for the display by clicking the Ek and Eb button
respectively. The binding energy is calculated from the source energy.

A particularly easy method of setting up spectra is to use the periodic table button:
Click the icon below the spectrum group table and click an element. A menu will appear
with a list of peaks that you can select. The spectrum will be set up with suggested para-
meters for scanning the peak. Remember to set a lens mode for the spectrum!


12

Further configuration options:
Click the button to add another spectrum to the group. This duplicates the selected spec-
trum, or the last spectrum if none is selected. A new line is added to the table with the para-
meters for the spectrum. To remove a spectrum, first select the row in the table, then click
the button. You can move a spectrum to a different position in the group using drag and
drop.
Add a data operation to the spectrum in the Plot View. The data operation is automatically
performed after the spectrum is acquired.
Add additional spectrum groups or spectroscopy experiments to the Experiment Editor in
order to run many measurements in one sequence.

Add other instruments or operations to the schedule.
13
3.1.5 Starting a Measurement

SpecsLab Prodigy performs a validation check on the experimental settings before starting
acquisition. In general, small inconsistencies in the settings are automatically corrected. If
there is a more serious problem in the configuration, an error message appears which tells
you how to fix the problem.

To acquire specified spectra:
1. Use one of the following methods:
Check the box in the leftmost cell for the spectrum you want to acquire. This action val-
idates the spectrum. If you have defined additional spectra, you can also check these
as you wish. Only spectra which have been selected will be acquired.
Select a number of spectra by holding down SHIFT (to select a range of items) or CTRL
(to add the selected item) and click the spectra you want to acquire, then click under
the spectrum group.
2. Click the button in the main toolbar. The selected spectra will be acquired.

To acquire all spectra:
1. Click the button in the main toolbar. A dialog will appear, asking if you want to run the
entire schedule.
2. Click Yes. All spectra will be acquired.

If you selected Notify to set up device when adding the source, a dialog will now appear to
prompt you to switch the source on with the correct settings.

Note
Devices controlled by SpecsLab Prodigy will be automatically switched on without requiring a
prompt. The status of each device is shown in the menu bar.


14

You can pause acquisition by clicking the icon or abort the scan with the icon. There is
also the "panic button" in the menu bar which allows you to switch off all connected instru-
ments.

The Plot View displays data as it is being acquired. For more information about viewing data,
please refer to:
"Plot View I: Features" on page 71, for display options in the Plot View.
"Plot View II: Data Operations" on page 85, for operations that you can perform on the
data.

You can also view 2D data in the Image View—see "Image View" on page 135.

After data acquisition, the spectrum is locked, as indicated by a icon. To unlock spectra:
1. Select the spectrum in the spectrum group. You can select a number of spectra by holding
down the SHIFT or CTRL keys, as described above.
2. Click . There is a warning that all data will be deleted from the selected spectra. Confirm
this to unlock the spectra. You can now edit the spectrum as necessary and reacquire.
3.1.6 Saving Data

SpecsLab Prodigy has an Autosave feature. This saves data during and at the end of acquis-
ition. In the event of a program crash or similar interruption, you can reload the file in order to
restore the settings and data. Clicking the Save icon next to the name will also save the current
status of the experiment.

Clicking the arrow next to the Save icon produces a menu with the following options:
Save the experiment.

Save As, which opens a dialog allowing you to specify a new name and location for the
15
experiment file.
Duplicate the experiment, with the experiment being saved under a new automatically gen-
erated name.
Export to various formats.

Note the following points about files:
You can set the location by clicking Settings and entering a path in the field provided. Click-
ing the ellipsis button opens a file browser so you can select a folder.
The default name of the file is the experiment type (e.g. Electron Spectroscopy) with a date
and time stamp.
SpecsLab Prodigy uses a binary format that contains all data and experimental details. You
can export data to different formats.

Note
As you can see from the screenshot below, SpecsLab Prodigy is able to export to the VAMAS
format . Importing from this format is also possible, but not all information in the experiment
will be saved for future use.

3.2 Scheduling Tasks

The Experiment Editor allows you to run a sequence of experiments. This is a very flexible sys-
tem that allows you to automate various tasks. Note the following points about the schedule:
The schedule runs from top to bottom, completing each task before starting the next.
By adding new spectroscopy experiments, you can define different excitation sources.
You can set up a sequence of different experiments.

If you only want to change the analyzer settings, it is best to add new spectrum groups to
16
an existing experiment—this provides a logical order and makes complex procedures
easier to follow.
You can drag and drop items in the schedule to rearrange the order of their execution.
3.2.1 Building Schedules

The fastest way to build up a complex experiment is to add a number of predefined templates
in a sequence. The screenshot below shows an example of an experiment built out of several
operations. The Survey + Ag 3d item is a template that is added repeatedly without the need
for further definition.

Note
Groups can also be saved as templates so that complex routines can also be added. See Using
Groups for more information.

The experiment can be started, as usual, by clicking . This will check and validate all parts of
the schedule and then sequentially run through the items.
3.2.2 Reusing the Schedule

A useful feature for quickly defining new experiments is the repeat function. This copies the
existing experiment, complete with all configuration details, to a new file. The copy does not
contain any data, and can therefore be immediately started without any further modifications.
This is a useful feature for semi-automated procedures, for example if identical measurements
are run on different samples.

To duplicate an experiment:

Click the icon in the Experiment Editor toolbar. A duplicate will be created. You will see 17
that the timestamp in the filename has been updated.
3.2.3 Saving a Schedule

If the schedule represents a commonly executed procedure, you can save it for reuse:
1. Click the icon. A Save dialog will open.
2. Select Prodigy Template (*.slt) from the File Type drop-down list.
3. Enter a name (including the .slt extension) and location for the schedule and click Save.

The schedule will be available in the Experiment Editor as one of the quick links.
3.3 Templates
Templates are reusable experimental configurations. You can save items in the Experiment
Editor together with their configurations for later use. This saves time when performing a
series of similar measurements, while reducing errors caused by incorrect configuration.

Note
You can also save an entire experiment as a template.

After creating a template, you can use it in other experiments. A template manager allows
you to remove unused templates.

Typical uses of templates include:
Defining an electron spectroscopy experiment with spectrum group(s) for commonly
used scans.
Setting up a number of devices.
Defining a group of actions (or other templates) to perform a complex sequence.

If you are using standard mode (not expert mode), templates are the normal way of operating
SpecsLab Prodigy.

Note
You can also save configurations in devices and recall them for use in experiments or stan-
dalone device controls.
3.3.1 Creating Templates

To create a template:
1. Add an item (e.g. Electron Spectroscopy, Device, etc) to the Experiment Editor.
2. Set up the item so that it is suitable for running in an experiment


Note
18
You can run an item in an experiment, then save it as a template when the experiment is fin-
ished.

3. Click and select Save as Template. A dialog will open.

4. Type a name for your template and click OK. Clicking the arrow reveals a list of other tem-
plates of this type.

Note
Templates are stored in the settings\ExperimentEditor\Templates folder of the SpecsLab
Prodigy installation directory.
3.3.2 Adding Templates to Experiments

To add a template to an experiment:
Click . If the entry in the menu has templates, there is an arrow on the right side. Moving
the mouse to the control unit will show all available templates for this type of control item.
Selecting a template will add it to the experiment.

Note
Selecting Default will add the item with no preset values.

19
3.3.3 Managing Templates
All templates you create are always available when you start SpecsLab Prodigy. You can
remove outdated templates using the template manager:
1. Click the icon in the Experiment Editor toolbar. The Template Manager dialog will open.

2. Select a template that you want to remove and click Delete Selected.

Note
Deleted templates cannot be recovered.

Note
To change a template name, load it, then save it with a new name. You can then delete the ori-
ginal.
3.4 Expert Mode

Expert mode allows full access to all features in the software. This is necessary for configuring
and optimizing experiments. For regular data acquisition, many of the features are not altered.
You can leave Expert Mode. This hides a number of parameters and options, leaving only those
which are actually used for running experiments. Building and running experiments involves
selecting tried and tested templates which are less prone to error and do not require such a
high level of expertise for operation.

To toggle Expert Mode:
Select Setup/ Expert Mode at the top right of the window. A tick indicates when SpecsLab
Prodigy is in Expert Mode.

20

21
Chapter 4 – Experiment Editor II: Schedule

Options
The schedule consists of a set of instructions and operations that make up an experiment. For
an introduction to preparing schedules, please see:
Creating a New Experiment
Building Schedules

Beyond the basics of setting up a scan, there are a number of additional options that you can
use. These are shown in the menu when you add an item to the Experiment Editor or to an Elec-
tron Spectroscopy experiment.

Some of these options may not be present in your version of SpecsLab Prodigy as they are
included in your configuration. The table below provides a short description of all possible fea-
tures.

If you would like to add an option to your configuration, please contact SPECS for details about
licensing.

Option Description
Auto Flood Gun Adjustment Varies the emission current of a flood gun while recording
(optional) test spectra. Selects an optimum emission current based on
the minimum peak width.
Auto Sample Height Adjust- Moves the sample position while measuring signal intensity.
ment (optional) Locates the optimum position for maximum intensity.
Device (standard) Adds a device (e.g. heater, manipulator, etc) to the schedule,
allowing you to perform an action with the equipment.
Electron Spectroscopy (stand- Sets up a source and analyzer.
ard)
Group (standard) Allows you to group other actions together to form logical
groups, adding structure to the schedule.
Pause (standard) Pops up a message prompting user action during a schedule.
Profiling (optional) Steps through a set of parameter values (e.g. manipulator
positions), taking spectra at each point.
Sleep (standard) Stops the schedule for a user-defined period.
Spectrum Group (standard) Defines settings for scanning data.
Sputter Depth Profiling Controls an ion gun for automating depth-profile exper-
(optional) iments.

22
4.1 Electron Spectroscopy
The electron spectroscopy experiment allows you to set up an analyzer and source ready for
data acquisition. You can add and configure other devices. These will be activated before the
experiment continues.

Note
See also Creating a New Experiment for a description of how to set up a standard electron
spectroscopy experiment.

An electron spectroscopy experiment must contain the following items:
Analyzer
Source

If you only have one analyzer or source, it will be added automatically. Otherwise, you will be
offered a choice of all available devices.

To add an electron spectroscopy experiment:
Click in the Experiment Editor and select Electron Spectroscopy. You can only add elec-
tron spectroscopy items directly to the Experiment Editor—they cannot be added to any
other item.

After setting up the experiment, you can add items to define the data acquisition procedure.
The most common item is a spectrum group.
4.2 Spectrum Group

A spectrum group contains analyzer settings and the parameters for one or more scans. The
workflow for creating and editing spectrum groups is described elsewhere. The following sec-
tions provide reference information about the features in a spectrum group:
Analyzer configuration.
Menus and context menus.
Spectrum definition.
Icons below the spectrum definitions.

To add a spectrum group:
In an electron spectroscopy experiment, click and select Spectrum Group.

Note
The icon in the main toolbar contains the usual controls for creating templates and unlocking
the contents of the group. In addition, it contains the same items as the context menu and
allows a convenient way to export all spectra in the spectrum group.

23
4.2.1 Spectrum Definition

The spectrum group contains a table which contains a set of definitions for spectra. You can
move a spectrum to a different position in the group or to another spectrum group using drag
and drop.

Which items are displayed in the manual depends on other settings. Please refer to the fol-
lowing:
Scan mode
Context menu

In addition, the analyzer manual has details of which lens modes are available.
4.2.2 Analyzer Configuration

There are a number of settings for the analyzer. These apply to all spectra in the group. The
table below lists the function of each setting.


24 Setting Description
Scan Mode See Scan Modes for a description of all available scan modes.
Scan Range Sets the range of the HSA 3500plus power supply. You should select the
lowest possible for your experiment, as the power supply is more accur-
ate in the lower ranges.
MCD Calibration Corrects energy shifts and intensity differences between different meas-
urement channels
Processing Order Determines the order that spectra are measured:
Consecutive—all spectra in the group will be measured con-
secutively.
Cyclic—depends on the number of scans defined. All energy regions
are measured once consecutively, then the scan returns to the start of
the group and goes through the group, as defined for each individual spec-
trum. This cycles until all scans are performed.
Transmission Selects a transmission function for your experiment.
Entrance Slit Notes the slit settings on the analyzer. You need to set these manually on
the analyzer. The transmission function is dependent on the slit settings.
Exit Slit SpecsLab Prodigy will check that the transmission function is suitable for
the selected slits.
Iris The iris setting of the analyzer. As with the slit settings, this is set manu-
ally on the analyzer and the value is recorded with the experiment. The
default value for the iris setting is the maximum, as defined in the con-
figuration tool.
Compact Data There are three options:
Off—the data is not compacted.
Combine Channels—the signals from individual channels in a mul-
tichannel detector are summed to a single value.
Sum Scans—when measuring a spectrum with several scans, the
intensities from the scans are summed into a single value.

Compacting data can significantly reduce file size. However, meas-
urements of individual channels or scans are lost.
4.2.3 Context Menu

Right-clicking on the spectrum definition table shows a context menu. The options in this menu
are listed in the table below.


25

Menu item Description
Copy Selected Spec- Copy and paste the selected spectrum(s). This allows you to quickly cre-
trum(s) ate duplicates of definitions in the spectrum group.
Paste
Enable Overwriting On selecting this item, the spectrum is marked red in the table. When you
Mode run the experiment, spectra are acquired normally until reaching the red
spectrum. The red spectrum is then repeated in a loop, with each acquis-
ition overwriting the previous results. This loop will continue until you
unselect overwriting mode—data acquisition will then continue through
the rest of the spectrum group. Canceling acquisition will also break the
loop.

This mode is useful for setting up or optimizing experiments.
Export Spectrum to Allows you to export the selected spectrum to VAMAS or XY format. See
file, VAMAS or XY "Exporting Data" on page 61 for more details.

These items are also available in the main toolbar, which allows all spec-
tra to be exported and in the icon below the table, which allows all selec-
ted spectra to be exported.
4.2.4 Menus
The icon in the main toolbar brings up a menu which contains the items shown in the table
below.

Menu item Description
Unlock and Clear Unlocks all spectra in the group, allowing you to modify the definition
All Data after running the measurement. This will delete all measured data in the
group.

26 Menu item Description
Save as Template Saves the group configuration as a template for future use.
Copy Copies the configuration. When you add an item to the Experiment Editor
(e.g. a Spectrum Group), you can paste this configuration.
Use Start/ End These two options determine the way you set up the energy range for
the experiment. The values are also dependent on whether binding or kin-
etic energy is selected.

Start/ End directly sets the minimum and maximum settings for the spec-
Use Center/ Width trum range. Center/ Width allows you to pick a central energy (e.g. a
peak position) and the total width of the spectrum. Although useful for
setting up spectra which examine a known peak position, this is espe-
cially useful for the snapshot scan mode, where the analyzer is not
scanned.
4.2.5 Tools
There are a set of icons below the list of spectrum definitions which add, remove or perform
actions on spectrum definitions. The table below lists function of each icon.

You can select multiple spectra as follows:
Hold SHIFT and click a spectrum to select a range.
Hold CTRL and click a spectrum to add it to the selection.

Icon Description
Adds a spectrum definition to the group. The values in the spectrum are based on the
currently selected spectrum or, if no spectrum is selected, on the last spectrum in the
table.
Deletes the selected spectra.
Shows the periodic table, if available. Selecting an element and excitation in the table
adds a suitable energy range to the spectrum definition.
Validates the selected spectra.
Uses the electron kinetic energy to define the spectrum.
Sets the energy settings for the spectrum definition to binding energy, as calculated
from the source energy.
Unlocks selected spectra, allowing you to modify the definition after measurement. This
will delete the data in the spectra.
Displays a menu with the same entries as the context menu.
4.3 Devices
You can add a device to your experiment and operate it. The devices available depend on the
configuration of your system.

27
In general, the settings for devices are intuitive. For a full description, please refer to the
manual of the instrument. The device control for the instrument usually has a similar method of
operation.

Note the following points about devices:
If you simply want to control the device, i.e. not operate it as part of an experiment, use the
device control.
A device in an experiment is normally part of the schedule and often in a group.
The settings for the device will remain as you set them until the experiment finishes, or
until you apply new settings. Thus, if you switch on a flood gun, it will stay on for the rest of
the experiment unless you include another device section to switch it off.

Note
You can add devices to Electron Spectroscopy experiments. Any parameters you set are valid
for the duration of the scan.

To add a device:
1. Click and select Devices. A new devices control item will be added.
2. Click a device. Controls for the device will appear.
3. Set the parameters for the device as desired. Clicking will reveal more parameters.
4. Add and configure other devices as necessary.

The settings for the device will be applied when you run the experiment and SpecsLab Prodigy
reaches the item in the schedule.
4.4 Pausing to Prompt User Action

The Pause action allows you to display a message during an experiment. The schedule is inter-
rupted until the message is accepted by the user.

To add a Pause to the schedule:
1. Click and select Pause from the menu.
2. Type a message into the field provided. This text will appear in the prompt


You can now add further items to the schedule. When running the experiment, the Pause item
28
will be executed as part of the schedule. SpecsLab Prodigy displays a dialog with the user
instructions:
Resume—Continues the experiment.
Stay Paused—Closes the dialog and pauses the schedule. You can make adjustments to
the rest of the schedule as necessary, then click . The schedule will restart after the
Pause item.

4.5 Adding Sleep Intervals

The Sleep item adds an interval to the schedule in which no actions are performed. Typical
uses of the Sleep feature are:
Adding a short break so that a device can initialize and come to stable operation.
Adding longer breaks so that the sample can cool down or the pressure can recover.

To add a Sleep item to the schedule:
1. Click and select Sleep to add a pause to the schedule.
2. Set the Sleep duration.

You can now add further items to the schedule. When running the experiment, the Sleep item
will be executed as part of the schedule. The menu bar shows the status of the Sleep as it is run-
ning.


29
4.6 Using Groups
As experiments increase in length and complexity, the schedule can quickly become long and
unreadable. Groups allow you to apply a hierarchy to the schedule, adding structure and group-
ing items into logical units.

To add a group to the schedule:
Click and select Group.

Groups are particularly well-suited to be saved as templates. You can create a common task
that uses a number of devices and save this as a template. Each time you need to perform this
task, you can insert the group template in the schedule.

Example
The following example shows how to create a group that contains commands for heating the
sample. It performs the following actions:
Uses the manipulator to move the sample to a "safe" position. This may be in the pre-
paration chamber, or simply away from the analyzer.
Heats the sample to a specified temperature for a specified time.

To define the group:
1. Click and select Group.
2. Click inside the group and select Devices. A list of all devices on your system will be
shown.

Note
If you accidentally add an item outside the group, you can drag and drop it into the correct pos-
ition.

3. Click SPECS 4 Axis Manipulator: Position. The controls for the manipulator will be
shown.
4. Click the drop-down list in the manipulator settings and select a position for the manip-
ulator.
5. Click EBH 300 and configure the electron beam heater so that it heats the sample to the
desired temperature.

NoteIt is a good idea to give items suitable names as you add them so you can easily identify
the functions of the group and its components.


30

6. Click inside the group and select Sleep.
7. Set a time for the sleep interval. The sample will be held at the temperature for this time.
8. Click inside the group and select Devices. Another devices section will be added to the
group.
9. Add an electron beam heater group to switch off the heating.


31

You can save the group as a template for future use:
Click in the main toolbar of the group (labeled "Heat to 800 K for 3 min" in this example)
and select Save as Template. A dialog will open allowing you to specify the name of the
template
4.7 Dimension Profiling

Dimension profiling allows you to change device parameters, running a spectrum group after
each change. A typical example would be to move a manipulator a fixed distance between
scans in order to build up a spatial chemical map of the surface.

As an example, the following procedure shows you how to use a manipulator to scan a series
of points on the sample to obtain spatial mapping of the surface.


32
Measurement points
Sample
Manipulator movement after each measurement
To continue the example, and thereby demonstrate the flexibility of the software, the exper-
iment will then ramp the temperature while performing the spatial mapping. Finally, there are
instructions on how to acquire and display data.

In principle, you can add dimensions for any item of equipment with adjustable operating para-
meters. For example, you can run a series of measurements using different HV settings in the
X-ray source in order to measure as a function of X-ray power. This makes the procedure
extremely powerful and flexible. Moreover, you can add many dimensions to the profile.
However, this can quickly lead to long measurements—measuring a grid of points 5 × 5 in size
leads to 25 scans. Adding a third dimension can quickly lead to hundreds of measurements in
the experiment.
4.7.1 Setting Up Devices

As usual, the first step in defining a new experiment is to set up the sources and analyzer. In
addition, you also need to add the equipment that is used in the profile.

For a position profile, a manipulator is required.

To set up the devices for a position profile:
1. Click Electron Spectroscopy in the Experiment Editor to start a new experiment.
2. Add a source and analyzer and define their properties.
3. Add the Manipulator: Position device to the experiment.
4. Select a preset position for the manipulator.

User-defined preset

33

Note
You can define presets in the manipulator Device Control. Set the desired position for the axes,
then click Add Position. You can then save the settings to a position file. This file will then
appear in the preset menu.
4.7.2 Defining the Profile

When defining a profile, you first need to select a parameter that will be varied during the
experiment. You then define the range of the parameter and the number of iterations for the
scan—the steps are equally spaced. You can also determine whether the settings in the profile
are absolute or relative:
Check Relative box—settings in the profile are relative to the settings defined when you
added the device to the experiment.
Uncheck Relative box—defined device settings are ignored and the absolute values
defined in the profile are used for controlling the equipment.

To define the profile:
1. Click the icon to add a profile.
2. Click Add New Dimension and select Manipulator X from the list. The manipulator will
move in the X direction between scans.
3. Set the following values (modify for your own requirements):
x: 0.0 mm
to 5.0 mm
Iterations in dimension 1: 6
Check Relative.

If we were to define a scan now, the following would occur:
The spectrum group would be scanned with the manipulator in its present position.
The manipulator would move 1 mm in the X direction.
The spectrum group would be scanned again.
The move/ scan procedure would continue, with the manipulator moving in 1 mm steps
until it had moved 5 mm from its initial position.

As an aside, you can add another parameter to this dimension. For example:

Click Add Parameter and select Manipulator Y from the list. A new line appears that
34
allows you to define movement of the Y axis. Both X and Y movements are performed
together, so the scan would follow a diagonal line (in the X–Y plane) on the sample surface.

Note
Clicking the icon will remove a dimension without affecting any other part of the con-
figuration.
4.7.3 Adding a Second Dimension

The previous section showed you how to define a profile for one dimension. You can add as
many dimensions as you like to an experiment—the limiting factor is the required meas-
urement time. After measuring points in the X direction, a natural step might be to add a dimen-
sion in the Y direction, in order to build up a 2D spatial map of the surface.

As an alternative, this section shows you how to use two dimensions with a sample heater and
manipulator. The sample will be heated to a set temperature, then measured along a set of pos-
itions, then the temperature changed before measuring again.

Note
It is not necessary to add all devices to the experiment before adding the profile. It is sufficient
to add the device before you want to add the dimension.

To add a temperature dimension to the profile:
1. Add the device E-Beam Heater EBH 150.
2. Select Temperature IR from the Mode drop-down list.
3. Click Add New Dimension and select E-Beam Heater (EBH 150): Temperature from the
list. The new dimension is added.
4. Set the values for the temperature settings, e.g. such as those in the screenshot below.


35

5. Add a new dimension for the X axis of the manipulator and define this for a series of pos-
itions.

If we were to define a scan now, the following would occur:
The sample would be warmed up to 300 K and the spectrum group once again recorded
over all X positions.
The spectrum group would be scanned at positions 0 mm to 5 mm in 1 mm steps.
The sample would be warmed up to 310 K and scanned at each position.
Scanning would continue until all positions have been recorded at all temperatures up to
400 K.
4.7.4 Running the Profile

After defining all the desired dimensions in the profile, you can add a spectrum group. As there
may be a large number of iterations in the profile, you should try to keep the scan duration as
short as possible:
Scan peaks of interest, rather than survey or other wide-range spectra.
Use larger energy step times and shorter dwell times.
Try to use snapshot mode to capture a small energy region without needing to scan.

To acquire spectra with the profile:
1. Click the icon to add a spectrum group to the profile.
2. Define the spectrum group in the normal way.
3. Click to validate the scan and start data acquisition.

36
The tool bar will show the progress of the profile as it runs. Data is shown in the Plot View. For a
better view of the scans, you can click to display the Z axis, then select Position for the Z axis.
You can also open the data in the Image View for an alternative visualization.

4.8 Depth Profiling

Depth profiling with an ion gun involves removing the surface layer(s) with ions, then meas-
uring the chemical composition of the newly exposed surface. In this way, you can measure the
bulk chemical composition of the sample.

The following sections guide you through the procedure for setting up sputter cycles, the ion
gun and other equipment , then running a depth profiling experiment in SpecsLab Prodigy.
4.8.1 Defining the Sputter Cycles

Depth profiling experiments involve measure–sputter–measure cycles. You need to specify the
length of each sputter cycle and the number of cycles. For ease of setup, you can specify a num-
ber of iterations for a given duration.

37
If you want to measure the sample before sputtering, set the duration of the first cycle to zero.

To define the sputter cycles
1. Click the icon to add a Sputter Depth Profile to the experiment.
2. Click the icon to add a new entry to the Sputter Cycles.
3. Edit the settings for the sputter cycles:
Duration sets the time that the ion gun is switched on.
#Iterations sets the number of times the sputter cycle is performed.
4. Add and define further entries as necessary.

4.8.2 Adding an Ion Source for Sputtering

The SPECS IQE 12/38 has a number of predefined settings. The IQE 12/38 manual describes
how to adjust these settings. You can recall one of these settings for the depth profiling exper-
iment. If you do not have a SPECS IQE 12/38, you can define a dummy. This records the set-
tings with the experimental data, while you operate the ion source manually.

To add an ion source to the depth profile configuration:
1. Click IQE 12/38: Operate in the Sputter Device section. A new field containing settings
for the sputter gun will be added.
2. Click the button to show more settings.


38

3. Edit the settings for the ion source:
VCU pressure is the regulating pressure to be set by the VCU 1000 valve control unit.
Thisi is not displayed if the VCU 1000 is not installed.
Select one of the pre-programmed settings for the IQE 12/38. These are defined in the
power supply for the IQE 12/38—please see the manual for further details.
If desired, define new settings for the spot X and Y width settings and emission current.
These settings will override those in the pre-programmed setting.

Note
The settings for a dummy source are similar to those for the "real" IQE 12/38. As with other
dummy sources, you have the option to ask for a prompt to control the device.
4.8.3 Completing the Sputter Cycle

There are some additional options that may be useful for your sputter experiment. You can set
these as you wish before defining the spectrum group.

To finish configuring the sputter cycle:
1. Add additional devices as necessary:
XR50 Hot standby—Used in conjunction with the XR50 source defined in the exper-
iment. Leaves the source in standby mode when not in use, rather than switching off.
Manipulator Constant Rotation—Allows you to set the manipulator to rotate at a
constant user-defined rate.
2. Set the behavior of the sputter device during data acquisition::
You can set the ion gun to standby (HV off, filament at standby level) or Emission On
(HV off, filament reduced to allow a small amount of emission). The latter setting
allows the ion gun to achieve stability more quickly when it is switched back on for the
next sputter cycle.

You can maintain the gas pressure during the measurement cycle. Only available if you
39
have a VCU 1000 installed.

4.8.4 Running the Depth Profile

Defining spectra for the depth profile experiment is the same procedure as for a normal scan.

To run the depth profile:
1. Click the icon to add a spectrum group to the depth profile.
2. Define the spectrum group in the normal way.
3. Click to validate the scan and start data acquisition.

Data is shown in the Plot View. For a better view of the scans, you can click to display the Z axis,
then select Etch Time for the Z axis. You can also view the data in the Image View. For more
information, please refer to:
"Changing the Axis Labels" on page 83.
"Displaying Spectrum Components" on page 72.
"Opening Data in the Image View" on page 136.


40
4.9 Auto Adjustment of Flood Gun

The auto adjustment of flood gun procedure assists you in automating experiments on insu-
lating surfaces. These surfaces charge up when exposed to X-rays as a result of pho-
toemission. This prevents reliable measurements of the surface, or even any measurement at
all.

In order to compensate for charging, a low energy electron source can irradiate the surface.
However, this damages the sample in many cases. The trade-off is peak quality against flood
gun emission current.

SpecsLab Prodigy optionally offers a means to automatically measure the full width at half max-
imum (FWHM) of a peak as a function of flood gun emission current. Following a series of
scans, it evaluates the data and finds the emission current with the smallest peak FWHM. Specs-
Lab Prodigy then sets the flood gun to this emission current and continues to run the exper-
iment.
4.9.1 Configuring Auto Flood Gun

You need to include and configure the following items in the Electron Spectroscopy experiment:

Analyzer.
41
Source.
Flood Gun. The auto flood gun adjustment routine starts with the emission current set for
this device. The emission current must be greater than zero.

Note
After producing a suitable configuration, you can save it as a template. You can then load this
for future experiments without needing to follow the whole procedure described here.

To configure the auto adjustment of flood gun procedure:
1. Click and select Sleep to add a pause to the schedule.
2. Set the Sleep duration to 1 minute. This will allow the flood gun to stabilize before the
optimization routine starts.

3. Click and select Auto Adjustment of Flood Gun to the schedule. This should appear
directly after the Sleep item.
4. Edit the settings. The table below describes each item. The screenshot shows typical set-
tings with a carbon 1s peak selected.

Parameter Description
Max. Emission The maximum flood gun emission current. The auto adjustment
routine will stop after measuring a spectrum at this flood gun
setting.
Emission Step The increase of emission current in each measurement.
Intermediate Emission Sets an earlier point for stopping the routine. If the auto adjust-
ment procedure has already located a minimum in the FWHM of
the measured peaks, it will stop and use the settings obtained.
Otherwise, the emission will be increased up to the limit given in
Max Emission.
Expected Peak Position (Ek) Enter the expected location of the peak (kinetic energy). Ideally,
this is the book value of the excitation. Due to charging, it will
have moved somewhat, but it will most probably appear some-
where in the scan range.
You can click the icon to display the periodic table and select
an excitation.
Final Pass Energy The initial pass energy of the analyzer is set to 50 eV for an

42 Parameter Description
exploratory scan. This decreases to 30 eV for the second scan.
You can define the pass energy for the subsequent scans. For
most purposes, 30 eV should be sufficient. If you require very
high resolution, you can reduce the pass energy at the cost of
count rate.
Lens Mode Set an appropriate lens mode for your analyzer. Medium Area
is suitable for most purposes.

5. Set up the analyzer parameters (Scan Mode, etc) in the normal way. If your detector has a
suitable number of channels, you can use Snapshot mode; otherwise, you need to use
Fixed Analyzer Transmission for a normal XPS scan. The other analyzer parameter should
be the same as those for your data acquisition.

You can now add a spectrum group to the With Optimized Emission section. below the auto
adjustment of flood gun procedure. All items in this section will be executed after the flood gun
emission current has been optimized. After running these items, the flood gun emission is
returned to the value you defined for the flood gun at the start of the experiment (with the ana-
lyzer and source settings).

Note the following points for running spectra in the With Optimized Emission section:
If no optimum emission current can be found, SpecsLab Prodigy will use the emission cur-
rent you defined for the flood gun at the start of the experiment.
After running the experiment, you can add new spectra to the With Optimized Emission
section. These will be run with the optimized emission current found in the previous run. If,
however, an optimum emission current has not been found, the optimization routine will
run again.
4.9.2 Running Auto Flood Gun

The auto adjustment of flood gun procedure runs as a part of the schedule. You can validate
the procedure separately to confirm that it is able to run by checking the validation box:

43

Otherwise, the procedure will be checked when you validate the whole experiment and will run
as scheduled after you click the icon.

The procedure performs the following steps:
1. Exploratory scan with pass energy of 50 eV and a step size of 1 eV. Although the peak is
likely to have shifted from its expected value, it should appear somewhere within this
region. SpecsLab Prodigy will locate the peak within this region.
2. Based on the peak found in the previous step, SpecsLab Prodigy will scan a smaller region
containing the peak. This is a higher precision scan with a 30 eV pass energy and a smaller
step size of 0.5 eV.
3. Having confirmed the position of the peak, a third scan is performed. Again, the step size is
smaller at 0.2 eV; the pass energy is a user-defined value. This is used as the basis for all
subsequent scans.
4. The emission current of the flood gun increases by a user-defined step and SpecsLab
Prodigy runs a scan based on the settings in the previous step. After each scan, SpecsLab
Prodigy performs a data operation to determine the FWHM of the peak. This step repeats
until the flood gun reaches an intermediate emission current.
5. On reaching the intermediate emission current, SpecsLab Prodigy evaluates the data. It
tries to fit a curve to the FWHM vs. Emission Current data set using a Savitsky-Golay curve.
If it finds a minimum, it skips to the last item in this list.
6. If no minimum is found in the previous step, the program will continue increasing the emis-
sion current and scanning until the maximum emission current is reached.

Note
If no obvious minimum is visible even at this point, the algorithm will still attempt to fit the data
and continue with the schedule. The results in this case may not be completely reliable.

7. SpecsLab Prodigy will set the emission current of the flood gun to the value obtained from
the fit and continue with the schedule. This value is shown in the Experiment Editor, as
shown below. The data obtained is displayed in the Plot View.


44
4.9.3 Results of Auto Flood Gun Procedure

As with other data obtained by SpecsLab Prodigy, you can view results in the Plot View. At first
sight, the results from the auto adjustment of the flood gun can appear to be a confusing
jumble. This section offers a few tips on using the Plot View to view the results.

Note
A Savitskz-Golay function fits the data. The minimum of this curve determines the emission cur-
rent used in the experiment. The parameters of this fit are not displayed in SpecsLab Prodigy—
only the results are available in the Auto Adjustment of Flood Gun item in the Experiment
Editor.

To view data from the auto adjustment of flood gun procedure:
1. Click the icon in the section of the Data Browser that corresponds to the data for the auto
adjustment of the flood gun. The section will expand to show the properties of the data.
2. Double click the Emission or Iteration field. A list will appear.
3. Click an entry in the list. The spectrum corresponding to this entry will be displayed in the
Plot View. Moving the scroll wheel on your mouse allows you to browse through the entries.

45

4. You can create a copy of the spectrum by clicking the and icons. A second line will
appear in the table. You can change the settings of this copy to display a second spectrum
in the Plot View. The screenshot below shows two spectra displayed in this way. The spec-
tra are fluorine peaks from PTFE, showing the effect of optimization.

4.10 Auto Sample Height Adjustment

The auto sample height adjustment feature changes the sample position until the optimum dis-
tance between the sample and analyzer is located.


The lens system on the front of a SPECS electron energy analyzer has a focus which determ-
46
ines the working point. For optimum performance, the sample should be exactly at this point.
This is particularly important for small excitation spots, such as from an electron gun or a syn-
chrotron.

SpecsLab Prodigy can control the manipulator while reading the signal intensity to locate the
working distance. After obtaining the signal intensity as a function of sample distance, Specs-
Lab Prodigy evaluates the optimum position and moves the sample accordingly.

Performing auto sample height adjustment typically involves the following steps:
1. Add an Electron Spectroscopy experiment and define your analyzer, source and other
devices as usual.
2. Click and select Auto Sample Height Adjustment.
3. Configure the auto sample height adjustment routine.
4. Define the rest of your experiment.
5. Run the experiment with the auto sample height adjustment routine.

When you start the experiment, SpecsLab Prodigy will run the auto sample height adjustment
as part of the schedule. Data is saved with the experiment and can be viewed at any time.
4.10.1 Configuring the Auto Sample Height Adjustment

To add auto sample height adjustment to the experiment:
Click at the desired point in the schedule and select Auto Sample Height Adjustment.

You need to include and configure the following items in the Electron Spectroscopy experiment:
Analyzer.
Source.
Manipulator: Position. You should set this to a position loaded from a template that you
know is near to the measurement position.

Note
After producing a suitable configuration, you can save it as a template. You can then load this
for future experiments without needing to follow the whole procedure described here.

Please note the following points when configuring the auto sample height adjustment routine:
The sample moves along the lens axis of the analyzer—this involves moving the X and/ or
Y axes of the manipulator. The movement of the axes is configured by SPECS. For this
reason, SpecsLab Prodigy may indicate different adjustments of X and Y manipulator set-
tings for each step.
After recording data at each step, SpecsLab Prodigy runs an arithmetic mean data oper-
ation. This calculates the mean value of the intensity of all points. As such, it is not

important whether a peak or a secondary electron signal is measured—only an intensity is
47
used.
Scan Mode: Use Snapshot mode to quickly measure the signal without needing to scan.
The other settings for setting up the analyzer (slit settings, configuration file, etc) need to
be the same as those for the spectrum group.
The "spectrum" is set up in the same way as a normal experiment. You can set the energy
to look at a peak energy or for secondary electrons.

The screenshot below shows a typical configuration after validation.

Following configuration of the auto sample height adjustment, you can add actions that take
place at the optimized position by clicking the icon and selecting an item, e.g. a spectrum
group. Please note the following points:
Only actions within the At Optimized Position group will be performed at the sample pos-
ition obtained
by the auto sample height adjustment. After completing actions in the At Optimized Pos-
ition group, the manipulator will move back to the position defined by the
Manipulator: Position device at the start of the Electron Spectroscopy experiment.
If you run the experiment again, having already found the optimum sample position, Specs-
Lab Prodigy assumes that the optimum position has not changed and uses the value
already obtained without running the routine again. However, if you close the Experiment
Editor and reopen the routine, the optimum position is measured again.
If you want the auto sample height adjustment to run again, you need to click the icon
and select Unlock and Clear All Data.


The screenshot below shows a spectrum group correctly nested in the schedule so that the
48
spectrum is scanned at the optimum sample position.

4.10.2 Running Automatic Sample Height Adjustment

Auto sample height adjustment is a part of the schedule. You can validate the procedure sep-
arately to confirm that it is able to run by checking the validation box:

Otherwise, the procedure will be checked when you validate the whole experiment and will run
as scheduled after you click the icon.

SpecsLab Prodigy makes a measurement at the current sample position before moving the
manipulator. If less than 1 cps per channel is measured, SpecsLab Prodigy will abort the auto
sample height adjustment and move to the next item in the schedule. Although this may occur
for trivial reasons (e.g. the source is not switched on), it may also be because the manipulator
is in the wrong part of the chamber—further movements may be unexpected and dangerous.

After locating the optimum position for the sample, i.e. the position with highest signal intens-
ity,SpecsLab Prodigy fits the data using a Savitsky-Golay curve to locate the maximum. It then
moves the sample to this maximum, and makes a final measurement at this new position. The
position is reported in the Experiment Editor. SpecsLab Prodigy then executes the next step in
the schedule.

49
Note
Only actions in the At Optimized Position group are performed at this position. After com-
pleting these actions, the manipulator moves back to the position set by the Manipulator: Pos-
ition device.

The data obtained from the auto sample height adjustment is saved in the experiment file with
any other data obtained. You can view this data in the Plot View or—better still—in the Image
View.

Note
There are occasional outliers in the data which may affect the evaluation of the position. For
this reason, you should select an energy that provides an adequate signal and is not unduly
affected by noise. Viewing auto sample height adjustment data allows you to judge the reli-
ability of the procedure.
4.10.3 Viewing Results of Auto Sample Height

As with other measurements, the Plot View shows data collected as part of the automatic
sample height adjustment. It is however better to use the Image View if you want to under-
stand the data.

Note
The Savisky-Golay fit and its parameters are not visible in SpecsLab Prodigy. Only the cal-
culated maximum is shown in the Experiment Editor after the procedure has finished.

To view the data in the Image View:
1. Select Views/ Image View from the menu bar to open the Image View. No data is dis-
played in the image because the axes of the image are not yet correctly set up.
2. In the Data Browser, select the spectrum corresponding to the automatic sample height
adjustment.
3. Click the icon to expand the spectrum properties. You should see the Arithmetic Mean
data operation.
4. Double click the Arithmetic Mean title bar so that a tick appears. This is now the active
data set for the image.

50

5. In the image, select the following axis settings:
Y axis: x (mm)
X axis: Iteration
You should now see the data presented in the image. The intensity at each position is rep-
resented by the color. You can drag the horizontal profile to see the intensity presented in
graphical form.

Note
The example above uses fewer points than the default settings for reasons of clarity.

51
Chapter 5 – Experiment Editor III: Reference

Information
This chapter contains useful reference information for using the Experiment Editor. It covers
the following topics:
Scan modes—their applications and settings.
Exporting data—procedures and file formats.
Instrument status—indicators and error messages.
5.1 Scan Modes

SPECS analyzers can operate in a number of different modes. You set the mode for each spec-
trum during definition in the Experiment Editor. Each mode has its own characteristics; avail-
able parameters and limits also vary between the modes.

The table below summarizes the available scan modes, together with a brief description of
their major uses. The following subsections describe the modes in more details.

Scan mode Description
Fixed analyzer trans- Normal scanning mode for XPS, UPS, ISS.
mission
Fixed retarding ratio Normal scanning mode for AES.
Fixed energy Measures single energy, ideal for analyzer set up and stability
checks.
Snapshot Uses energy resolution of multi-channel detectors for fast peak
measurements.
Detector voltage scan For finding optimum detector operating voltage.
Constant final state Scans photon energy (synchrotron) and measures fixed kinetic
energy. For band structure mapping experiments.
Constant initial state Scans photon energy (synchrotron) and scans kinetic energy.
For band structure mapping experiments.
5.1.1 Fixed Analyzer Transmission

Fixed analyzer transmission (FAT) mode allows you to scan through the kinetic energy while
holding the incident excitation energy constant. It is the most commonly used mode for XPS,
UPS and ISS.

The pass energy is held constant during the scan, so that the energy resolution of the spec-
trometer is constant throughout the scan. The retarding potential of the analyzer is varied in
order to measure different kinetic energies.

52
Measurements are normally performed with a fixed excitation energy, e.g. an X-ray gun. You
can easily set up measurements defined in terms of the binding energy, as well as kinetic
energy.
S ettings

Setting Dependencies Description
Name Free text Name of the spectrum.
Scans - Number of scans performed.
Start Start < End Start energy (eV). For binding energy,
the initial binding energy.
End End > Start Final energy (eV). For binding energy,
the final binding energy.
Step 0 < Step < ceil(End − Start) / Step Energy step between measurement
points.
Values Values = (ceil(End − Start) / Step) + 1 Total number of values measured.
Dwell - Measurement time for each point.
LensMode - See analyzer manual for available
lens modes.
Epass - Analyzer pass energy.
Duration Duration = Dwell*Scans*(End − Start) / Total time taken for measurement
Step (info only).
Comment Free text Additional comment about the spec-
trum.

5.1.2 Fixed Retarding Ratio

Fixed retarding ratio (FRR) allows you to scan through the kinetic energy while holding the incid-
ent excitation energy constant. Unlike Fixed Analyzer Transmission, the pass energy is not

held constant—the ratio of retarding potential to pass energy is constant. This means that the
53
energy resolution is lower at higher kinetic energies.

Although this mode is rarely used for photoelecton spectroscopy because of the non-constant
energy resolution, it is the mode best suited to AES. Auger data tables are compiled from res-
ults obtained using a cylindrical mirror analyzer (CMA). Using the PHOIBOS analyzer in
FRR mode has the same characteristics as a CMA, so you can use the data directly without any
further correction.
S ettings

Start Start < End Start energy (eV). For binding energy,
the initial binding energy.
End End > Start Final energy (eV). For binding energy,
points.
lens modes.
RetRatio RetRatio = (Ekin − Work function)/ Epass Retarding ratio. The dependency
show its relation to the pass energy.
Work function is set in the Device
Control.
Step (info only).
trum.


54
5.1.3 Fixed Energies

The fixed energy (FE) mode is a simple mode that allows you to monitor a single kinetic energy
for a specified time. Particles with a defined kinetic energy pass through the analyzer and are
detected. This mode is used when setting up or checking the operation of the analyzer, as well
as for investigating the stability of the excitation source.

Since the mode measures intensity as a function of time, signals from multiple channels are
not of interest. SpecsLab Prodigy therefore treats all channels as a single detector and sums
the signal from all channels.
S ettings

Start Start < End Kinetic energy (eV).
LensMode - See analyzer manual for available lens
modes.
Duration Duration = Dwell*Values*Scans Total time taken for measurement (info
only).
Comment Free text Additional comment about the spectrum.

Data is displayed in the Plot View as intensity vs Values. If you set the dwell time to 1 s, the X
axis is therefore effectively measured in seconds.


55
5.1.4 Snapshot
The analyzer is not scanned in snapshot mode. Data is collected from all channels of the
detector without performing any averaging. The spectrum shows the energy distribution of the
particles that pass through the analyzer with its current settings.

A typical use for snapshot mode is to position the detection energy at the top of a peak and
record the signal. This allows faster data acquisition for the limited energy range compared to
FAT. Snapshot measurements are usually best suited to CCD and DLD detectors, which have
hundreds of channels and can show the peak shape. They are also possible with five or nine
channel detectors; however, the energy resolution is comparatively poor.

If you want to use the analyzer in snapshot mode, you should calibrate the detector so that the
signal delivered by each channel is normalized.
S ettings

The center/ width configuration mode is particularly useful for snapshot mode:
Right-click the spectrum settings table and select Use Center/Width from the context
menu.

Center - Kinetic energy/ binding energy at the
center channel.
Width Final energy (eV). For binding energy,
Step - Calculated energy step between
measurement points.

56 Setting Dependencies Description
Values Values/Channel number must be an Total number of values measured.
integer. Validation of scan corrects to
nearest integer.
lens modes.
Duration Duration = Dwell*Scans*Values Total time taken for measurement
(info only).
trum.
5.1.5 Detector Voltage Scan

The detector voltage scan (DVS) changes the detector voltage while holding the detected
energy constant. Since channel electron multipliers degrade with use, you can use this mode to
find the correct operating voltage for the detector.

When examining the results of a DVS, it is best to view the individual channels by selecting
Separated in the data browser. This allows you to check the performance of the individual
channel electron multipliers.

Please also refer to the detector manual for more information.

Caution!
You can destroy your detector if you set Udet End too high. Refer to the test
report for your detector to find suitable operating voltages.
S ettings

Name Free text Name of the scan.
Start Start < End Start voltage (V).
End End > Start Final voltage (V).
Step 0 < Step < ceil(End − Start) / Step Voltage step between measurement
points.
Values Values = ceil(End − Start) / Step Total number of values measured.
LensMode - Use a mode such as large area to
allow high transmission of electrons.

Setting Dependencies Description 57
Ekin - Measured kinetic energy. This
should be a background level with
some signal—not a peak energy!
Step (info only).
Comment Free text Additional comment about the scan.

The results of a detector voltage scan are displayed in the Plot view. You need to select
Detector Voltage in the X axis in order to display the data. You can find the operating voltage
with the cursor. The detector voltage is set in the device control for the analyzer.

5.1.6 Constant Final State

Constant final state (CFS) mode involves scanning the photon energy while detecting a single
kinetic energy. The resulting scans show intensity as a function of binding energy. This mode
ensures that you only measure occupied states in the sample.


This mode is only available when you select a beamline as your source.
58

Measurements with multiple channels are not suitable with this mode, since you are only
examining a single kinetic energy. SpecsLab Prodigy therefore treats all channels as a single
detector and sums the signal from all channels.
S ettings

Start Start < End Source start energy (eV). For binding
energy: (Source energy − Kinetic
energy).
End End > Start Source final energy (eV). For binding
energy).
points.
lens modes.
Ekin - Measured kinetic energy.
Step (info only).
trum.

The X-axis in the Plot View shows the difference energy (source energy + kinetic energy). When
using binding energy definitions, binding energy is shown.
Examp le
The screenshot below shows a spectrum with a set of typical parameters for a measurement
with CFS. The data acquired from these parameters represent a binding energy of 80–90 eV.


59

As an explanation, the following steps take place in an experiment with these parameters:
1. Monochromator moves to 100 eV.
2. Analyzer measures electrons with energy 20 eV for 0.1 s dwell time.
3. Monochromator moves to 100.1 eV.
4. Analyzer measures with energy 20 eV, monochromator moves an increment of 0.1 eV. This
is repeated until the monochromator reaches 110 eV.
5.1.7 Constant Initial State

Constant initial state (CIS) mode involves scanning the photon energy while simultaneously
scanning the detected kinetic energy. When the photon energy is changed, the detected kinetic
energy of the analyzer is changed by the same amount. In this way, the same binding energy is
always measured. This allows you to measure the density of states in unoccupied states.

This mode is only available when you select a beamline as your source.

Measurements with multiple channels are not suitable with this mode, since you are only
examining a single kinetic energy. SpecsLab Prodigy therefore treats all channels as a single
detector and sums the signal from all channels.
S ettings

Start Start < End Source start energy (eV). For binding
energy).
End End > Start Source final energy (eV). For binding

60 Setting Dependencies Description
energy).
points.
lens modes.
Ekin - Measured kinetic energy.
Step (info only).
trum.

The X-axis in the Plot View shows the difference energy (source energy + kinetic energy). When
using binding energy definitions, binding energy is shown.
Examp le
The screenshot below shows a spectrum with a set of typical parameters for a measurement
with CIS. The data acquired from these parameters represent a kinetic energy of 20–30 eV.

As an explanation, the following steps take place in an experiment with these parameters:
1. Monochromator moves to 100 eV.
2. Analyzer measures electrons with energy 20 eV for 0.1 s dwell time.
3. Monochromator moves to 100.1 eV.
4. Analyzer measures electrons with energy 20.1 eV for 0.1 s dwell time
5. Monochromator moves an increment of 0.1 eV, analyzer measures an increment of 0.1 eV.
This is repeated until the monochromator reaches 110 eV.

61
5.2 Exporting Data
There are a number of ways to export data obtained from measurements. These allow you to
import the data into other programs for further analysis and processing.

The following export formats are supported:
Prodigy template file—the entire experiment is saved as a template, rather than just part
of the configuration.
VAMAS—a standard data exchange format.
XY—exports the data in space-delimited columns with header information.
XML—the native file format of SpecsLab2. This allows you to share your data with Spec-
sLab2 users.

Note
The transmission function, if included in the spectra, is also exported.

You can automatically export data to any of these formats after acquisition:
1. Click the File Settings button in the Experiment Editor toolbar. The export settings will
appear.

2. Check the export format that you want to save. After acquisition, the data is automatically
saved in the selected format.

You can also export the current experiment:

Click the arrow next to the icon in the Experiment Editor toolbar. A menu will appear allow-
62
ing you to export the experiment.

To export data from a single spectrum:
Right-click the spectrum in the spectrum group and select Export Spectrum Data from
the context menu. A Save dialog will appear, allowing you to select the name, location and
file type (XY or VAMAS) for the exported data.
5.2.1 VAMAS Files

VAMAS format1 is a standard that allows interchange of data from SpecsLab Prodigy with other
programs such as CASA XPS.

Note
SpecsLab Prodigy is able to read VAMAS files and import the data. Importing follows the nor-
mal procedure for opening a file.

When exporting a number of spectra, each spectrum is saved in its own VAMAS file.

By default, the export file is saved in a new directory at the same location as the autosaved
data file. You can override this setting and specify a different save location.

Note
Not all metadata generated by SpecsLab Prodigy is saved in the VAMAS file. This does not
affect the import into third-party programs.

For reference, the table below describes the VAMAS format.

Item descrip- Sample
Line Sample entry Item description Line
tion entry
Format identifier 1 VAMAS Surface Source azimuth 43 180
Chemical
Analysis Standard
Data Transfer
Format 1988 May 4
Institution iden- 2 Specs Analyzer mode 44 FAT
1 . The Versailles Project on Advanced Materials and Standards (VAMAS) introduced a standard data exchange format specifically
designed for the interchange of data for analysis methods such as UPS, XPS, AES and many others. It is capable of storing elemental
maps, depth profiles, and data sequences. The VAMAS format used by SPECS conforms to ISO 14976. See, for example, "VAMAS Sur-
face chemical analysis standard data transfer format with skeleton decoding programs", W.A. Dench, L.B. Hazell, M.P. Seah, Surf.
Int. Anal. 13, p. 63–122 (1988).

Item descrip- Sample 63
tion entry
tifier
Instrument model 3 PHOIBOS HSA3500 Analyzer resolution 45 100
i.d. DLD 150 characteristic
R6-WAL[HWType
30:106] DLD
Operator i.d. 4 – Magnification of ana- 46 1
lyzer
Experiment i.d. 5 ? Magnification of ana- 46 1
lyzer
# Comment lines 6 1 Analyzer work function 47 4.6
Comment lines 7 Created by Specs- Target sample bias 48 0
Lab
Prodigy,
Version 2.83-
r17331
Experiment mode 8 NORM Analysis width x, mu 49 0
Scan mode 9 REGULAR Analysis width y, mu 50 0
# Regions 10 4 Analyzer axis polar 51 0
angle
# Variables 11 1 Analyzer azimuth 52 0
# Parameter 12 Step Species 53 Silicon
exclusion entries
# Manual items 13 d Transition state 54 Silicon
# Future exper- 14 0 Charge of analyzed 55 -1
iment items particle
# Future block 15 0 Abscissa label 56 kinetic energy
entries
# Blocks 16 1 Abscissa units 57 eV
Block i.d. 18 Silicon Abscissa start 58 1379.31
Sample i.d. 20 Cycle1 Abscissa increment 59 0.05
Year 4 digits 21 2010 # Corresponding vari- 60 15
ables
Month 22 06 Corresponding vari- 61 counts_0
able label
Day 23 24 d= none 62 d
Hour 24 14 Signal mode 91 pulse counting
Minute 25 45 Signal collection 92 1
time/channel
Second 26 00 # Scans for this block 93 20
# Hours + GMT 27 1 Signal time correction 94 0
# Lines in block 28 6 Sample normal tilt 95 0

64 Item descrip- Sample
tion entry
comment
Technique 35 XPS Sample normal azi- 96 0
muth
source 37 Al Sample rotation angle 97 0
Source energy 38 1486.6 # Additional params 98 0
Source strength 39 300 # Ordinate values 99 3315
Source width x , 40 500 Min y 100 31
mu
Source width y , 41 500 Max y 101 10877
mu
Source polar 42 54
angle

Data points
terminator end of experiment
5.2.2 XY Format

The XY format is a simple format that contains:
Header information about the measurement and the export details.
The numerical data from the scan in two space-separated columns.

Results are saved in a simple space-delimited X Y format. You can specify if individual spectra
or channels are to be saved—the file then contains a set of measurements concatenated into
one file with a single set of metadata (if specified for export). Each measurement is identified
with a title. The export format is readable in a text editor or spreadsheet.

When you check the XY box in the Export Settings, the following settings appear:
Location: By default, the export file is saved in a new directory at the same location as the
autosaved data file. You can override this setting and specify a different save location.
Output: This gives you the option of saving the data from spectra in one file or each spec-
trum in a separate file.
Parameters: Checking the boxes in this table determines the contents of the export file.
The metadata contains details of the experimental setup.


65
5.3 Instrument Status

SpecsLab Prodigy offers two ways of checking the status of an experiment:
Status indicators for each device currently being used.
Error messages to describe problems in the schedule.
5.3.1 Status Indicators

The menu bar of SpecsLab Prodigy shows icons of all devices that are currently connected in
the program. The color shows the status of each device, as listed in the table below.

Note
Each device has its own icon and is displayed separately in the toolbar. The table below only
shows the analyzer icon.

Indicator Status
Device inactive.
Device in operation and working correctly.
Set up device ready for operation.
Device error.

If a device is disconnected in the software, it is not shown in the menu bar.

66
5.3.2 Dealing with Errors
After configuring an experiment, you need to validate, either by checking the box next to items
in the schedule, or by pressing and validating the entire schedule. SpecsLab Prodigy checks
that the items can be run. If problems appear, they are indicated by the symbols in the table
below.

Error sym-
Comments
bol
Warning. The instrument may not perform correctly, but operation is possible.
On double-clicking the symbol, an error message will appear to explain the
cause of the error. After reading and understanding the message:
Click Acknowledge to dismiss the error symbol and continue.
Click OK to continue, but the error will still be shown.
Error. The experiment cannot run. An error message will inform you of the
reason for the error. Perform the following checks:
The instrument is switched on.
All electrical connections and interlocks are correct.
The IP address is set correctly.

The following example shows some of the features available when errors appear, explaining
how you can locate and solve errors. As you can see, there are four items in the schedule: Two
Electron Spectroscopy experiments, a Sleep command and a Group which can contain addi-
tional items.


67

The first Electron Spectroscopy group has a warning, while the second Electron Spectroscopy
experiment and the Group have errors. An error message provides information about the
cause of the errors. Remember that the experiment will still run with a warning, so this not
shown in the error message.

Warning in Electron Spectroscopy 1
We see that there is a warning in the first Electron Spectroscopy group, so we expand the
group by clicking the button. There are two spectrum groups in this experiment.

Importantly, the warning symbol has moved to show us which spectrum group has the prob-
lem. We can therefore focus on this group.

Expanding the spectrum group shows us the spectrum that is causing the problem. Clicking the
symbol produces a message that tells us the transmission function is not suitable for the slit set-

tings. We can either acknowledge this (the error will go away) or click OK to continue the meas-
68
urement, but with the error still shown.

Error in Electron Spectroscopy 2
Solving the error for the second Electron Spectroscopy experiment is fairly easy. SpecsLab
Prodigy cannot find an analyzer for the experiment, so the analyzer needs to be defined.

Error in Group
Groups allow you to create hierarchies in the schedule. As with the warning described pre-
viously, the error symbol shows you that the failure lies somewhere within this group. On
expanding the group, the symbol moves to show the item that is causing the problem.


For hierarchies with many levels, the error symbol will move as you expand the hierarchy until
69
you locate the source of the problem. In this case, SpecsLab Prodigy cannot connect to a
sample heater. Looking in the Devices item, we see the heater that is causing the trouble.

The table above lists the typical reasons for this kind of error so that you can find why SpecsLab
Prodigy cannot connect to the device.

This page intentionally left blank.
70

71
Chapter 6 – Plot View I: Features
The Plot View contains a chart that displays data from selected regions. You can choose which
data is shown in the Data window; you can also create additional Data windows in order to com-
pare spectra.

Chapter 6 – shows the main sections in the Plot View.

The following sections describe the features present in the Plot View. Data operations, which
perform calculations on acquired spectra, are described in "Plot View II: Data Operations"
on page 85.
6.1 Data Browser

The data browser displays all spectra from the experiment as well as data operations per-
formed on the spectra. You can change the appearance of the line in the Plot View and hide
spectra.
By clicking the icon, you can see more information about the spectrum, including which
spectrum components are displayed and additional data display settings.


Note
72
The columns in the table (e.g. Scan in the screenshot below) depend on what data is available
in the scan. For a single-scan, single-channel data set, for example, no column would be shown.

Many of the features have an impact on the display of the spectrum in the Plot View. These fea-
tures are described in the following sections:
Displaying components of spectra.
Changing the appearance of data.
Showing/ hiding spectra.
Changing the settings.
6.1.1 Displaying Spectrum Components

By default, the total signal intensity is displayed in the Plot View. You can change the display so
that individual channels (for multichannel detectors) or individual scans (when multiple passes
are scanned in the spectrum) are show. Other scanning options, such as depth profiling, con-
tain additional components that can be selected. Clearly, the options available depend on your
configuration and experiment type.

As an example, to display individual channels in a spectrum:
Double-click the Combined button under En. Chn and select Separated from the drop-
down list.


73
You can show the individual channels on the Z-axis:
1. Click the icon in the toolbar.
2. Select Channels for the Z axis label.
6.1.2 Setting Color and Appearance of Data

There are a number of different linestyles and data markers that you can use to display your
data. You can access these as follows:
1. Select the line of the spectrum in the legend. The color, linestyle and width are shown.
2. Edit the linestyle accordingly. The plot is updated as soon as you select a setting.
3. Click Done or anywhere outside the selection box to close the box.

6.1.3 Showing and Hiding Spectra

You can toggle the visibility of each spectrum in the Plot View for the purposes of clarity or com-
parison.

To toggle the visibility of a spectrum in the plot, use one of the following methods:
Click next to the spectrum that you want to show or hide and select Toggle Visibility from
the menu. You can also use the entries in this menu to toggle all child items in the hier-
archy or to hide all others.
Double click the name of the spectrum or data operation. The axes in the plot are auto-
matically scaled to the displayed spectra.


74

Visibility of spectra is indicated by a line next to its description. The color of this line is the same
as that displayed in the plot.

You can only remove a spectrum completely from the data browser by deleting its data and
then removing its from the spectrum group:
1. Select the spectrum (or spectra) in the Experiment Editor and click . SpecsLab Prodigy
will prompt you before the data is deleted.
2. Click the icon to remove the definition of the spectrum from the group.
6.1.4 Adding New Spectra

You can add new spectra based on existing measurements. These spectra belong to the same
spectrum group and have the same settings, except for the selected energy range. After study-
ing or analyzing a spectrum, you can make new measurements based on areas of interest in
the data.

There are two options for adding spectra:
Adding an exact copy of the spectrum, or the range selected in the spectrum.
Adding a copy of the spectrum or selected area with a 0.1 eV step size.

To add a new spectrum:
1. Select a spectrum in the Data Browser.

2. Click one of the following icons at the bottom of the Data Browser:
75
Adds an exact copy of the spectrum, or the range selected in the spectrum.
Adds a copy of the spectrum or selected area with a 0.1 eV step size (detailed
copy).
The new spectrum will be added to the Spectrum Group in the Experiment Editor. The energy
range of the spectrum depends on the following, in order of priority:
1. The area selected in the plot.
2. The zoomed area visible in the plot.
3. The whole spectrum.

You can further edit the configuration in the spectrum group as necessary and start the meas-
urement in the Experiment Editor to acquire the data.
6.1.5 Additional Data Display Settings

By clicking the Settings button for a spectrum in the legend, you can display and adjust addi-
tional settings that affect the appearance of the data in the Plot View. The table below lists the
settings.

Setting Description
Energy correction Allows you to add an energy shift to the spectrum, e.g. a work function
correction. You can enter a value using the keyboard, with the up and
down arrows or—on selecting the number in the pop-up—with the
mouse wheel. The original data (saved with the experiment) is not
affected by this action, but exported data does contain these shifts.
Normalize by You can acquire other signals (such as sample current) during data
acquisition and use this to normalize the signal. This menu allows you to
select which data source is used for normalization.
Channel allocation You can apply an interpolation to data obtained from multi-channel
detectors. Apportioning or nearest neighbor approaches are available.
More information about this procedure is provided in the SPECS soft-
ware note "Acquiring Data with Multi- Channel Systems", included in the
Documents/Additional Information folder of the SpecsLab Prodigy install-
ation directory
6.2 Toolbar Controls

The toolbar in the Plot View contains controls to perform the following actions:
View peak energies with the periodic table (optional feature).
Set cursor positions.
Select a region of interest in the spectrum.
Toggle the grid display.

Toggle the Z axis display.
76
Zoom.
6.2.1 Setting the Cursor Position

You can add cursors to the chart in the Plot View. A cursor is a cross that allows you to look at X
and Y values. Typically, you can use them for checking peak positions and heights. There are
two cursors that can be set independently.

When setting cursors, note the following points:
If you select another mouse tool (e.g. the Zoom mode), the cursor is sticky and remains in
its position until you reactivate the cursor.
You can toggle the operation of each or both of the cursors by selecting the appropriate
entry in the cursor menu. Keyboard shortcuts also allow you to toggle the cursors.
If you display both cursors at the same time in the chart, the toolbar shows the difference
between the positions of the two centers.

When setting cursors in the chart:
1. Click the icon in the toolbar or press C to toggle the cursors.
2. Add a cursor:
Left-click in the plot to add the yellow cursor.
Right-click to add the blue cursor.
6.2.2 Selecting an Area

You can set the position of both cursors with one action. In this case, the area between the two
X coordinates is also displayed.

To select an area with cursors:
1. Click the icon.
2. Click a point in the chart and drag the mouse to a second point. This produces a shaded
area. You can perform data operations on this region—see Performing Data Operations
for more information.


77
6.2.3 Displaying the Grid in the Plot View

You can switch on a grid to help you judge the position and height of peaks in the spectrum:
Click the grid icon in the Plot View. This button toggles the display of the grid.

The grid lines are shown for major ticks on the axes. The intervals between the major ticks
depend on the scaling of the plot—see "Zooming and Autoscaling in the Data Window" on
page 77.
6.2.4 Zooming and Autoscaling in the Data Window

The Data Window automatically zooms to show the selected plot or operation in the data
browser. If nothing is selected in the Data Browser, the range is adjusted to show all spectra
and operations.

The toolbar contains two icons, and , which respectively allow you to zoom in and out of
the plot in steps.

To display the complete plot again, double click in the plot area. Alternatively, click the icon
in the toolbar. The button rescales the chart so that Y = 0 is shown.

You can also define an area of the plot in order to inspect items of particular interest:
1. Click the icon to activate zoom mode.

2. Click and drag the mouse to form a rectangle in the Plot View. When you release the mouse
78
button, the plot shows the selected area. Scroll bars on the top and right side of the plot
allow you to move to other areas of the plot.
6.2.5 Displaying the Z Axis

You can display a Z axis in the Plot View. The scale of the Z axis depends on the type of data in
the spectrum, which data components are displayed and the selection of the Z axis label. For
more information about these topics, please refer to:
"Displaying Spectrum Components" on page 72.
"Changing the Axis Labels" on page 83.

To toggle the appearance of the Z axis:
Click the icon in the Plot View toolbar.

6.2.6 Copying an Image to the Clipboard

Clicking the icon will copy the plot (with axes) exactly as it appears in the Plot View. You can
paste the bitmap into other applications.

79
6.2.7 Printing the Plot View
The toolbar contains icons for a print preview and for printing the plot. The following inform-
ation is printed:
The plot in the Plot View, including all visible spectra and data operations.
A legend, showing the experimental parameters for each spectrum. The entries in the
legend are color coded.

The print preview window allows you to see the page before it is sent to the printer. The toolbar
contains a number of controls for changing the orientation and page size, as well as changing
the appearance of the preview.

To print the Plot View:
Click the icon in the Plot View toolbar. The standard MS Windows print dialog will open,
allowing you to configure and start the print job.

80
6.3 Periodic Table
The periodic table contains a set of databases for the XPS, UPS and AES transitions of all ele-
ments. It allows you to easily identify peaks in the plot view, as well as providing additional
methods for performing peak operations.

To open the periodic table:
Click in the toolbar of the Plot View.


81
6.3.1 Identifying Peaks using the Periodic Table
There are a number of options that you can select to affect the way peak identifications are
added to the spectrum. These are listed in the table below.

Feature Description
Excitation The excitation energy used to measure the data.
energy
XPS Shows lines for XPS.
AES Shows lines for AES.
Main lines Only shows the most intense lines for the selected element. Hovering the mouse
only over the line will show all lines of the element.
References Displays the database reference for each displayed peak.

For identification of peaks in the spectrum, you can use the automatic peak identification fea-
ture or manually select peaks. Expand the sections below for more information about these pro-
cedures.

Automatic peak identification
The automatic peak identification feature can be useful to help you identify unknown peaks in
the spectrum. Note the following points:
Some of the peaks may be included because their energy is close to that of a peak in the
spectrum. The identification of a peak does not necessarily mean that the element is
present in the sample.
Artifacts and spikes in the data may be identified as peaks.
Not all peaks of an element will be shown. This generally applies to weak peaks of the ele-
ment which are hidden in the noise level of the data.
Hovering the mouse over the peak identification label in the spectrum or over the identified
element in the periodic table will show all peaks for that element in the spectrum.

As a result of these points, checking the Main Lines Only box is a good idea to reduce the num-
ber of false identifications.

To use automatic peak identification:
1. Select a spectrum in the Data Browser. The peak identification feature will be run on this
spectrum.
2. Click Peak Identification. SpecsLab Prodigy will locate all peaks in the spectrum and
match them to values in the databases.

Manually selecting peaks for an element

If you expect an element to be present in the spectrum, you can show the database values for
82
the peaks:
Click the element in the table. All peaks for the element will be displayed in the spectrum.

Manually selecting peaks for an element
If you expect an element to be present in the spectrum, you can show the database values for
the peaks:
Click the element in the table. All peaks for the element will be displayed in the spectrum.

Right-clicking the element shows a list with the transitions for the element. You can select one
of these transitions to add the peak to the Selected Transitions pane.

Clicking Deselect All Elements will remove all peak identifications from the spectrum. If you
have selected any peaks, these will not be removed.
6.3.2 Selecting Peaks

You can select peaks of interest. These are highlighted in the Plot View and listed in a table next
to the periodic table. You can perform operations on the selected peaks.

There are two ways to select peaks in the spectrum:
Click the icon in the label of the peak. The icon will change to to show it is pinned.
Right-click an element in the table and select a peak from the menu.

In both cases, the selected peak will be displayed in a table next to the periodic table. You can
select peaks in this table and perform actions on them:
Shows all peaks for the selected element.
Adds detailed spectra for all selected peaks.
Performs an operation on the selected peak(s). The element name and transition is
included in the parameters of the operation.


83

To remove selected peaks:
Select one or more peaks in the Selected Peaks table and click . If no peaks are selec-
ted, all will be deleted when you click .
6.4 Changing the Axis Labels

You can change the labels of the X, Y and Z axes so that they present different quantities. The
options available depend on the axis selected as well as the type of spectrum.

To change the axis label:
1. Move the mouse over the axis label. It will change into a drop-down list.
2. Click the drop-down list and select the desired label.

84

85
Chapter 7 – Plot View II: Data Operations
SpecsLab Prodigy offers a variety of operations that you can perform on spectra in the Plot
View. This chapter describes how to perform data operations and contains descriptions of all
operations.

There are essentially two methods of running data operations:
Setting up the operation before running the experiment. The operation is performed and
updated after each scan. Such an approach is ideal as part of a template.
Running an operation on a region of interest in an acquired spectrum as part of the data
analysis.

For all other features in the Plot View, please refer to "Plot View I: Features" on page 71. Data
operations in the Image View are covered in "Performing Operations in the Image View" on
page 142.
7.1 Defining Data Operations before Measurement

You can define a data operation as part of the experiment configuration. The operation is per-
formed after the experiment runs. In this case, you typically know what form of data analysis is
required (for example, FWHM calculation) and want this automatically performed. In particular,
if you save the experiment as a template, the definition for the data operation is also saved.

Note
This approach is also useful if you are using overwrite mode (see ). In this case, the spectrum is
scanned repeatedly—you can perform an operation after each scan to check current per-
formance.

To define a data operation:
1. Define a spectrum in the Experiment Editor.
2. Select the spectrum in the Experiment Editor or in the legend of the Plot View.
3. Click and select an operation from the menu, e.g. an FWHM operation as shown in the
picture below. The operation will be performed on the selected area and displayed in the
data browser below the selected spectrum.


86

4. Set the color, linestyle and width of the operation. This is the same procedure as for spec-
trum data—see "Setting Color and Appearance of Data" on page 73.
5. Click the arrow next to the operation to display the settings.
6. If you want to restrict the range over which the calculation is performed, check the Restrict
Range box and enter the start and end energies for the calculation.

7. Edit the input parameters in the table as necessary and click Apply. See the page for the
data operation for a description of the input parameters.


The data operation is now defined for the spectrum. You can now:
87
Run the experiment to take the spectrum. The data operation will be performed at the end
of each scan.
Save the experiment (or spectrum group) as a template. The configuration for the data
operation will be saved with the template and will be used every time you use the template.
7.2 Performing Operations on Regions of Interest

After acquiring a spectrum, you can run data operations on the whole spectrum or a specific
region of interest. The operations provide you with some useful tools for analysis.

Note
If you do not select a region of interest in the following procedure, the data operation will be
performed on the whole spectrum or the zoomed area in the view.

To perform a data operation on a region of interest:
1. Select a spectrum in the Experiment Editor or in the legend of the Plot View. This is the tar-
get spectrum for the operation.
2. Click the icon in the Plot View toolbar.
3. Select a region in the plot. The operation will be performed on the data in this region.

4. Click and select an operation from the menu, e.g. an FWHM operation as shown in the
picture below. The operation will be performed on the selected area and displayed in the
data browser below the selected spectrum.

88

5. Click the arrow next to the operation to display the input and output parameters. You can
alter range of the calculation as well as its input parameters. The list of input and output
parameters depends on the operation selected (see the Online Help for more inform-
ation).


89
7.3 Normalizing Spectrums

You can measure signals from other equipment while taking data. A typical example would be
the sample current in order to find the relative source intensity. After measuring this data, you
can normalize the acquired data to this signal.

To normalize spectra, perform one of the following:
Click the icon next to the experiment you want to normalize and select an item from the
Normalize by list. The normalization will be applied to all spectra in the experiment.
Click the icon next to the spectrum group you want to normalize and select an item from
the Normalize by list. The normalization will be applied to all spectra in the group.
7.4 Annotation Syntax

Some of the data operations display text on the chart. This is usually a summary of the cal-
culation and some explanatory text. The information displayed is determined by a command
string in the settings dialog for the operation. You can modify this string to change the inform-
ation.


The syntax used to write annotations is similar to the printf command of the C language.
90

Note
Each operation which has an annotation has a pre-defined setting. You can use this as an
example and as a basis for further modification.
S yntax
The annotation syntax is summarized as follows:

< x [ . m ] [ *f ] : { { @ [ n ] } | { [n] . g } }>

Note
Square brackets indicate optional terms; the pipe symbol | indicates OR.

Item Description
x Parameter name. This is the name shown in the table of output parameters.
m [ value | error].
*f Scale factor (useful if kcps instead of cps etc).
@ The @ sign indicates that the default number format is to be used when displaying res-
ults.
n Field width (number of digits, width = digits + sign + separator sign).
g Fixed-point arithmetic.
P arameters
All output parameters in the data operation can be used in the annotation.
Default numb er fo rmat

When using the default number format (with the @ symbol), the value is scaled to lie between 1
and 1000 (exclusive) and the prefix used to form decimal multiples and submultiples of the unit
is set accordingly. Additionally the standard deviation appears in parenthesis in a standard
abbreviated form. This is the rounded two digit integer value of the standard deviation after nor-
malization by the magnitude of the parameter value’s last digit.

Some examples of how numbers are displayed in the standard format:
(3435.3518 ± 85.613096) cps is abbreviated to 3.435(86) kcps
(881.62159 ± 0.00087205) eV is abbreviated to 881.62159(87) eV
(11403390.1 ±5130.74971) cps is abbreviated to 11.4034(51) Mcps
(2.668437 ± 0.00006868) eV is abbreviated to 2.668437(69) eV
Examp le
The following example shows how a typical definition and how it relates to displayed text.


Annotation [newline] [newline]
91
definition S-B = <Signal-BG:@>\nFWHM = <FWHM:@>\nArea = <Area:@>
Displayed S-B = 156 kcounts

text FWHM = 4.891 eV
Area = 11.66 Mcps eV

Note
The default settings in the software for data operation provide further examples.
7.5 Peak Operations

The peak operations allow you to perform various operations on peaks in spectra for eval-
uation purposes. The following operations are available:
Peak area—calculate the area under a peak.
Peak fit —uses a user-selected algorithm to find the height and width of a peak.
Peak FWHM —finds the width of a peak.
Peak identification—matches peaks in a spectrum to values in a database.
Peak Location—analyzes the points at or near a peak and finds the position of the peak.
7.5.1 Peak Area

The peak area operation constructs a series of trapeziums between adjacent data points to the
background line, calculates their area and sums the total area.

Restrict range
The operation runs with the selected region of interest. This region is shown in the Restrict
Range section. If no region is selected, the operation runs on the whole spectrum.

You can change the region of interest using one of the following methods:
Check the Restrict Range option box and enter start and end values in the fields provided.
The operation will run again automatically in the specified range.

Select the operation in the data browser, then drag the bars at the edge of the operation
region. The screenshot below shows a range selected for a background subtraction oper-
ation.


Note
92
The shaded area has the same color as the operation. You can change this by clicking the line
of the operation and selecting a new color.

Unchecking this box will set the range to the whole spectrum.

Input parameters
The input parameters allow you to alter the operation. The table below lists all the input para-
meters for the Peak Identification operation. After setting the parameters, click Apply to run
the operation with the new settings.

Input parameter Value
Element name Optional. Enter an element symbol. This will be sent to the
output parameters when you click Apply. This setting is
used for further quantitative evaluation of the spectrum
area (if available) and can be added to the data in the peri-
odic table (if available).
Element transition Optional. Enter the name of the transition. See Element
name above for more details.
Compound Optional. Enter the name of the compound in the sample.
See Element name above for more details.
Label Optional. Enter a reference label for the measurement. See
Element name above for more details.
Background method Choose a background subtraction method. The default is

Input parameter Value 93
linear.
Left background points These values determine how many points in the back-
ground are used in the background calculation. Setting the
value to zero means that the number will be selected auto-
matically.
Right background points As Left background points above.
Annotation Defines the text shown in the plot—see "Annotation Syn-
tax" on page 89.

There are two buttons below the input parameter table:
Apply—runs the operation with the selected input parameters.
Reset Params—sets the input parameters to their default values.

The Output Parameters section contains the results of the operation.

7.5.2 Peak Fit

The Peak Fit operation fits a user-selected function to the selected peak.

You can select which background operation is used (see "Background" on page 105 for a
description of all available options) and set the fitting algorithm to operate on asymmetrical
peaks, as necessary.

Restrict range

94


ation.

Note


Input parameters
The input parameters allow you to alter the operation. The table below lists all the input

parameters for the Peak Identification operation. After setting the parameters, click Apply to
95
run the operation with the new settings.

Background method See Background for a description of all available back-
ground subtraction methods.
Peak shape Select the function used to calculate the peak shape. The
sections below describe the options.
Asymmetric peak Check this if the peak shape is asymmetric.
FWHM annotation Defines the text shown in the plot—see "Annotation Syn-
tax" on page 89.
Peak annotation Defines the text shown in the plot—see "Annotation Syn-
tax" on page 89.



The following sections describe the different available fitting methods

DSG—Doniac-Sunjic-Gauss

Theoretical considerations of the energy loss of photoelectrons in metals lead to the asym-
96
metrical Doniac-Sunjic function:

DS ( x ; α , F , E ) =
cos ( πα
2
+ (1 − α ) rct n ( x f− e )) (1)
1− α
2 2
(f + (x − e ) ) 2

where:
α is the asymmetry parameter—with α = 0, this is equivalent to a Lorenzian
e is related to the position of maximum intensity
f is related to the half-width

In the DSG fit, the Doniac-Sunjic is convoluted with a Gaussian:

DSG (x ; α , f DS , eDS , fG , eG ) = DS (x ; α , f DS , eDS ) * G (x ; α , fG , eG ) (2)

where:
e is related to the position of maximum intensity in the D-S function
DS
e is the peak position of the Gaussian
G
f is related to the half-width in the D-S function
DS
f is the half-width of the Gaussian.
G

GLP—Gauss-Lorenz Product
The Gauss-Lorenz product results from multiplying Gaussian and Lorenzian functions together:

 (x − E ) 
2
(3)
exp−4ln 2(1 − m ) ⋅ 
 2
F 
 
GLP (x ; F , E , m ) = 2
(x − E )
1 − 4m
F2

where:
E is the center of the curve
F is the half-width
m is a mix parameter

GLS—Gauss-Lorenz Sum
The Gauss-Lorenz product results from adding Gaussian and Lorenzian functions together:


 (x − E )2  m (4)
97
GLS (x ; F , E , m ) = (1 − m )exp−4ln 2 2 + 2
 F  1 + 4 (x − E )
F2

where:
F is the half-width
m is a mix parameter

Voigt
In order to obtain a realistic line shape for peaks in a spectrum, a Voigt function is used. This is
a convolution of a Gaussian and Lorenzian function:

V (x ; E , FG , F i ) = G (x ; FG , E ) * L(x ; FL , E ) (5)

where:
F is the half-width of the Gausssian
G
F is the half-width of the Lorenzian
L

The numerical solution of the convolution integral is very time consuming. For this reason,
SpecsLab Prodigy uses an approximation based on the principle of Fourier transformations
such that the Fourier transform is equal to the product of the individual Fourier transforms:

Ϝ(g * f ) = Ϝ(g ) ⋅ Ϝ(f ) (6)
7.5.3 Peak FWHM

The Full Width at Half Maximum operation uses a smoothing spline calculation. It automatically
performs a background subtraction before determining the peak width.

You can select which background operation is used (see "Background" on page 105 for a
description of all available options) and set the fitting algorithm to operate on asymmetrical
peaks, as necessary. The FWHM annotation defines the text shown in the plot—see "Annota-
tion Syntax" on page 89 for details.

Restrict range


98

ation.

Note


Input parameters


Element name Optional. Enter an element symbol. This will be sent to the
output parameters when you click Apply. This setting is
used for further quantitative evaluation of the spectrum
area (if available) and can be added to the data in the peri-
odic table (if available).
Element transition Optional. Enter the name of the transition. See Element
name above for more details.
Compound Optional. Enter the name of the compound in the sample.
See Element name above for more details.
Label Optional. Enter a reference label for the measurement. See
Element name above for more details.
Background Method Select a method. See Background for a description of all
the options.
Asymmetric Peak Check this if the peak shape is asymmetric.
FWHM-Annotation Defines the text shown in the plot—see "Annotation Syn-
tax" on page 89.
Automatic Range The operation can select the area to the left and right of the
peak in order to optimize the background subtraction.




100
7.6 Peak Identification

The peak identification operation matches peaks in your data to values in a database. It is a con-
venient way to identify unknown elements in a spectrum.

To run the peak identification operation:
1. Select a spectrum in the Data Browser.
2. If necessary, select a region of interest for the operation.
3. Click the icon and select Peak Operations/ Peak Identification from the menu. The
operation will run and its parameters and results will be displayed below the selected spec-
trum. The results will also be shown in the Plot View.

The section below describe the parameters and results.

Restrict range



101

ation.

Note


Input parameters

Restrict to specific elements Enter an element symbol, e.g. Ag (case sensitive).
Energy tolerance to associate Set the shift allowed from the literature value for the assign-

102 Input parameter Value
peaks [eV] ment.
FWHM theshold

Apply—runs the operation with the selected input parameters
Reset Params—sets the input parameters to their default values


7.6.1 Peak Location

The Peak Location operation fits a quadratic function to the topmost region of the peak for cal-
ibration purposes (peak location), following the procedure of Anthony and Seah1 .

Restrict range

1 M.T. Anthony and M.P. Seah, "XPS: Energy calibration of electron spectrometers. 1—An absolute, traceable energy calibration and
the provision of atomic reference line energies", Surf. Interface Anal . 6, 95 (1984); M.P. Seah, "Measurement: AES and XPS", J. Vac.
Sci. Technol. A 3, 1330 (1985)

103

ation.

Note


Input parameters

104
Left data points These values determine how many points on each side of
the maximum are used in the calculation. Setting the value
to zero means that the number will be selected auto-
matically—top 5% of the peak and at least enough points
for fit.
Right data points As Left data points above.
Asymmetric Peak Check this if the peak shape is asymmetric.
Background slope Check this if the background has a slope. You should not
use a sloping background when fitting peaks for energy
scale calibration. As discussed by Powell1 , this can intro-
duce systematic errors.
Peak-Annotation Defines the text shown in the plot—see "Annotation Syn-
tax" on page 89.


Equation (7) shows how the peak location is calculated.

 2 (7)
Ix = Ic ⋅ exp−4ln 2 ⋅    + S ⋅ (x − c ) + B
x−c
 g
 FWHM(1 ± α )  
 

where:
I is the intensity at x
x
I is the intensity at the center
c
c is the peak maxima value of x
α is an asymmetric factor
S is the sloping background value
B is the constant background intensity
g


1 C.J. Powell, "Energy Calibration of X-ray Photoelectron Spectrometers. II. Issues in Peak Location and Comparison of Methods",
Surf. Interface Anal. 25, 777-787 (1997)

105
7.7 Fitting Operations

The fitting operations menu contains the following items:
Fermi Edge—find the position and width of the Fermi edge.
Background—various methods of background subtraction. These are also used in other
operations for peak fitting.
7.7.1 Background
The background operation allows you to subtract the background of a selected region accord-
ing to a preset algorithm.

Restrict range



106
ation.

Note


Input parameters

Optimize Range The range of the operation is optimized so that the lowest
reasonable background is achieved.
Method Select a background subtraction method. The various meth-
ods available are described below.


107

The following background subtraction methods are available:

None
No algorithm is used. The results from this setting are a straight line at Intensity = 0.

Linear
This is a simple subtraction in which draws a straight line between two suitable points.

The endpoints are calculated by selecting several points from the extremes within the visible
regions along the energy axis and performing a linear least square fit to those points. This kind
of background does not represent a physical background.

Shirley
The Shirley background1 determines the background intensity at a point by means of an iter-
ative analysis.

The background at a given kinetic energy E(i) is proportional to the intensity area above the
background between the given energy and the maximum energy boundary N.

Equation (8) shows the calculation method for the Shirley background.

N
(8)
bi = k ∑ pj
j =i +1

This is run iteratively. In the first iteration the background is set to zero. In the i-th channel, the
signal s is the sum of the background b and the peak intensity p . The calculation is repeated
i i i
until the change in results is below the desired error. k is determined to fit the background at
the high kinetic energy side.

The method assumes that the energy loss function for electron scattering is constant. As in the
case of the linear background, the extremes correspond to the visible region or to the value
determined through range optimization. The boundary conditions for the calculations are
determined in the same manner as the extreme points for the linear background calculation.

Tougaard
A physical model of the background is based upon the elastic and inelastic loss processes in
1 D.A.Shirley, "High-Resolution X-Ray Photoemission Spectrum of the Valence Bands of Gold", Phys. Rev. B, 5, 5, 4709 (1972)

the solid. Tougaard and Sigmund showed1 that if j(E) is the measured flux of emitted electrons
108
at energy E from a homogenous solid, the primary excitation spectrum F(E) is given by:

∞
E′ − E (9)
F ( E ) = j (E ) − B ∫ ⋅ j (E ′) d E ′
22
E (C + (E ′ − E ) )

7.7.2 Fermi Edge

The Fermi edge operation calculates a fit to the Fermi edge. As well as finding the position, you
can use it for energy scale calibration or for finding the FWHM of the Fermi edge. The Fermi
edge is modeled using an error function:

h   2 ln 2  (10)
y= ⋅ 1 + erf( x 0 − x ) ⋅
2 FWHM 
  

1 S.Tougaard and I.Sigmund, "Influence of elastic and inelastic scattering on energy spectra of electrons emitted from solids", Phys.
Rev. B, 25, 4452 (1982)

where h is the height of the error function. The rest of the data is fitted with straight lines which
109
can have different gradients, as seen in the figure above. The formula can also be convoluted
by another function which adds the peak broadening due to temperature. This convolution is
not performed with a set temperature of 0 K.

Note
Noisy data or "unexpected" slopes can cause the algorithm to fail.

You can restrict the range over which the operation is applied.

Restrict range


ation.

Note


110


The screenshot below shows a fit with the calculated results.

Note
Noisy data or "unexpected" slopes can cause the algorithm to fail.

The Fermi edge is modeled using an error function:

111
h   2 ln 2  (11)
y= ⋅ 1 + erf( x 0 − x ) ⋅
2 FWHM 
 

where h is the height of the error function. The rest of the data is fitted with straight lines which
can have different gradients, as seen in the figure above. The formula can also be convoluted
by another function which adds the peak broadening due to temperature. This convolution is
not performed with a set temperature of 0 K.
7.8 Smoothing Operations

The smoothing operations provide a set of methods for processing the appearance of raw
data:
Despiking—removes anomalous spikes from the signal.
Noise settings—estimates the noise in a signal from a CCD detector.
Savitsky-Golay smoothing—a method of smoothing that also allows the calculation of
derivatives in the data.
Smoothing spline—fits a spline to the selected data.
7.8.1 Despiking
The despike filter removes spikes from spectra which may occur due to some external event
(e.g. sparks) and replaces them with the mean values of the neighbor values by additionally
adding some typical noise distribution.

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ation.


Note
112


Input parameter
The input parameter allows you to alter the operation. The table below lists the input para-
meter for the Despike operation. After setting the parameter, click Apply to run the operation
with the new settings.

Threshold A multiple of the expected rms noise threshold.

Apply—runs the operation with the selected input parameter.
Reset Params—sets the input parameter to its default value.


113
7.8.2 Noise Settings

The Noise operation estimates the intensity scaling for CCD detector measurements. This cal-
culates a factor for the noise based on the standard deviation from the average signal.
SPECS detectors typically produce a noise factor in the range 0.95–1.05. Consistent noise levels
outside this range may indicate a fault with the detector.

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ation.

Note


114


Input parameters

Smoothing Parameter Enter the error variance. The calculation uses this to min-
imize an unbiased estimate of the true mean square error
and thereby determines the degree of smoothing.
If the error variance is not known, set this to –1. The routine
minimizes the generalized cross validation to determine the
degree of smoothing. This approaches the limit of min-
imizing the true mean square error.
Noise-Annotation Defines the text shown in the plot—see "Annotation Syn-
tax" on page 89.



115
7.8.3 Savitzky Golay Smooth

The idea behind data smoothing is the signal is slowly varying and also corrupted by noise.
Sometimes it can be useful to replace each data point by a local average of surrounding data
points. Since nearby points measure very nearly the same underlying signal, averaging can
reduce the level of noise without significant change the signal (and the containing information)
obtained.

SpecsLab Prodigy offers a particular type of low-pass filter, well-adapted for data smoothing,
called Savitzky-Golay1 .

Restrict range

1 A. Savitzky and M.J.E. Golay. "Smoothing and differentiation of data by simplified least square procedures", Anal. Chem., 36(8),
1627−1639, 1964

116

ation.

Note


Input parameters


See also the background section below for more information about the input parameters.
117

Left Data Points Number of points to the left of the current data point.
Right Data Points Number of points to the right of the current data point. This
is usually set to the same value as the Left Data Points
value.
Polynom Order When using derivatives, you should set this value to 4 or
higher.
Derivation Order Allows you to calculate numerical derivatives. Setting this
value to 1 gives a first order derivative.


Background theory
Savitzky-Golay filters were initially (and are still often) used to render visible the relative widths
and heights of spectral lines in noisy spectrometric data. A digital filter is applied to a series of
equally spaced data values f = f ( t ) , where t = t + i Δ for some constant sample spacing Δ
i i i 0
and i = … −2, −1, 0, 1, 2, …. The simplest type of digital filter replaces each data value f by a lin-
i
ear combination g of itself and some number of nearby neighbors,
i

nR
(12)
gi = ∑ cn ⋅ f i + n
n = − nl

Here nL is the number of points used to the left of a data point i , i.e. before it, while nR is the
number used to the right, i.e. after. As a starting point for understanding Savitzky-Golay filters,
consider the simplest possible averaging procedure: For some fixed nL = nR, compute each g i
as the average of the data points from f − nL to f + nR . This is sometimes called moving win-
i i
dow averaging and corresponds to the equation above with constant:

1 (13)
c=
nL + nR + 1

If the underlying function is constant, or is changing linearly with time (increasing or decreas-
ing), then no bias is introduced into the result.

The points at the right of the data point in the averaging interval are usually balanced by those
at the left. A bias is introduced, however, if the underlying function has a non-zero second deriv-
ative. At a local maximum, for example, moving window averaging always reduces the function

value. In the spectrometric application, a narrow peak has its height reduced and its width
118
increased. Since these parameter are themselves of physical interest, the bias introduced is dis-
tinctly undesirable.

The idea of Savitzky-Golay filtering is to find filter coefficients cn that preserve higher
moments. SpecsLab Prodigy fits a polynomial of degree M in i, to the values f − nL … f + nR. For
i i
a more detailed description please refer to the paper by Savitzky and Golay.

7.8.4 Smoothing Spline

The smoothing spline operation calculates an interpolating natural cubic spline curve which
smooths a given set of data points, using statistical considerations to determine the amount of
smoothing required. The smoothing factor can be set (0–1) to determines the degree of
smoothing.

Restrict range



119
ation.

Note


Input parameters

Smoothing Factor Enter the error variance. The calculation uses this to min-
imize an unbiased estimate of the true mean square error
and thereby determines the degree of smoothing.
If the error variance is not known, set this to –1. The routine
minimizes the generalized cross validation to determine the
degree of smoothing. This approaches the limit of min-

120 Input parameter Value
imizing the true mean square error.
Smoothing-Annotation Defines the text shown in the plot—see "Annotation Syn-
tax" on page 89.


The Output Parameters section contains the results of the operation:
RMS—the root mean square of the signal.
Poisson factor—The RMS value divided by the square root of the signal. For an ideal Pois-
son distribution, this will be exactly 1. Significant deviations from 1 (e.g. 1.5) may indicate
errors in the way the detector counts the signal.

7.9 Miscellaneous Operations

The miscellaneous operations are a collection of other functions that do not fit in with other
operations. Operations available are:
Arithmetic mean—calculate the average value of points in a selected region.
Dead time correction—compensate for the dead time in detector acquisition.
Least squares gradient —calculates the gradient at each point in the spectrum using a
first order least squares fit.
Linear operations—add offsets and scaling factors to data.

Spin Asymmetry for VLEED—calculate the spin component of a signal from a spin-
121
resolved detector.
7.9.1 Arithmetic Mean

The arithmetic mean function sums the intensity of all data points and divides this figure by the
number of data points. The result is the mean intensity of the data collected. You can restrict
the range over which the mean is calculated.

Restrict range


ation.

Note


122


7.9.2 Dead Time Correction

This operation corrects the measured data by dead time considerations. After each point is
recorded, there is a dead time before the next point can be recorded. For an ideal counter with
a non-extended dead time t, the measured count rate N’ and the true count rate N is given by


N (14)
N′ = 123
1 + Nt

Please see your detector manual for more information about dead time factors. The
SPECS technical note "CEM Dynamic Range" also contains some details about the dead time.

You can restrict the range over which the operation is applied.

Restrict range


ation.

Note


124


7.9.3 Least Squares Gradient

The least squares gradient function calculates the gradient of the spectrum at each point,
based on a user-defined window size. The result is a derivative of the spectrum. This reduces

the noise level in the signal. Peak positions are then located at the zero point in the derivative
125
curve.

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ation.

Note


126

Input parameters

Half Window Size Half width of the sampling region in eV. See below for more
information.


The half window size determines the energy range used for the calculation:

ΔE = E i ± Half Window Size

Where Ei is the current data point used in the calculation. A first order least squares fit is cal-
culated using the data points in this energy region.

7.9.4 Linear Operations

Using linear operations, you can scale and shift your data on the X and Y axes.

Restrict range

127


ation.

Note


Input parameters

128

Energy Offset Moves the spectrum (or the selected region) by the offset in
eV, i.e. along the X axis.
Energy Scaling Scales the spectrum (or the selected region) by the given
factor in the horizontal direction.
Count(rate) Offset Moves the spectrum (or the selected region) by the offset in
counts or count rate, i.e. along the Y axis.
Count(rate) Scaling Scales the spectrum (or the selected region) by the given
factor in the vertical direction.


There are no output parameters for this operation—the results are shown in the Plot View. The
screenshot below shows a data set shifted in intensity and energy.


129
7.9.5 Spin Asymmetry for VLEED
The asymmetry operation evaluates the asymmetry of spin-resolved spectra and can only be
used with spin detectors. If you have two spectra which are recorded with opposing spin dir-
ections (for example with different magnetizations or opposing collection geometry), you can
derive the asymmetry function from the two signals according to the following relation:

S −S (15)
A1 = 1 2
S 1+ S 2

Schedule setup
As well as requiring a special detector, the schedule setup is different from the standard data
acquisition. This is necessary in order to allow for the magnetization cycles between meas-
urements.

The screenshot below shows a typical schedule for acquiring spin resolved data. Note the fol-
lowing points:
Devices: In addition to the analyzer and source, you need to include devices for the spin
detector controller and the magnetic pulse control.
Sleep: Provides a pause while the magnetic pulse control charges and magnetizes the spin
target.
Step Profile: Changes the target magnetization, with a spectrum measured at each setting.
Sleep: Once again, this allows the magnetization to take place before the measurement
starts.
Spectrum Group: The normal definition for the spectrum.

Note
You can also include a Loop before the step profile to perform a number of iterations of the
experiment.


130

Input parameters
meters for the Spin Asymmetry for VLEED operation. After setting the parameters, click Apply
to run the operation with the new settings.

Asymmetry Cycle The name of the step profile used for the magnetization of

the target. This is the same as the name shown in the Exper-
iment Editor.
Summation Cycle You can leave this setting as "Loop". If a loop is used for a
number of iterations of the experiment, this is taken into
account. In the case of no loop being used, this section is
ignored.
Asymmetry Cycles Size This should be the number of cycles in the magnetization
step profile that is included in the Experiment Editor.
Asymmetry Forward Direction This parameter, together with Asymmetry Backward Dir-
ection, determines which scan measures positive spin and
which negative. One parameter must be OFF, the other ON.
If you change these values, the result of the calculation will
be reflected around the horizontal axis.
Asymmetry Backward Direction See Asymmetry Forward Direction above.

Output parameter
There is only one output parameter:
Use Summation Cycle—This box is checked if a loop is used in the calculation.


132

133
Chapter 7 – Chemical Databases
SpecsLab Prodigy has several databases which contain information about excitation levels of
elements and compounds, AES excitations, electron mean free path values, etc. These are
used for features such as peak identification. The Chemical Databases view allows you to view
the information in the databases and also to add your own databases.

To open the Chemical Databases view:
Select Views/ Chemical Databases from the menu bar.
7.10 Viewing Pre-Installed Databases

Pre-installed databases are supplied by SPECS and can be viewed. The table below provides an
overview of the controls that are active for viewing databases.

Feature Description
Database Type A drop-down list showing all the databases available. This includes
user-defined databases.
Filter Filters the displayed entries according to the entered criterion. All fields
in the displayed databases are used for matching.
Reload all Databases Reloads all the databases.
Priorities This pane shows all databases that contain data for the selected data-
base type. You can order them by drag and drop or by using the and
arrows. The order determines the priority of the database. Lower
databases are only used if the value is not present in any higher data-
bases.
Toggles the availability of the database. Databases with a line through
them are not used.
Table The main area of the view, showing the entries in the database. You
can sort the entries in the database by clicking the header of a column.
Export Opens a dialog so that you can export the database as a csv file.
Allows you to create a new database.

The grayed out buttons below the table are used for editing user databases and cannot be
used for the pre-installed databases.


134
7.11 Creating and Editing User Databases

In order to protect the values in the pre-installed databases, they cannot be edited. However,
you may need to supplement the databases with additional values or with corrections. You can
create a database and edit its values. Note the following points:
A database is in CSV format. Although it is not possible to import a database into SpecsLab
Prodigy, you can create a new database and then edit its CSV file in a spreadsheet pro-
gram.
If you are correcting values in other databases, you should move your new database to the
top of the priority list.

To create a new database:
1. Click . A dialog will appear for you to enter the name of your new database. The new
database is added at the top of the Priority pane (that is, it has top priority—you can move
it down if you wish).
2. Select the database in the Priority pane. The main area will be empty except for the name
of the database and its location
3. Click Edit Database. The databases in the Priority pane will be grayed out.
4. Click . A new row is added to the table.
5. Enter values in the fields.
6. Click Save. Your values will be saved to the database.

There are other controls below the table that are useful:
removes the currently selected row.
Discard removes all changes to the database and reverts to the last saved version.
Export opens a dialog allowing you to save the contents of the database in csv format.

135
Chapter 8 – Image View
The Image View displays two dimensional data. Frequently, this will be the energy and non-
energy axes from a CCD camera or delayline detector. However, you can use the Y axis to dis-
play other information, such as etching time in a depth profile experiment.

The 2D viewer displays the contents of a single region. You can open a number of 2D viewers if
you want to view more than one region.

In addition to displaying data, the 2D viewer offers features for data analysis as well as con-
figuring the spectrometer with a CCD detector:
Selecting regions of interest in the data and zooming the image.
Setting cursors to mark positions in the image.
Viewing profiles of the data.
Changing the color coding and display threshold in the image.
Data operations.

136
8.1 Opening Data in the Image View
To open the Image View:
Select Views/ Image View from the menu bar. The Image View will open, showing the cur-
rently selected spectrum. All other spectra will be shown in the legend—you can select a
spectrum to view it individually.

The Image View can display data in two dimensions. If the spectrum contains more than two
dimensions, the view requires user input to determine how the data is to be displayed. You can
change the axis settings or change the data settings in the legend. Using a combination of the
following two methods will allow you to display the data in exactly the way you want.

Note
By comparison with the Plot View, multi-dimensional data is condensed into simple intensity vs
energy. In that case, if you want to display additional dimensions on the Z axis, you first have to
select which dimension is to be displayed.
Data b ro wser settings

The data browser is described in detail in "Additional Data Display Settings" on page 75—all
information there also applies to the legend in the Image View. For the present purpose, it is
worth focusing on the spectrum components, as shown in the figure below.

This example shows a depth profile experiment, where etch time can be used as an axis. To
reduce the number of dimensions so that the spectrum can be displayed:
Select an individual etch time from the drop-down list. The spectrum will then display intens-
ity on the Y axis against energy on the X axis.

You can change the Y axis by selecting different spectrum components:
Selecting Separated for Channels will put the channel number on the Y axis.
Selecting All (or an individual scan number) for Scan will put the scan number on the Y
axis.

The images below show a comparison of different displays of the same data.


137
Y axis lab el
The axis labels contain all available dimensions. You can therefore change the axis label to tell
SpecsLab Prodigy how it should display data. For the above example, using a depth profile scan:
Hover the mouse pointer over the Y axis label and select Etch Time from the drop-down
list. The data will be displayed with the etch time on the Y axis.


138
X axis lab el
The X axis always contains the options for showing kinetic energy and binding energy. Some
types of experiment may also give you the option for changing the X axis setting. For example,
in slab imaging scans, the X axis will give you the option of Focus Displacement so that you can
show one of the profiling parameters on the X axis.
8.2 Image Pane

The main part of the Image view is the image pane. This shows the data from the selected
region.

When you move the mouse within the image pane, the coordinates and intensity of the indic-
ated pixel is shown next to the pointer.
8.3 Horizontal and Vertical Profiles

The horizontal and vertical profile panes show one dimensional views of the data from the
2D image. The data in the profiles shows the summed up intensity in the image or region of
interest . The profiles also show the results of profile operations (i.e. Gaussian or Fermi edge
fits).

There are handles on the edge of the pane bordering on the image. These allows you to resize
the pane.

By default, the data in the profiles is shown. You can hide the data:
Click the icon in the toolbar.

To hide the vertical profile pane:
Click the icon in the toolbar. The vertical profile pane and the histogram will be hidden.
Click the icon
again to show them.

139
To hide the horizontal profile pane:
Click the icon in the toolbar. The vertical profile pane and the histogram will be hidden.
Click the icon
again to show them.
8.4 Histogram
The histogram is shown in the bottom right corner of the 2D viewer. It shows a distribution of
the colors in the image. The shape of the histogram is produced by counting the number of
pixels within a fixed intensity range of a given image.

You can restrict the displayed color range by changing the selected area in the histogram. This
is especially useful if you want to suppress noise, which is situated in the left hand part of the
histogram. To change the displayed color range:
1. Click the histogram and drag the mouse. Release the mouse when you have selected the
desired area. Only pixels with the selected colors are displayed—all others are shown as
maximum or minimum intensity.
2. Fine tune the region by entering numbers or clicking the arrows in the fields below the his-
togram. The numbers represent the minimum and maximum limits to the selected range.

Right-clicking the histogram produces a context menu. The table below describes the actions
available in the context menu.

Item Description
Copy Profile Data Copies the data in the histogram to the clipboard. The data depends on
the Intensities setting in the Histogram Ranges dialog—using this
setting, you can restrict the amount of data copied to the clipboard.
Histogram Ranges Opens the Histogram Ranges dialog. In this dialog, you can:
Set which intensities are displayed in the histogram. With user
defined values, the histogram is redrawn so that only the intensities

140 Item Description
selected are displayed. This does not affect the appearance of the data
in the main view.
Set the sampling rate for the intensities. A lower number of
samples increases the peak height in the histogram, while also increas-
ing the granularity.
Color Trans- The sub context menu contains the following items:
formation Range Autoscale—Cancels any range selected in the histogram so that all
colors are displayed in the viewer.
User Defined—Adds the limit fields below the histogram so you
can define a range. This option is automatically selected when you
define a range in the histogram.
Change Colormap The sub context menu contains a number of different color schemes
that you can select to view the data.
Use Zoomed Area When checked, the histogram is calculated based on the contents of
the zoomed area of the image pane. If it is not selected, all data in the
region. is used in calculating the histogram.
Enable Histogram When checked, the histogram is updated following changes to the
image pane (e.g. due to zooming or data acquisition). If it is not selec-
ted, the histogram is not updated. This can speed up operation if you
have performance problems.
8.5 Cursor and Zoom Controls

You can change the zoom and cursor settings, as well as toggling the grid. The picture below
has an overview of the controls available. Each of these are described in their own section.


141
8.5.1 Setting Cursor Positions
You can set the position of two cursors in the 2D viewer. These allow you to mark the position
of peaks and other features; you can, for example, use them to measure the distance or energy
difference between features.

When setting cursors, note the following points:
If you select another mouse tool (e.g. the Zoom mode), the cursor is sticky and remains in
its position until you reactivate the cursor.
The and icons toggle the display of the cursors in the image pane.

To display a cursor in the image pane:
1. Click the icon or the icon. These activate the yellow and blue cursors respectively.
2. Click a point in the chart. The cursor will be displayed with the center at the selected point.
The status bar at the bottom of the 2D viewer will show the coordinates of the cursor cen-
ter point.
8.5.2 Selecting a Region of Interest (ROI)

You can select a region of interest (ROI) of the image. Data operations and analysis will be per-
formed on this ROI, rather than the whole image. The selection is a cross, containing a hori-
zontal and vertical section of the image.

To select an ROI in the image pane for analysis:
1. Click the icon in the toolbar.
2. Click a point in the image pane. A red cross will be displayed with its center at the selected
point. The cross is semi-transparent with bold lines at its edge.
3. Click and drag the horizontal and vertical red lines at the edge of the cross until you
achieve the desired area. Alternatively, edit the numbers to change the start and end pos-
itions of the X and Y coordinates for the selection (in pixels). You can enter numbers or click
the up/ down arrows to change these settings.

To hide the selection:
Click the button in the toolbar. This toggles the display of the ROI.
8.5.3 Zooming in the 2D Viewer

You can zoom into an area of the chart in order to inspect items of particular interest:
1. Click the icon to activate zoom mode.
2. Click and drag the mouse to form a rectangle in the image pane. When you release the
mouse button, the image shows the selected area.

3. To display the complete image again, double click in the image pane. This fits the image to
142
the image pane.

You can also click the icon to show each data point as a single pixel in the image pane.
8.5.4 Toggling between Pixels and Physical Units

Clicking the in the toolbar of the Image View toggles the units of the display:
Camera pixels.
Physical units, e.g. mm or degrees, depending on the mode of acquisition.
8.5.5 Displaying the Grid in the 2D Viewer

You can switch on a grid to help you view features in the image pane:
Click the grid icon in the toolbar. This button toggles the display of the grid.
8.6 Performing Operations in the Image View

There are a number of operations you can perform on an image or a region of interest (ROI)
which are useful for instrument calibration or data evaluation. The interface for the operations
consists of three drop-down lists:
Image—operations on the image.
Profiles—operations on the selected profiles in the horizontal and vertical profile panes.
Op. Result—display a dialog with large text so you can read operation results at a dis-
tance.

The following tables describe the available features in these three lists.

Image operations

Operation Description
No Operation None of the calculations in the drop-down list are performed.
Center/ Integral Calculates the center point of the image (X, Y coordinates) and the total
number of counts. If you have selected a range with the profile marker, the
point calculated is the center of the profile.
X Line Fit Fits a line to the data in the X direction. It reports the angle of the line from
the horizontal. You need to select an ROI.

This feature is useful when setting up the analyzer in conjunction with a test
grid, e.g. when determining the angular resolution of the detector.

Operation Description 143
Y Line Fit Fits a line to the data in the Y direction. It reports the angle of the line from
the vertical. You need to select an ROI.

This feature is useful when setting up the analyzer in conjunction with exit
slit setting A, e.g. aligning the camera.

Profile operations

Operation Description
No Operation None of the calculations in the drop-down list are performed.
Gauss Fits a Gaussian profile to the selected region in the horizontal and vertical
profile panes. The calculation reports the center postion of the fitted peak
and its FWHM. If the data are not suitable for a fit, a message appears to
say the calculation is impossible. This may be the case in one profile pane;
it does not affect the calculation in the other pane.

You need to select an ROI in order to run this operation. You should also
select Show Physical Units from the image context menu for meaningful
results
Fermi Edge Locates the Fermi edge in the selected region in the horizontal and vertical
profile panes. The calculation shows a line fitting the Fermi edge and
reports the position and FWHM. If the data are not suitable for a fit, a mes-
sage appears to say the calculation is impossible. This may be the case in
one pane; it does not affect the calculation in the other pane.

You need to select an ROI in order to run this operation. You should also
select Show Physical Units from the image context menu for meaningful
results

Displaying operation results
You can display the results in large text, so they can be seen at a distance. Results from all oper-
ations are shown:
Grab the horizontal split bar at the top of the image and drag it down.

Note
If the view is not wide enough to see all results, a scroll bar is included.


144

145
Chapter 9 – Live View
The Live View allows you to view the signal received by the detector in real time. This is primar-
ily of interest for 2D detectors which record an image. The Live View is generally used for the
following purposes:
Viewing a 2D image while setting up the analyzer, e.g. for angular dependence calibration.
Checking the mapping area of the detector.
Viewing the image during data acquisition.

The Live View also allows you to check for hot pixels in the camera.

This chapter is divided into the following topics:
Viewing an image in the Live View.
Available features in the Live View.
Active area and channels.
9.1 Opening the Live View

The Live View displays regular updates of the data whenever the detector is in operation. This
means that you can watch live images during regular data acquisition by simply opening the
Live View from the Views menu.

A common use for the Live View is to see the image as you change analyzer parameters. In this
case, you can use the Live View in conjunction with the analyzer Device Control, as described
below.

Note
The refresh rate of the image in the Live View is 1 s.

To obtain an image in the Live View:
1. Locate the analyzer control in the Device Control View.
2. Click Control to connect to the analyzer. If you have already been using the analyzer for
experiments, it will already be connected.
3. Edit the analyzer settings as required. For setting up the analyzer, it is normal to set the kin-
etic energy and pass energy to the same value.


146

4. Click Activate to send the operating values to the analyzer.
5. Select Views/ Live View from the menu bar to open the Live View
6. Click in the toolbar to start viewing the image.

9.2 Features and Options in the Live View

Visually, the Live View is very similar to the Image View and it shares a lot of functionality. The
table below lists the features and explains their operation.

You can hide or display the various panes in the view by grabbing the horizontal and vertical
split bars and dragging them.


147

Feature Description
Zoom controls. See "Zooming in the 2D Viewer" on page 141
Cursor controls. See "Setting Cursor Positions" on page 141
Grid. See "Displaying the Grid in the 2D Viewer" on page 142
Region of interest controls. See "Selecting a Region of Interest
(ROI)" on page 141.
Toggle display of traces in horizontal and vertical profiles.
Operation menu Drop-down list for image operations. See "Performing Operations
(default: No Image Op.) in the Image View" on page 142.
/ Start/ stop live image view.
Raw Data Allows you to select between raw data and channel data views.
Described fully in "Active Area and Channels" on page 148.

148 Feature Description
Toggles the display of the active area.
Opens the Calculate Hot Pixel dialog. See "Removing Hot Pixels"
on page 150.
Results pane Shows the results of the operation in large text for easy reading at a
distance. See also Performing Operations in the 2D Viewer.
Image pane Displays the live image. Right-clicking this area opens a context
menu—see "Image Pane" on page 138 for a description.
Horizontal/ vertical pro- Shows a cross section of the data signal when a region of interest is
files selected. See "Horizontal and Vertical Profiles" on page 138.
Histogram Shows the color distribution in the image. See "Histogram" on
page 139.
9.3 Active Area and Channels

The active area is the area of the image recorded during data acquisition. In order to maximize
the signal from the detector, you should set the active area as large as possible. However, the
image is circular, so you need to set the largest area within the circle, so that all channels have
equal weight.

Data is recorded in channels rather than as raw pixels. The number of pixels is divided exactly
by the number of channels defined, and the signal summed over these pixels. Although this
reduces the resolution of the image, the noise is also reduced.

Viewing the active area
To view the active area:
Click the icon in the Live View. The active area is shown in the image.

The active area is set in the Device Control:
Click the arrow in the analyzer device control to show more settings, then select the
Detector tab. The picture below shows how the settings relate to the image.


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Viewing channels
To view the channels:
Click the Raw Data button and select Channel Data. The image then shows the image
within the active area. The pixels in the raw data view are summed together into channels,
as shown in the picture below.

Incorrect channel settings and pixel coordinates
The number of channels must divide exactly into the number of pixels. If not, pixels at the edge
of the image will not be measured because there are not enough to form a complete channel.

If you set a channel number that does not divide exactly into the pixel number, a warning mes-
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sage will appear. By showing the active area, you can see the discrepancy caused by an incor-
rect channel number:
The red area is the active area. All data within this area is recorded.
The dotted yellow area is the area defined by the channel number. These channels are not
recorded during data acquisition.

By zooming into the area, you can see the pixel coordinates (with current intensity).

Changing detector settings
You cannot change detector settings while it is in operation. To change settings:
1. Click Stop to switch off the detector.
2. Make the desired changes.
3. Click Apply and Save.

You need to disconnect and reconnect the analyzer Device Control to see the effect of the
changes.

Note
See also the PHOIBOS Device Control for more information about detector settings.
9.4 Removing Hot Pixels

Hot pixels are individual pixels on the CCD with higher intensity than their surrounding area.
They can appear as small pixel sized bright points of light on longer exposures. You can con-
figure SpecsLab Prodigy to ignore hot pixels—the pixels are not displayed or recorded.


Note
151
This procedure involves manually editing the MS Windows registry. This ensures that you know
precisely what changes are being made. With an automated process, a simple error would "sim-
ulate" a broken camera; the source of the problem might be hard to identify.

To remove hot pixels:
1. Click the icon in the toolbar of the Live View.. The Calculate Hot Pixel dialog will open.
2. Enter a threshold value. When the mouse pointer hovers over a pixel, it shows "(x,y coordin-
ates) intensity". You can therefore find the intensity of the pixel.
3. Click Calculate. All pixels with an intensity above the threshold value are identified as hot
pixels. The Hot Pixel field shows the number of hot pixels identified.
4. Click Show Details. A list of hot pixels is shown, showing the coordinates and intensity of
each hot pixel.

5. Check the list carefully to confirm that all identified pixels really are hot pixels.
6. Click Apply. The list of hot pixels is copied to the clipboard.
7. Start the MS Windows registry editor, e.g. by selecting Start/ Run and entering regedit in
the Run dialog.
8. Locate the registry entry HKEY_LOCAL_MACHINE\SOFTWARE\Wow6432Node\SPECS\Spec-
sLab Prodigy\Devices\PhoibosND\Configuration\Detector\ImageProcessing.

9. Double-click the HotPixelList key.
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10. Paste the contents of the clipboard into the Value field. You will see a list of coordinates
with the format:

PointVec: (x1,y1),(x2,y2),...

11. Click OK and close the registry editor. The hot pixels will now be ignored by SpecsLab
Prodigy when acquiring data.
12. Restart the PHOIBOS Device Control (disconnect the analyzer in the Device Control, then
click Control to reestablish the connection) to make sure the changes are accepted.

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Chapter 10 – Live Parameter View
The Live Parameter View displays the current value of user-specified device parameters. Most
operating parameters of installed equipment are available and you can select which ones to
view depending on your current activity.

Note
Detector and analyzer parameters (e.g. data signal) cannot be observed using the Live Data
View. The Live View and data acquisition procedures are intended for use with detectors and
analyzers.

Parameter values are displayed in a large font, allowing you to read them from a distance. You
can therefore make adjustments on the chamber while reading the current instrument para-
meters on the computer screen.

To open the Live Parameter Data View:
Select Views/ Live Parameter View from the toolbar. The view will open at the bottom of
the main window. You can move this to a new position as desired.

The following procedures and features are available:
Selecting parameters for display.
Changing the mode of display .


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10.1 Selecting Parameters
No parameters are selected when you open the Live Parameter View. You can add parameters
individually or by loading a configuration. You can also remove any parameters from the view.

Note
Parameters are grayed out if the device is not connected. In this case, go to the Device Control
for the instrument and connect it.

Adding parameters to the Live Parameter View
To add parameters:
1. Click the Add Parameter button. A menu showing all installed equipment will appear.
2. Move the mouse pointer to an item of equipment. A submenu will appear showing all avail-
able operating parameters for the equipment.
3. Select a parameter. The parameter will now be listed in the left side of the view. This is reg-
ularly updated.

You can select a number of parameters, each of which will be shown separately.

Saving configurations
You can save the configuration (i.e. which parameters are selected for display, not their val-
ues). This allows you to easily display a group of parameters for a particular purpose.

To save a configuration:
1. Click the icon next to the drop-down menu. A Save dialog will open.


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2. Enter a name for your configuration. This will be saved with a .cfg extension in the set-
tings\ParameterLiveView directory of the installation folder.

Loading configurations
You can recall a saved configuration:
Click the drop-down menu and select a configuration from the list.

Removing parameters
You can remove parameters from the Live Data View:
Click the icon next to the parameter. The parameter is removed from the view.
10.2 Viewing Live Parameters

The Live Parameter View shows the current value of selected parameters in a large, easy to
read font. The default setting for parameters is to show the absolute value. For each or all para-
meters, you can display a reference value and the delta (difference) from the reference:
1. Set the parameter to a base value that is to be used for comparison.
2. Click . The reference value will be "frozen" in the left column. The right column will now
show the delta (difference) from the reference.

To set all parameters to reference and delta values:
Click in the toolbar.

When one or more reference value is selected, two columns of numbers are displayed. The
number in the right column changes as you make adjustments. Since there may be a mixture of
absolute and delta values, you need to know how to identify the type of value:
If only one value is shown, it is the absolute value.
If two values are shown, the left value is the reference value; the right is the delta.

Example
The screenshot below shows three parameters:
Mass Flow: Only one value is shown, so this is the absolute value.
Sensor A: Two values are shown. The left is the reference, the right is the delta from the ref-
erence.

Emission: This is grayed out and no values are shown. The device (FG 22 flood gun) is not
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connected.


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Chapter 11 – Live Data View
The Live Data View displays the variation of selected parameters over time. You can save the
data for later examination in the Data History View. Most operating parameters of installed
equipment are available, although some of these parameters are not of interest for data
recording.

Note
Detector and analyzer parameters (e.g. data signal) cannot be observed using the Live Data
View. The Live View and data acquisition procedures are intended for use with detectors and
analyzers.

You can adapt the selection of parameters and according to your experimental requirements,
e.g. monitoring the pressure during bakeout, producing a record of automated processes or
recording equipment parameters during measurements.

To open the Live Data View:
Select Views/ Live Data View from the toolbar. The view will open at the bottom of the
main window. You can move this to a new position as desired.

The following procedures and features are available:
Selecting parameters.
Viewing options.
Saving data.
Clearing data.


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11.1 Selecting Parameters

No parameters are selected when you open the Live Data View. You can add parameters indi-
vidually or by loading a configuration from a template. You can also remove any parameters
from the view.

Note
If no data is displayed after selecting a parameter, the device is probably not connected. In this
case, go to the Device Control for the instrument and connect it.

Adding parameters to the Live Data View
To add parameters:
1. Click the Add Parameter button. A menu showing all installed equipment will appear.
2. Move the mouse pointer to an item of equipment. A submenu will appear showing all avail-
able operating parameters for the equipment.
3. Select a parameter. The parameter will now be listed. A plot will also appear in the view
showing the status of the parameter. This is regularly updated.

You can select a number of parameters, each of which will be shown in its own plot.


159

Saving configurations
You can save the configuration (i.e. which parameters are selected for display, not their val-
ues):
1. Click the icon next to the drop-down menu. A Save dialog will open.

2. Enter a name for your configuration. This will be saved with a .cfg extension in the set-
tings\LiveData directory of the installation folder.

Loading configurations
You can recall a saved configuration:
Click the drop-down menu and select a configuration from the list. Live updates for all para-
meters in the configuration will start.

Removing parameters

You can remove parameters from the Live Data View:
160
Click the icon next to the parameter. The parameter is removed from the list and its
data window closed. Updating for this parameter will stop and no more data will be logged.
11.2 Viewing Live Data

The data for each parameter is shown in its own data window.

Toggle parameter visibility
When you select a parameter, a data window is automatically displayed. You can toggle the vis-
ibility of each parameter:
Click the check box next to the parameter. When ticked, a data window showing the live
data is shown. When empty, the data window is not displayed, but the data is still updated
for the parameter and written to a log file, if Autosave is selected.

Changing the time axis setting
By clicking the time axis label, you can change the way the time is displayed:
Relative time: Time relative to the start of reading data in the Live Data View, i.e. after the
first parameter was selected or after data was cleared.
Universal Time: The system clock time in UTC.
Local time: The system clock time with local settings.

Displaying most recent data
You can restrict the time axis so that it only displays recent data:
1. Check the show last box. The time axes of all data windows will be set to show a 10 min
(default setting) time period.
2. Enter a new time in minutes or use the up/ down arrows to adjust the time range.

Zoom
You can zoom into areas in the data windows:

Click and drag the mouse to form a rectangle in one of the data windows. When you
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release the mouse button, the plot shows the selected area. Note the following points:
The X axis is the same for all data windows. Moving the scroll bar on the X axis will
move the X scroll bars for all data windows. Thus, the same time frame is shown for all
data sets.
The Y axis is rescaled for the selected data window—other data windows are not
affected. If necessary, a scroll bar will appear on the Y axis.
Although the Live Data View is still continuously updated, the time axis is not
updated—the zoomed area is always shown. The Y axis in the zoomed window is also
not updated.

To remove the zoom from a window:
Double-click in any data window. All data windows will be restored to their full extent.

Cursor
You can place a cursor in a data window:
Right-click a point in the data window. The cursor will appear with its center at the mouse
pointer.

The position of the cursor stays constant. Due to data updating, this means it will appear to
move to the left (if you have not used zoom), as it continues to show the selected time.
11.3 Saving Live Data

You can save the data in the Live Data View for later examination in the Data History View.
There is also an autosave feature which saves the data in 60 s intervals.

Data is saved in a binary format with the .slh extension.

To save the current contents of the Live Data View:
1. Click the icon in the toolbar. A Save dialog will open.
2. Select a location and name for the file and click Save.

If autosave is activated, it will save data to this file.

To activate autosave:
1. Set the parameters that you want to record.
2. Check the Autosave box in the toolbar of the Live Data View. Autosave will then start.

If a file is not already listed in the field, a Save dialog will open so that you can specify a file for
the data. Alternatively, you can click the icon to create a new file, then click Autosave.

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11.4 Clearing the Live Data View
You can clear the data from the Live Data View:
Click . This removes all data from all parameters in the Live Data View. Live data acquis-
ition will restart.

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Chapter 12 – Data History View
The Data History View is the counterpart to the Live Data View. It allows you to load and view
data saved in the Live Data View. This arrangement allows you to view live data and old data
logs simultaneously.

To open the Data History View:
Select Views/ Data History View from the toolbar. The view will open at the bottom of the
main window. You can move this to a new position as desired.

You can perform the following actions in the Data History View:
Open data.
View data.
Save copies of the data.


164
12.1 Opening Data History
The Data History View can display data saved in the Live Data View. The data is saved in .slh
SpecsLab history format.

To open data history:
1. Click . A file browser will open.
2. Select a .slh file and click Open. The data will be loaded. Each parameter will be displayed
in its own data window.

There are a number of options for viewing the data.
12.2 Viewing Data History

The data for each parameter is shown in its own data window.

Toggle parameter visibility
On loading a data history file, data windows are automatically displayed for each parameter.
You can toggle the visibility of each parameter:
Click the check box next to the parameter. When ticked, a data window showing the data
history is shown.

Changing the time axis setting
By clicking the time axis label, you can change the way the time is displayed:
Relative time: Time relative to the start of reading data in the Live Data View, i.e. after the
first parameter was selected or after data was cleared.
Universal Time: The system clock time in UTC.
Local time: The system clock time with local settings.

Zoom
You can zoom into areas in the data windows:
Click and drag the mouse to form a rectangle in one of the data windows. When you
release the mouse button, the plot shows the selected area. Note the following points:

The X axis is the same for all data windows. Moving the scroll bar on the X axis will
165
move the X scroll bars for all data windows. Thus, the same time frame is shown for all
data sets.
The Y axis is rescaled for the selected data window—other data windows are not
affected. If necessary, a scroll bar will appear on the Y axis.

To remove the zoom from a window:
Double-click in any data window. All data windows will be restored to their full extent.

Cursor
You can place a cursor in a data window:
Right-click a point in the data window. The cursor will appear with its center at the mouse
pointer.
12.3 Saving Data History

You can make a copy of the data history:
Click . A Save dialog will open, allowing you to select a new name and location for the
file.

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167
Chapter 13 – Detector Calibration
Detector calibration is a procedure that corrects the peak height and position of channels. It
does this by comparing measurements to a reference scan and modifying the energy and/ or
intensity scales.
13.1 Calibration Procedures

Measured peak positions can shift for different lens modes and slit settings. This is caused by
the changing incidence angle of electrons onto the entrance slit. The spread in energy around
the pass energy E , ΔE , is given by:
p an

ΔE n W α2 (16)
= −
E p ss 2R 0 4

where:
W = (W1+ W2)/2 is the average of the widths of the electron beam at the entrance and exit
slits in the
energy direction.
α is the average angular width of the electron distribution.
R is the radius of the hemispherical energy filter.
0

There are calibration settings included in SpecsLab Prodigy that provide a good correction to
this effect. However, not all lens/ slit combinations are calibrated and you may find that the
approximation for your combination is not sufficient. After performing the detector calibration,
you can use it for this lens/ slit combination in future experiments.

The figure below shows the individual channels measured in a scan using a CCD detector. As
you can see, the peak position is different in each channel. This produces a broadening of the
summed peak which needs to be corrected. It is also possible that the peak position shifts as a
function of pass energy. You can see this by recording a series of spectra at different pass ener-
gies and observing the peak positions in the Plot View.


168

The Detector Calibration View allows you to calibrate the energy position and detector gain set-
tings to compensate for the above effects. The basic procedure for calibration is:
1. Find a suitable reference area.
2. Measure this area at different pass energies. These will be calibrated.
3. Perform the calibration.
4. Save the calibration.

The screenshot below shows the difference between uncalibrated data (left) with calibrated
data (right).

There are two different calibration algorithms, which are applied to these use cases:
Fixed analyzer transmission (FAT) mode, to calculate the energy shifts of the channels.

Snapshot mode, to calculate energy shifts and gains of the channels.
169
Replace, to replace the calibration used in a data set to that in another calibration file.

These are described in the following sections.
13.1.1 Calibrating Fixed Analyzer Transmission Groups

In fixed analyzer transmission mode, the analyzer scans the kinetic energy of the incident
particles at a fixed pass energy. You can scan in this mode by selecting the analysis mode
FixedAnalyzerTransmission when setting up the spectrum group.

Note
If the calibration procedure does not succeed, check that the count rate is high enough. This is
a problem for regions with low pass energies. Also, you should ensure that SpecsLab Prodigy
can detect the peaks by using Operations/ Peak Location. If the peak cannot be detected, cal-
ibration will fail. For this reason, you should check that all energy channels show a peak—some-
times, channels at the edge do not show a complete peak.

To perform a calibration for fixed analyzer transmission groups:
1. Create a new spectrum group for the calibration.
2. Scan a number of spectra, each with the same parameters but different pass energies (e.g.
5, 10, 20, 50 eV pass energies). These allow the detector to be calibrated for each pass
energy.
3. Select Views/ Detector Calibration from the menu bar. The Detector Calibration View will
open.


170

4. Select a spectrum group from the Group drop-down list. Calibration is performed on this
group.
5. Select an entry from the Calibration Type drop-down list:
Peak—the peak is used as the calibration point.
Fermi Edge—the Fermi edge will be used as the calibration point rather than a peak.
6. Set values for Ek min and Ek max, if necessary. These settings restrict the range used in
the calibration. By default, the values in the Ek min and Ek max fields are the parameters
you entered when defining the spectra.
7. Click Calculate Shifts. The calibration will be performed. The new values will be displayed
in the table.You will also see the peaks updated in the view pane after the calibration is per-
formed.

This calculation is only applied to the data in the Detector Calibration View. To apply the results
to the spectrum data:
Click Apply to Group. The calculated values are updated in the data file. You can see the
results, for example, in the Plot View.

171
You can reset the results of the calculation:
Click Reset Shifts. This sets Shift = 0 for all channels (it does not return the values to their
previous settings). If necessary, you can also update the data to these values by clicking
Apply.
13.1.2 Calibrating Snapshot Fixed Analyzer Transmission Groups

You can use snapshot mode when acquiring data. In this case, the spectrum is generated by
reading out the whole detector array at once—there is no averaging over the channels.

The SFAT detector calibration procedure requires two spectrum groups, recorded with the fol-
lowing scan modes:
Fixed Analyzer Transmission—to calculate a linear fit over the energy range.
Snapshot—to record the relative intensities of each channel.

The figure below shows the effect of calibration. The FAT scan is a flat background energy scan.
The Snapshot scan shows the different contributions from each channel. Calibration works by
fitting a straight line to the spectrum measured in FAT mode. This is used with the values from
the snapshot spectrum to calculate the gain factors for each channel. The gain factors are
equal to the inverse of the average number of counts for each channel (energy value) in the
snapshot spectrum divided by the value obtained from the linear fit for the corresponding
energy value.

Note
The maximum absolute value of the residuals (i.e. the difference between the scan mode
intensity and the linear fit for all the energy values measured) should be less than 5% of the
energy averaged number of counts. If the residuals are greater, the spectrum is either too
noisy or not sufficiently flat. In this case the procedure will fail.


You should remember the following points when calibrating the snapshot mode:
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The SFAT procedure only calibrates gain corrections for the channels. Energy shifts are not
calculated.
Calibration uses a linear fit, so the count rate in the spectrum should be constant, i.e. there
should be a flat background signal with no peaks. An example is the 817–812 eV binding
energy in the silver spectrum.
You should ensure that the average number of counts is similar for each measurement by
taking into account the number of energy channels N, e.g.
10 scans, dwell time 1 s for the scan mode
100 scans, dwell time N × 0.1 s for the snapshot mode

To perform a calibration for SFAT spectra:
1. Create two spectrum groups for the calibration. One needs to have the scan type Fixed Ana-
lyzer Transmission, the other Snapshot.
2. Record spectra for both spectrum groups using an energy region that shows a flat back-
rgound signal.
3. Select Views/ Detector Calibration from the menu bar. The Detector Calibration View
will open.
4. Click the SFAT tab.


173

5. Select a group from the Group drop-down list in the Gains (SFAT) section.
6. Set values for Ek min and Ek max, if necessary. These settings restrict the range used in
the calibration. By default, the values in the Ek min and Ek max fields are the parameters
you entered when defining the spectra.
7. Click Calculate. The calibration will be performed. The new values will be displayed in the
table. If the data window is open, you will also see the peaks updated after the calibration is
performed.

This calculation is only applied to the data in the Detector Calibration View. To apply the results
to the spectrum data:
Click Apply. The calculated values are updated in the data file. You can see the results, for
example, in the Plot View.

You can undo the results of the calculation:

Click Reset Gains. The spectra will be returned to their original values. If necessary, you
174
can also update the data to these values by clicking Apply.
13.1.3 Replacing a Calibration

When you define an experiment, you can specify a calibration file which is applied to the res-
ults. If necessary, you can replace the calibration file so that the data is corrected with another
detector calibration. This procedure allows you to change the calibration file in arbitrary data
sets.

To replace a calibration file for a data set:
1. Select the Replace tab in the Detector Calibration view.
2. Select a spectrum group from the Group drop-down list. The data will be loaded into the
table.
3. Click Load. A file browser dialog will open.
4. Select the calibration file that you want to use to calibrate the data in the table.
5. Click Apply to Group. The calibration file will be applied to the data.
13.2 Managing Dataset Files

SpecsLab Prodigy stores calibration data in text files known as dataset files. There is a text file
for each dataset file. After installation, the dataset files are stored in the data-
base\datasetCalib1d folder in your SpecsLab2 installation directory. Calibration files have a
.calib1d extension. You can open these files in a text editor to view their contents; however, you
should not change their contents.
13.2.1 Saving Calibrations

You can save a calibration for future use. When you save a dataset file, it is available in the
Experiment Editor as par t of the definition of the spectrum group.


175
To save a calibration:
1. Perform the calibration as described in the previous sections.
2. Click Save. A Save dialog will open.
3. Select a location for the file and enter a filename. The .calib1d extension will be added auto-
matically to the name.
4. Click Save. The dataset file will be saved.
13.2.2 Loading Calibrations

When you load a dataset file, it is applied to the currently selected spectrum group in the
Detector Calibration View. This allows you to see the effect of a different calibration on existing
data.

To load a dataset file:
1. Select Views/ Detector Calibration from the menu bar. The Detector Calibration View will
open.
2. Select a spectrum group from the drop-down list in either the FAT or SFAT tabs.
3. Click Load. A file browser will open.
4. Locate the dataset file you want to load. The file must have a .calib1d extension.
5. Click Open. The calibration settings are opened and displayed in the table. The plot in the
Detector Calibration View shows that the calibration has been applied to the spectra.

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177
Chapter 14 – Transmission Function
The transmission function is a property of the analyzer that determines the intensity of the
measured signal under different experimental conditions.

The transmission function is dependent on the following factors:
Lens transmission, which is determined by integrating curve intensity as a function of
retarding ratio.
Analyzer transmission, which is proportional to the pass energy.
Detector transmission, which depends on the conversion voltage.

These quantities are multiplied to give the transmission function. In general, it is necessary to
determine the transmission function for
Each lens mode.
Each combination of entrance and exit slits.
Each size of the excitation spot on the sample.

SPECS supplies a set of transmission functions for a few combinations.

Note
If a transmission function is not available for your chosen combination, you need to either use a
transmission function for a similar combination (this will produce a warning when you validate
the experiment) or measure a new transmission function—please contact SPECS for advice.

For quantitative analysis of data, it is essential to use a transmission function, as this ensures
the correct ratios in peak areas. It is important to note that SpecsLab Prodigy does not include
the transmission function when displaying or evaluating data. You can however export spectra
with the transmission function in VAMAS or XY format.

The transmission function view allows you to see the transmission function used with a spec-
trum and to change the transmission function if necessary. To open the transmission func-
tion view:
Select Views/ Transmission Function from the menu bar. The transmission function view
will open.


178
14.1 Viewing the Transmission Function

When you open the transmission function view, the Transmission Correction tab is displayed.
This shows the following:
A plot of the transmission function as a function of electron kinetic energy.
A table containing metadata for the transmission function.

The transmission function shown is for the currently selected spectrum in the experiment
editor.

Note
The numbers in the Y-axis of the plot are arbitrary units. In applying a transmission function,
you lose the measured intensities of the peaks, but gain the correct relative intensities.

Note
Angle-resolved measurements require a transmission function for each angle. In order to use
a transmission function for angle-resolved modes, you need to select Use Image Mapping in
the Detector section of the PHOIBOS device control. This only applies to 2D detectors.


179
14.2 Selecting a Transmission Function

You can select a transmission function as part of defining a spectrum group:
Select an item from the Transmission drop-down list in the spectrum group definition. In
addition to the transmission functions for specific setups, there is also a default trans-
mission function as well as a constant value, which is equivalent to not applying a trans-
mission function.

Each spectrum in a spectrum group can use a different lens mode. Since the transmission func-
tion is dependent on the lens mode, SpecsLab Prodigy automatically applies the correct trans-
mission function for the lens mode. The picture below shows the file structure of the
transmission functions. As you can see, the folders determine the analyzer, detector and slit
settings. Each lens mode has its own transmission function file.

Note
The SpecsLab Prodigy is normally under C:\Program Files (x86)\ .

If a suitable transmission function is not available, a warning will be shown when you validate
the experiment. SpecsLab Prodigy deals with missing transmission functions as follows:
The default transmission function is used.
If the default is also not available, a constant value is used.


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14.3 Replacing the Transmission Function

The Replace Transmission tab allows you to specify the transmission function in spectra.

To replace the transmission function:
1. Select the Replace Transmission tab in the transmission function view.
2. Select a spectrum group in the experiment editor. All spectra in the group will be listed in
the transmission function view, along with their transmission function (if any).

Note
If you select an element in the experiment editor that contains more than one spectrum group,
all spectra in all affected groups will be selected.

3. Select a transmission function from the drop-down list at the bottom left of the trans-
mission function view. Selecting Load from this list opens a file browser dialog, allowing
you to select a transmission function from the file system.
4. Click Replace TF Data. The transmission functions in all spectra listed in the transmission
function view will be replaced by the selected transmission function.


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182

183
Chapter 15 – Device Controls
SpecsLab Prodigy is able to control a variety of SPECS equipment. The Device Control view
provides an overview of all available SPECS instruments in your system and allows you to set
their operating parameters.

The contents of the Device Control view consist of a group of modules which depend on your
system configuration. For this reason, the view is not discussed in this manual. Please refer to
the manual of the equipment for a description of its Device Control.

In particular, there is a Device Control used to directly control and report the voltages in your
analyzer and detector. This is essential when setting up the analyzer, as well as for calibration
and test purposes. The Device Control is described in the analyzer manual.

Note
All modules are documented in the SpecsLab Prodigy Online Help.

15.1 Arranging Devices

You can arrange devices in the Device Control view:
1. Click and hold the title bar of a device.
2. Drag the mouse to a new position in the view. A blue line will appear at the mouse position:
Horizontal—the device control will be moved to this position in the column.
Vertical—a new column will be created at this position.

3. Release the mouse button. The device control will appear in the new position.
184

You can save the layout by selecting Layout/ Save Current Layout from the menu bar.

The Devices pane on the left contains an overview of all dis-
played devices. Clicking a device in this list will jump to the
selected device in the main pane.
15.2 Device Control Toolbar

There is a toolbar in the Device Control view. The actions of the features in the toolbar affect all
devices. It also shows the connected devices and their status.

Show/ hide inactive devices
Clicking this icon toggles the display of devices in the Device Control view. You can set it so that
only connected devices are visible. If you have many devices in your system, this can improve
the readability of the view.

All devices are shown in the Devices pane on the left side of the view. You can connect to
devices by checking the option box in the Devices pane. After connecting, the device control is
shown in the main pane.

185
Disconnect from all devices
Clicking this icon disconnects all devices.

Send devices to safe state
On clicking this icon, all connected devices are put into a safe state. The meaning of "safe
state" is device dependent.

Devices
The toolbar also contains icons showing the status of connected devices.

Note
Each device has its own icon and is displayed separately in the toolbar. The table below only
shows the analyzer icon.

Indicator Status
Device inactive.
Device in operation and working correctly.
Set up device ready for operation.
Device error.
15.3 Unknown Devices

Unknown devices are indicated by a question mark icon. This is shown when a file contains
details of a device, but the device is not configured in SpecsLab Prodigy. This may occur for the
following reasons:
When data acquired on one installation of SpecsLab Prodigy is opened in another.
If a device is reconfigured. The configuration in the data file is then different from the cur-
rent configuration in SpecsLab Prodigy.

Although it is not configured, the data file contains metadata which describes the device. This
metadata is shown in SpecsLab Prodigy with the settings used in the experiment. In most
cases, this should be sufficient for you to see what equipment was used and the operating para-
meters.

The screenshot below shows two unknown devices. The analyzer (left) has been correctly iden-
tified, while the X-ray source is recognized only as a source with the correct excitation energy.


186

187
Index
2 C
2D View See Image View Calibration

2nd Window 4 File 10, 174-175
Procedure 167, 169, 171
A
CCD
Abort 14 Active area 148
Absolute Values 155 Calibration 167
Acquire 13 Hot pixel 150
Active Area 148 Center/ Integral 142
Add Copy Of Spectrum 74, 82 Center/ Width 26
Add Spectrum 11 Change Colormap 140
Analysis Mode Channels
Constant final state 57 Allocation 75
Constant initial state 59 Calibrate 167, 169, 172
Detector voltage scan 56 CCD definition 148
Fixed analyzer transmission 51 Display 72
Fixed energies 54 Channeltron 56
Fixed retarding ratio 52 Clone Spectrum 74, 82
Snapshot 55 Color Transformation Range 140
Analyzer 8 Consecutive 10
Annotation 89 Constant Final State 57
Apportioning 75 Constant Initial State 59
Arithmetic Mean 121 Copy Profile Data 139
Asymmetric Peak 95, 104 Correct Transmission Function 178-179
Auto Flood Gun Adjust 40 Count Offset 126
Parameters 42 Count Scaling 126
Procedure 42 Cursor
Auto Sample Height Adjust Data history view 164
45
Configuration Image view 141
46
Procedure Live data view 160
48
Automatic Range Plot view 76
99
Autosave Cycling 9
14
Autoscale D
2D viewer 141
Axis Labels 83, 137 Data Appearance 73
Data Browser 71, 136
B Data History View 163-165
Background Subtraction Data Operation
Data operations 105 Region 87

188
Dead Time Correction 122 G
Delete Spectrum 11, 73
Delta Values 155 Gauss 143
Depth Profile 36 Grid
Derivation Order Image view 142
117
Despiking Plot view 77
111
Detector Calibration Group 16, 29, 66
167
Detector Settings 150 H
Detector Voltage Scan 56
Device 8 Half Window Size 126
Ion Gun 37 Hide Data 73
Item in electron spectroscopy 26 Histogram 139
Manipulator 32 Horizonal Profile 138
Sample Heater 34 Hot Pixel 150
Device Control 183 Hot Standby 38
Dimension 31, 33-34
I
Duplicate Spectrum 74, 82
Image Operations 142
E
Image Pane 138
EBH 150 34 Image View 49, 135
Electron Gun 7 Operations 142
Emergency Off 3, 13 Instrument Status 65
Enable Histogram 140 Interpolation 75
Energy Offset 128 Ion Source 7, 37
Energy Scaling 128 Iterations 33
Energy Tolerance 101
K
Error Function 108
Errors 66 Keep Pressure 38
Experiment Editor 7 Kinetic Energy 26
Expert Mode 19
Export 25, 61 L
Eye Icon 73
Label Syntax 89
F Least Squares Gradient 124
Legend See Data Browser
FAT See Fixed Analyzer Transmission Lens Mode 11
Fermi Edge Transmission Function 177
Plot View 108 Lens Voltage 10
Filter Database 133 Line Style 73
Fixed Analyzer Transmission 51 Linear Background 107
Fixed Energy 54 Linear Operations 126
Fixed Retarding Ratio 52 Live Data View 157-158, 160-162
Flood Gun 40 Live Parameter View 153-155
FRR See Fixed Retarding Ratio Live View 145
FWHM Threshold 100 Load Layout 3

189
M R
Mapping Reference Values 155

Detector 148 Region Of Interest 141
Profile 33 Relative 33
Menu Bar 3 Remove Spectrum 11
Moving View 3 ROI See Region Of Interest
N S
Nearest Neighbor 75 Sample Heating 34

Noise 113 Save 14
Normalize Spectra 89 Save Layout 3
Scan 11
O Scan ID 72
Optimize Range 85, 106 Scan Mode 9
Overwriting 25 Constant final state 57
Constant initial state 59
P Detector voltage scan 56
Fixed analyzer transmission 51
Panic Button 3, 14 Fixed energies 54
Pause 27 Fixed retarding ratio 52
Pause Scan 13 Snapshot 55
Peak Area 91 Schedule 16
Peak Fit 93 Search Database 133
Peak FWHM 97 Second Window 4
Peak Identification 81, 100 Selected Peaks 82
Peak Location 80, 93, 102 Settings
Periodic Table 11, 80 Data browser 75
Physical Units 142 Electron spectroscopy 9
Pixels 142 Experiment editor 14
Plot View 71, 85 SFAT 171
Data Browser 71 Shirley Background 107
Toolbar 75 Sleep 28, 30, 41
Point Style 73 Slit Settings 10, 177
Poisson Factor 120 Smoothing
Polynom Order 117 Sasvitsky Golay 115
Print 79 Spline 118
Priority (Database) 133-134 Snapshot 55
Processing 10 Calibration 171
Profiles (2D) 138 Source 7
Profiling Spatial Map 33
Depth 36 SpecsLab2 61
Dimensions 32 Spectrum Group 9
Spline 118
Sputter Cycle 36

190
Sputter Depth Profile 37 Zoom
Start/ End 26 Data history view 164
Status 65 Image view 141
Synchrotron 58-59 Live data view 160
Syntax 89 Plot view 78
Template 17
TF See Transmission Function
Time Axis
Data history view 164
Live data view 160
Toggle Visibility 73
Toolbar
Image view 135
Live View 145-146
Plot view 75
Tougaard Background 105
Transmission Function 177
Replace 180
Select 179
View 178
Use Zoomed Area 140
Validate 13
VAMAS 62
VCU Pressure 37
Vertical Profile 138
Visibility Of Spectra 74
X-Ray Source 7
X Profiling 33
XY Export 64
Y Line Fit 143
Z Axis 36, 39, 73, 78

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SpecsLab Prodigy

Data Acquisition and Experiment Control Software Package

User Manual 4.12.0r49869 | March 31, 2015

Chapter 2 – Interface Overview

Chapter 3 – Experiment Editor I: Basic Use

Chapter 4 – Experiment Editor II: Schedule Options

SpecsLab Prodigy 4.12.0r49869 March 31, 2015 iii

Chapter 5 – Experiment Editor III: Reference Information

Chapter 6 – Plot View I: Features

iv March 31, 2015 SpecsLab Prodigy 4.12.0r49869

Chapter 7 – Plot View II: Data Operations

Chapter 7 – Chemical Databases

Chapter 8 – Image View

Chapter 9 – Live View

SpecsLab Prodigy 4.12.0r49869 March 31, 2015 v

Chapter 10 – Live Parameter View

Chapter 11 – Live Data View

Chapter 12 – Data History View

Chapter 13 – Detector Calibration

Chapter 14 – Transmission Function

Chapter 15 – Device Controls

vi March 31, 2015 SpecsLab Prodigy 4.12.0r49869

1.2 Starting SpecsLab Prodigy

SpecsLab Prodigy4.12.0r49869 | March 31, 2015

SpecsLab Prodigy4.12.0r49869 | March 31, 2015

Chapter 2 – Interface Overview

2.1 Menu Bar

2.2 Managing Views

SpecsLab Prodigy4.12.0r49869 | March 31, 2015

2.3 Opening a Second Window

SpecsLab Prodigy4.12.0r49869 | March 31, 2015

2.4 Scrollbar Navigation Markers

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SpecsLab Prodigy4.12.0r49869 | March 31, 2015

Chapter 3 – Experiment Editor I: Basic Use

3.1 Measuring a Spectrum

3.1.1 Adding a Source

SpecsLab Prodigy4.12.0r49869 | March 31, 2015

3.1.2 Adding an Analyzer and Other Devices

SpecsLab Prodigy4.12.0r49869 | March 31, 2015

3.1.3 Creating a Spectrum Group

SpecsLab Prodigy4.12.0r49869 | March 31, 2015

SpecsLab Prodigy4.12.0r49869 | March 31, 2015

SpecsLab Prodigy4.12.0r49869 | March 31, 2015

SpecsLab Prodigy4.12.0r49869 | March 31, 2015

3.1.5 Starting a Measurement

SpecsLab Prodigy4.12.0r49869 | March 31, 2015

3.1.6 Saving Data

SpecsLab Prodigy4.12.0r49869 | March 31, 2015

3.2 Scheduling Tasks

SpecsLab Prodigy4.12.0r49869 | March 31, 2015

3.2.1 Building Schedules

3.2.2 Reusing the Schedule

SpecsLab Prodigy4.12.0r49869 | March 31, 2015

3.2.3 Saving a Schedule

3.3.1 Creating Templates

SpecsLab Prodigy4.12.0r49869 | March 31, 2015

3.3.2 Adding Templates to Experiments

SpecsLab Prodigy4.12.0r49869 | March 31, 2015