Fully convolutional networks for 2D segmentation#204

Merged

lamblin merged 96 commits intomasterfrom

Jun 15, 2018

Commits on Dec 14, 2017

first commit

StephanieLarocque
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images for fcn and unet

StephanieLarocque
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small changes

StephanieLarocque
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fixed details

adri-romsor
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polyps dataset explanation + metrics

StephanieLarocque
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jaccard visualisation

StephanieLarocque
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code for fcn8, miss dataset_loaders

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small changes

StephanieLarocque
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small changes

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old build instructions

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fixed fcn8

adri-romsor
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cortical

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ray

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remove file

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remove dependance from metrics.py

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remove dependance from model_helpers.py

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big brain images

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added reference captions

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global dataset loader from fvsin

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first commit for cortical layers segmentation

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first commit

StephanieLarocque
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cortical layers

StephanieLarocque
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cortical layers updated

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cortical layers imagse

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Feedback comments from PascalLamblin

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fixing small details on the metrics

adri-romsor
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dataset explanation addeed

StephanieLarocque
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small changes

StephanieLarocque
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reviewed 1d segm

adri-romsor
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Delete fcn_1D_segm.txt

StephanieLarocque
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fix for FCN32-16-8 description

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FCN description fixed

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typo

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fix figure labelling

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explanation ground truth vs predicted segmentation

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figure 4 description

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deleted files

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first commit for fcn1D segmentations

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edited text, including 2D-> 3D changes

Konrad Wagstyl
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lasagne recipe unet implementation

StephanieLarocque
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unet update

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added code

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changes in the prerequisite

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small corrections

adri-romsor
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references fixed

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acknowledgements

Konrad Wagstyl
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fix website links

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polyps results image

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no change

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update from pascal comment

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small changes

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delete unet.py (previous version)

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small change

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cleaned dataset loader

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relative paths

StephanieLarocque
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cleaned dataset loader

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deleted file

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relative paths

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with BN

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small changes

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Rename code/Unet_lasagne_recipes.py to code/unet/Unet_lasagne_recipes.py

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first commit

StephanieLarocque
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dataset loader for unet and fcn8

StephanieLarocque
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fixed path for unet.py

StephanieLarocque
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adde training loop link

StephanieLarocque
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fix dataset loader for em, name for polyps

StephanieLarocque
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fix import

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small change

StephanieLarocque
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small change

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fix input dim and details

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import conv2DDDNlayer

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saving stuff

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small changes

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accuracy import fix

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small change

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load data from train file

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data link

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removed files .pyc

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index updated with new links

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ref for dataset loaders

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remove loading pretrained weights

StephanieLarocque
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update in loading data parameters

StephanieLarocque
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added requirements for lasagne, datasetloaders and simple ITK

StephanieLarocque
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specify that data augmentation is used

StephanieLarocque
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data augmentation fixed

StephanieLarocque
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fix in shared_path for config.ini

StephanieLarocque
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More small fixes

lamblin
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Fix warnings in doc generation

lamblin
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Remove files that are not used any more

lamblin
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Formatting

lamblin
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Changes to help unet run

lamblin
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added per class jaccard

adri-romsor
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Results for unet

lamblin
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Preload data for 1D cortical dataset

lamblin
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Commits on Jan 12, 2018

Update segmentation tutorials and .gitignore.
notoraptor
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Commits on Jun 15, 2018

Add final scores and training times for FCN 2D segmentation
lamblin
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