.gitignore
Dockerfile
LICENSE.md
Multi-GPU Training.md
PostProcessSegmentationMask.py
README.md
cli.py
conftest.py
environment.yml
mkdocs.yml
notes_for_code_testing.md
setup.cfg
setup.py
test.py
train.py
Datasets/Sample_Dataset/test/22_2.png
Datasets/Sample_Dataset/test/34_3.png
Datasets/Sample_Dataset/test/6_2.png
Datasets/Sample_Dataset/test/799_2.png
Datasets/Sample_Dataset/test_DeepLIIF_results/22_2_fake_B_1.png
Datasets/Sample_Dataset/test_DeepLIIF_results/22_2_fake_B_2.png
Datasets/Sample_Dataset/test_DeepLIIF_results/22_2_fake_B_3.png
Datasets/Sample_Dataset/test_DeepLIIF_results/22_2_fake_B_4.png
Datasets/Sample_Dataset/test_DeepLIIF_results/22_2_fake_B_5.png
Datasets/Sample_Dataset/test_DeepLIIF_results/22_2_real_A.png
Datasets/Sample_Dataset/test_DeepLIIF_results/34_3_fake_B_1.png
Datasets/Sample_Dataset/test_DeepLIIF_results/34_3_fake_B_2.png
Datasets/Sample_Dataset/test_DeepLIIF_results/34_3_fake_B_3.png
Datasets/Sample_Dataset/test_DeepLIIF_results/34_3_fake_B_4.png
Datasets/Sample_Dataset/test_DeepLIIF_results/34_3_fake_B_5.png
Datasets/Sample_Dataset/test_DeepLIIF_results/34_3_real_A.png
Datasets/Sample_Dataset/test_DeepLIIF_results/6_2_fake_B_1.png
Datasets/Sample_Dataset/test_DeepLIIF_results/6_2_fake_B_2.png
Datasets/Sample_Dataset/test_DeepLIIF_results/6_2_fake_B_3.png
Datasets/Sample_Dataset/test_DeepLIIF_results/6_2_fake_B_4.png
Datasets/Sample_Dataset/test_DeepLIIF_results/6_2_fake_B_5.png
Datasets/Sample_Dataset/test_DeepLIIF_results/6_2_real_A.png
Datasets/Sample_Dataset/test_DeepLIIF_results/799_2_fake_B_1.png
Datasets/Sample_Dataset/test_DeepLIIF_results/799_2_fake_B_2.png
Datasets/Sample_Dataset/test_DeepLIIF_results/799_2_fake_B_3.png
Datasets/Sample_Dataset/test_DeepLIIF_results/799_2_fake_B_4.png
Datasets/Sample_Dataset/test_DeepLIIF_results/799_2_fake_B_5.png
Datasets/Sample_Dataset/test_DeepLIIF_results/799_2_real_A.png
Datasets/Sample_Dataset/test_cli/22_2.png
Datasets/Sample_Dataset/test_cli/34_3.png
Datasets/Sample_Dataset/test_cli/6_2.png
Datasets/Sample_Dataset/test_cli/799_2.png
Datasets/Sample_Dataset/test_groundtruth/22_2.png
Datasets/Sample_Dataset/test_groundtruth/34_3.png
Datasets/Sample_Dataset/test_groundtruth/6_2.png
Datasets/Sample_Dataset/test_groundtruth/799_2.png
Datasets/Sample_Dataset/train/Bladder1.png
Datasets/Sample_Dataset/train/Lung1.png
Datasets/Sample_Dataset/val/Bladder1.json
Datasets/Sample_Dataset/val/Bladder1.png
Datasets/Sample_Dataset/val/Lung1.json
Datasets/Sample_Dataset/val/Lung1.png
Datasets/Sample_Dataset/val/metrics.json
DeepLIIF_Statistics/ComputeStatistics.py
DeepLIIF_Statistics/Create_Loss_Diagram.py
DeepLIIF_Statistics/HelperFunctions.py
DeepLIIF_Statistics/PostProcessSegmentationMask.py
DeepLIIF_Statistics/README.md
DeepLIIF_Statistics/Segmentation_Metrics.py
DeepLIIF_Statistics/environment.yml
DeepLIIF_Statistics/fid.py
DeepLIIF_Statistics/fid_official_tf.py
DeepLIIF_Statistics/inception_score.py
DeepLIIF_Statistics/swd.py
ImageJ_Plugin/.gitignore
ImageJ_Plugin/README.md
ImageJ_Plugin/pom.xml
ImageJ_Plugin/images/roi_step01.png
ImageJ_Plugin/images/roi_step02.png
ImageJ_Plugin/images/roi_step03.png
ImageJ_Plugin/images/roi_step04.png
ImageJ_Plugin/images/roi_step05.png
ImageJ_Plugin/images/roi_step06.png
ImageJ_Plugin/images/roi_step07.png
ImageJ_Plugin/images/roi_step08.png
ImageJ_Plugin/images/roi_step09.png
ImageJ_Plugin/images/roi_step10.png
ImageJ_Plugin/images/step01.png
ImageJ_Plugin/images/step02.png
ImageJ_Plugin/images/step03.png
ImageJ_Plugin/images/step04.png
ImageJ_Plugin/images/step05.png
ImageJ_Plugin/images/step06.png
ImageJ_Plugin/images/step07.png
ImageJ_Plugin/images/step08.png
ImageJ_Plugin/images/step10.png
ImageJ_Plugin/src/main/java/org/nadeemlab/deepliif/DeepliifClient.java
ImageJ_Plugin/src/main/java/org/nadeemlab/deepliif/DeepliifException.java
ImageJ_Plugin/src/main/java/org/nadeemlab/deepliif/FileHelper.java
ImageJ_Plugin/src/main/java/org/nadeemlab/deepliif/InferencePlugin.java
ImageJ_Plugin/src/main/java/org/nadeemlab/deepliif/InteractionPlugin.java
ImageJ_Plugin/src/main/java/org/nadeemlab/deepliif/MutableHTMLDialog.java
ImageJ_Plugin/src/main/java/org/nadeemlab/deepliif/OverlayCreator.java
ImageJ_Plugin/src/main/java/org/nadeemlab/deepliif/ResultHandler.java
ImageJ_Plugin/src/main/java/org/nadeemlab/deepliif/RoisInferencePlugin.java
ImageJ_Plugin/src/main/java/org/nadeemlab/deepliif/UIHelper.java
ImageJ_Plugin/src/main/resources/plugins.config
Image_Processing/Augmentation.py
Image_Processing/Image_Processing_Helper_Functions.py
Registration/README.md
Registration/Registration_App.py
Sample_Large_Tissues/ROI_1.png
Sample_Large_Tissues/ROI_127.png
Sample_Large_Tissues/ROI_153.png
Sample_Large_Tissues/ROI_46.png
Sample_Large_Tissues/ROI_7.png
Scripts/download_pre_trained_model.sh
Scripts/download_training_sets.sh
assets/.METADATA/.gitkeep
assets/.METADATA/.version.json
assettypes/.gitkeep
deepliif/__init__.py
deepliif/postprocessing.py
deepliif/postprocessing__OLD__DELETE.py
deepliif.egg-info/PKG-INFO
deepliif.egg-info/SOURCES.txt
deepliif.egg-info/dependency_links.txt
deepliif.egg-info/entry_points.txt
deepliif.egg-info/requires.txt
deepliif.egg-info/top_level.txt
deepliif/data/__init__.py
deepliif/data/aligned_dataset.py
deepliif/data/base_dataset.py
deepliif/data/colorization_dataset.py
deepliif/data/image_folder.py
deepliif/data/single_dataset.py
deepliif/data/template_dataset.py
deepliif/data/unaligned_dataset.py
deepliif/models/CycleGAN_model.py
deepliif/models/DeepLIIFExt_model.py
deepliif/models/DeepLIIFKD_model.py
deepliif/models/DeepLIIF_model.py
deepliif/models/SDG_model.py
deepliif/models/__init__ - different weighted.py
deepliif/models/__init__ - multiprocessing (failure).py
deepliif/models/__init__ - run_dask_multi dev.py
deepliif/models/__init__ - time gens.py
deepliif/models/__init__ - timings.py
deepliif/models/__init__ - weights, empty, zarr, tile count.py
deepliif/models/__init__.py
deepliif/models/att_unet.py
deepliif/models/base_model.py
deepliif/models/networks.py
deepliif/options/__init__.py
deepliif/options/base_options.py
deepliif/options/processing_options.py
deepliif/options/test_options.py
deepliif/options/train_options.py
deepliif/scripts/train.py
deepliif/stat/__init__.py
deepliif/util/__init__.py
deepliif/util/checks.py
deepliif/util/get_data.py
deepliif/util/html.py
deepliif/util/image_pool.py
deepliif/util/util - modified tensor_to_pil.py
deepliif/util/util.py
deepliif/util/visualizer.py
docs/README.md
docs/ImageJ/README.md
docs/ImageJ/images/roi_step01.png
docs/ImageJ/images/roi_step02.png
docs/ImageJ/images/roi_step03.png
docs/ImageJ/images/roi_step04.png
docs/ImageJ/images/roi_step05.png
docs/ImageJ/images/roi_step06.png
docs/ImageJ/images/roi_step07.png
docs/ImageJ/images/roi_step08.png
docs/ImageJ/images/roi_step09.png
docs/ImageJ/images/roi_step10.png
docs/ImageJ/images/step01.png
docs/ImageJ/images/step02.png
docs/ImageJ/images/step03.png
docs/ImageJ/images/step04.png
docs/ImageJ/images/step05.png
docs/ImageJ/images/step06.png
docs/ImageJ/images/step07.png
docs/ImageJ/images/step08.png
docs/ImageJ/images/step10.png
docs/cloud/README.md
docs/deployment/README.md
docs/deployment/images/deepliif_torchserve_workflow.png
docs/images/DeepLIIF_logo.png
docs/images/overview.png
docs/installation/README.md
docs/testing/README.md
docs/training/README.md
docs/training/images/IHC_Gen.jpg
images/DeepLIIF_logo.png
images/IHC_Gen3.png
images/deepliif-imagej-demo.gif
images/deepliif-imagej-roi-demo.gif
images/deepliif-stitch-demo-01.gif
images/deepliif-website-demo-04.gif
images/deepliif_torchserve_workflow.png
images/overview.png
images/target.png
model-server/config.properties
model-server/deepliif_workflow.yaml
model-server/deepliif_workflow_handler.py
model-server/model_requirements.txt
model-server/net_handler.py
model-server/resnet.py
model-server/unet.py
tests/test_args.py
tests/test_cli_inference.py
tests/test_cli_serialize.py
tests/test_cli_train.py
tests/test_cli_trainlaunch.py
tests/util.py