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