├── .gitignore ├── DeepSTORM3D ├── GenerateTrainingExamples.py ├── PSF_Learning.py ├── Testing_Localization_Model.py ├── Training_Localization_Model.py ├── assessment_utils.py ├── cnn_utils.py ├── data_utils.py ├── helper_utils.py ├── loss_utils.py ├── physics_utils.py ├── postprocess_utils.py └── vis_utils.py ├── Demos ├── Results_Learned_demo5 │ ├── checkpoint.pth.tar │ ├── learning_results.pickle │ ├── setup_params.pickle │ ├── weights_best_jaccard.pkl │ └── weights_best_loss.pkl ├── Results_Tetrapod_demo2 │ ├── checkpoint.pth.tar │ ├── learning_results.pickle │ ├── setup_params.pickle │ ├── weights_best_jaccard.pkl │ └── weights_best_loss.pkl ├── Results_Tetrapod_demo3 │ ├── checkpoint.pth.tar │ ├── learning_results.pickle │ ├── setup_params.pickle │ ├── weights_best_jaccard.pkl │ └── weights_best_loss.pkl ├── parameter_setting_demo1.py ├── parameter_setting_demo2.py ├── parameter_setting_demo3.py ├── parameter_setting_demo4.py └── parameter_setting_demo5.py ├── Docs └── demo1_documentation.pdf ├── Experimental_Data ├── Learned_demo5_frm1 │ └── telomeres1.tif ├── Learned_demo5_frm2 │ └── telomeres2.tif ├── Tetrapod_demo2 │ ├── 1.tif │ ├── 10.tif │ ├── 11.tif │ ├── 12.tif │ ├── 13.tif │ ├── 14.tif │ ├── 15.tif │ ├── 16.tif │ ├── 17.tif │ ├── 18.tif │ ├── 19.tif │ ├── 2.tif │ ├── 20.tif │ ├── 21.tif │ ├── 22.tif │ ├── 23.tif │ ├── 24.tif │ ├── 25.tif │ ├── 26.tif │ ├── 27.tif │ ├── 28.tif │ ├── 29.tif │ ├── 3.tif │ ├── 30.tif │ ├── 31.tif │ ├── 32.tif │ ├── 33.tif │ ├── 34.tif │ ├── 35.tif │ ├── 36.tif │ ├── 37.tif │ ├── 38.tif │ ├── 39.tif │ ├── 4.tif │ ├── 40.tif │ ├── 41.tif │ ├── 42.tif │ ├── 43.tif │ ├── 44.tif │ ├── 45.tif │ ├── 46.tif │ ├── 47.tif │ ├── 48.tif │ ├── 49.tif │ ├── 5.tif │ ├── 50.tif │ ├── 6.tif │ ├── 7.tif │ ├── 8.tif │ └── 9.tif └── Tetrapod_demo2_crop │ ├── 1.tif │ ├── 10.tif │ ├── 11.tif │ ├── 12.tif │ ├── 13.tif │ ├── 14.tif │ ├── 15.tif │ ├── 16.tif │ ├── 17.tif │ ├── 18.tif │ ├── 19.tif │ ├── 2.tif │ ├── 20.tif │ ├── 21.tif │ ├── 22.tif │ ├── 23.tif │ ├── 24.tif │ ├── 25.tif │ ├── 26.tif │ ├── 27.tif │ ├── 28.tif │ ├── 29.tif │ ├── 3.tif │ ├── 30.tif │ ├── 31.tif │ ├── 32.tif │ ├── 33.tif │ ├── 34.tif │ ├── 35.tif │ ├── 36.tif │ ├── 37.tif │ ├── 38.tif │ ├── 39.tif │ ├── 4.tif │ ├── 40.tif │ ├── 41.tif │ ├── 42.tif │ ├── 43.tif │ ├── 44.tif │ ├── 45.tif │ ├── 46.tif │ ├── 47.tif │ ├── 48.tif │ ├── 49.tif │ ├── 5.tif │ ├── 50.tif │ ├── 6.tif │ ├── 7.tif │ ├── 8.tif │ └── 9.tif ├── Figures ├── locsoverlay.gif └── masklearninganimation.gif ├── LICENSE ├── Mat_Files ├── mask_learned.mat ├── mask_tetrapod.mat └── mask_tetrapod_printed.mat ├── README.md ├── demo1.py ├── demo2.py ├── demo3.py ├── demo4.py ├── demo5.py ├── environment_linux.yml └── environment_windows.yml /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EliasNehme/DeepSTORM3D/HEAD/.gitignore -------------------------------------------------------------------------------- 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