├── .gitignore ├── 0_get_masks.ipynb ├── 1_data_process_MoNuSAC.ipynb ├── 2_extract_patches_sliding.ipynb ├── 2b_trainval_split.ipynb ├── 3_train.ipynb ├── 3b_validate_and_compute_PQ.ipynb ├── 3c_load_test_data.ipynb ├── 4_inference.ipynb ├── 4b_inference.ipynb ├── ISBI 2020 MoNuSAC Workshop Challenge Paper.pdf ├── README.md ├── environment.yml ├── experiment ├── 2_extract_patches.ipynb ├── 400.mat ├── 401.mat ├── a.mat ├── a.png ├── a_mask.png ├── b.mat ├── eda.ipynb ├── m1.png ├── mask2.png ├── x.tif ├── y_ep.tif └── y_ly.tif ├── get_cell_count.ipynb ├── gpu_test.ipynb ├── media ├── network.png ├── result1.png ├── result2.png ├── result3.png └── result4.png ├── others ├── 2_extract_patches.ipynb ├── 3b_extract_patches_sliding.ipynb ├── resulta.png └── resultb.png ├── reference_notebooks ├── Binary_mask_generation.ipynb ├── Cell_counting.ipynb ├── Panoptic Quality.ipynb └── n-ary_mask_generation.ipynb ├── submission ├── README.txt ├── test_environment.yml └── the_great_backpropagator_testing_code.py └── test_environment.yml /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hasibzunair/MoNuSAC-ISBI-2020/HEAD/.gitignore -------------------------------------------------------------------------------- /0_get_masks.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hasibzunair/MoNuSAC-ISBI-2020/HEAD/0_get_masks.ipynb -------------------------------------------------------------------------------- /1_data_process_MoNuSAC.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hasibzunair/MoNuSAC-ISBI-2020/HEAD/1_data_process_MoNuSAC.ipynb -------------------------------------------------------------------------------- /2_extract_patches_sliding.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hasibzunair/MoNuSAC-ISBI-2020/HEAD/2_extract_patches_sliding.ipynb -------------------------------------------------------------------------------- /2b_trainval_split.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hasibzunair/MoNuSAC-ISBI-2020/HEAD/2b_trainval_split.ipynb -------------------------------------------------------------------------------- /3_train.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hasibzunair/MoNuSAC-ISBI-2020/HEAD/3_train.ipynb -------------------------------------------------------------------------------- /3b_validate_and_compute_PQ.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hasibzunair/MoNuSAC-ISBI-2020/HEAD/3b_validate_and_compute_PQ.ipynb -------------------------------------------------------------------------------- /3c_load_test_data.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hasibzunair/MoNuSAC-ISBI-2020/HEAD/3c_load_test_data.ipynb -------------------------------------------------------------------------------- /4_inference.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hasibzunair/MoNuSAC-ISBI-2020/HEAD/4_inference.ipynb -------------------------------------------------------------------------------- /4b_inference.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hasibzunair/MoNuSAC-ISBI-2020/HEAD/4b_inference.ipynb -------------------------------------------------------------------------------- /ISBI 2020 MoNuSAC Workshop Challenge Paper.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hasibzunair/MoNuSAC-ISBI-2020/HEAD/ISBI 2020 MoNuSAC Workshop Challenge Paper.pdf -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hasibzunair/MoNuSAC-ISBI-2020/HEAD/README.md -------------------------------------------------------------------------------- /environment.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hasibzunair/MoNuSAC-ISBI-2020/HEAD/environment.yml -------------------------------------------------------------------------------- /experiment/2_extract_patches.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hasibzunair/MoNuSAC-ISBI-2020/HEAD/experiment/2_extract_patches.ipynb -------------------------------------------------------------------------------- /experiment/400.mat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hasibzunair/MoNuSAC-ISBI-2020/HEAD/experiment/400.mat -------------------------------------------------------------------------------- /experiment/401.mat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hasibzunair/MoNuSAC-ISBI-2020/HEAD/experiment/401.mat -------------------------------------------------------------------------------- /experiment/a.mat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hasibzunair/MoNuSAC-ISBI-2020/HEAD/experiment/a.mat -------------------------------------------------------------------------------- /experiment/a.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hasibzunair/MoNuSAC-ISBI-2020/HEAD/experiment/a.png -------------------------------------------------------------------------------- /experiment/a_mask.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hasibzunair/MoNuSAC-ISBI-2020/HEAD/experiment/a_mask.png -------------------------------------------------------------------------------- /experiment/b.mat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hasibzunair/MoNuSAC-ISBI-2020/HEAD/experiment/b.mat -------------------------------------------------------------------------------- /experiment/eda.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hasibzunair/MoNuSAC-ISBI-2020/HEAD/experiment/eda.ipynb -------------------------------------------------------------------------------- /experiment/m1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hasibzunair/MoNuSAC-ISBI-2020/HEAD/experiment/m1.png -------------------------------------------------------------------------------- /experiment/mask2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hasibzunair/MoNuSAC-ISBI-2020/HEAD/experiment/mask2.png -------------------------------------------------------------------------------- /experiment/x.tif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hasibzunair/MoNuSAC-ISBI-2020/HEAD/experiment/x.tif -------------------------------------------------------------------------------- /experiment/y_ep.tif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hasibzunair/MoNuSAC-ISBI-2020/HEAD/experiment/y_ep.tif -------------------------------------------------------------------------------- /experiment/y_ly.tif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hasibzunair/MoNuSAC-ISBI-2020/HEAD/experiment/y_ly.tif -------------------------------------------------------------------------------- /get_cell_count.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hasibzunair/MoNuSAC-ISBI-2020/HEAD/get_cell_count.ipynb -------------------------------------------------------------------------------- /gpu_test.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hasibzunair/MoNuSAC-ISBI-2020/HEAD/gpu_test.ipynb -------------------------------------------------------------------------------- /media/network.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hasibzunair/MoNuSAC-ISBI-2020/HEAD/media/network.png -------------------------------------------------------------------------------- /media/result1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hasibzunair/MoNuSAC-ISBI-2020/HEAD/media/result1.png -------------------------------------------------------------------------------- /media/result2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hasibzunair/MoNuSAC-ISBI-2020/HEAD/media/result2.png -------------------------------------------------------------------------------- /media/result3.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hasibzunair/MoNuSAC-ISBI-2020/HEAD/media/result3.png -------------------------------------------------------------------------------- /media/result4.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hasibzunair/MoNuSAC-ISBI-2020/HEAD/media/result4.png -------------------------------------------------------------------------------- /others/2_extract_patches.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hasibzunair/MoNuSAC-ISBI-2020/HEAD/others/2_extract_patches.ipynb -------------------------------------------------------------------------------- /others/3b_extract_patches_sliding.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hasibzunair/MoNuSAC-ISBI-2020/HEAD/others/3b_extract_patches_sliding.ipynb -------------------------------------------------------------------------------- /others/resulta.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hasibzunair/MoNuSAC-ISBI-2020/HEAD/others/resulta.png -------------------------------------------------------------------------------- /others/resultb.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hasibzunair/MoNuSAC-ISBI-2020/HEAD/others/resultb.png -------------------------------------------------------------------------------- /reference_notebooks/Binary_mask_generation.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hasibzunair/MoNuSAC-ISBI-2020/HEAD/reference_notebooks/Binary_mask_generation.ipynb -------------------------------------------------------------------------------- /reference_notebooks/Cell_counting.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hasibzunair/MoNuSAC-ISBI-2020/HEAD/reference_notebooks/Cell_counting.ipynb -------------------------------------------------------------------------------- /reference_notebooks/Panoptic Quality.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hasibzunair/MoNuSAC-ISBI-2020/HEAD/reference_notebooks/Panoptic Quality.ipynb -------------------------------------------------------------------------------- /reference_notebooks/n-ary_mask_generation.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hasibzunair/MoNuSAC-ISBI-2020/HEAD/reference_notebooks/n-ary_mask_generation.ipynb -------------------------------------------------------------------------------- /submission/README.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hasibzunair/MoNuSAC-ISBI-2020/HEAD/submission/README.txt -------------------------------------------------------------------------------- /submission/test_environment.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hasibzunair/MoNuSAC-ISBI-2020/HEAD/submission/test_environment.yml -------------------------------------------------------------------------------- /submission/the_great_backpropagator_testing_code.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hasibzunair/MoNuSAC-ISBI-2020/HEAD/submission/the_great_backpropagator_testing_code.py -------------------------------------------------------------------------------- /test_environment.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hasibzunair/MoNuSAC-ISBI-2020/HEAD/test_environment.yml --------------------------------------------------------------------------------