├── .gitignore ├── LICENSE.md ├── README.md ├── docs ├── jupyter notebook │ └── Run ShapeAE from notebook.ipynb ├── pre-post-processing │ ├── Calculate IoU .ipynb │ ├── Create cylinder and ellipse shapes.ipynb │ ├── Evaluate and plot features.ipynb │ ├── Extract Features from 2D Microscope.ipynb │ ├── Extract Features from 3D Shapes.ipynb │ ├── Extract features from 2D segmentation.ipynb │ └── Red blood cell random forest classification.ipynb └── sample │ ├── image │ ├── A_cell_clusters000604.tif │ ├── A_cell_clusters000605.tif │ ├── A_cell_clusters000606.tif │ ├── A_cell_clusters000607.tif │ ├── A_cell_clusters000608.tif │ ├── A_cell_clusters000609.tif │ ├── A_cell_clusters000610.tif │ ├── A_cell_clusters000611.tif │ ├── A_cell_clusters000612.tif │ ├── A_cell_clusters000613.tif │ ├── A_cell_clusters000614.tif │ ├── A_cell_clusters000615.tif │ ├── A_cell_clusters000616.tif │ ├── A_cell_clusters000617.tif │ ├── A_cell_clusters000618.tif │ ├── A_cell_clusters000619.tif │ ├── A_cell_clusters000620.tif │ ├── A_cell_clusters000621.tif │ ├── A_cell_clusters000622.tif │ ├── A_cell_clusters000623.tif │ ├── A_cell_clusters000624.tif │ ├── A_cell_clusters000625.tif │ ├── A_cell_clusters000626.tif │ ├── A_cell_clusters000627.tif │ ├── A_cell_clusters000628.tif │ ├── A_cell_clusters000629.tif │ ├── A_cell_clusters000630.tif │ ├── A_cell_clusters000631.tif │ ├── A_cell_clusters000632.tif │ ├── A_cell_clusters000633.tif │ ├── A_cell_clusters000634.tif │ ├── A_cell_clusters000635.tif │ ├── A_cell_clusters000636.tif │ ├── A_cell_clusters000637.tif │ ├── A_cell_clusters000638.tif │ ├── A_cell_clusters000639.tif │ ├── A_cell_clusters000640.tif │ ├── A_cell_clusters000641.tif │ ├── A_cell_clusters000642.tif │ ├── A_cell_clusters000643.tif │ ├── A_cell_clusters000644.tif │ ├── A_cell_clusters000645.tif │ ├── A_cell_clusters000646.tif │ ├── A_cell_clusters000647.tif │ ├── A_cell_clusters000648.tif │ ├── A_cell_clusters000649.tif │ ├── A_cell_clusters000650.tif │ ├── A_cell_clusters000651.tif │ ├── A_cell_clusters000652.tif │ ├── A_cell_clusters000653.tif │ ├── A_cell_clusters000654.tif │ ├── A_cell_clusters000655.tif │ ├── A_cell_clusters000656.tif │ ├── A_cell_clusters000657.tif │ ├── A_cell_clusters000658.tif │ ├── A_cell_clusters000659.tif │ ├── A_cell_clusters000660.tif │ ├── A_cell_clusters000661.tif │ ├── A_cell_clusters000662.tif │ ├── A_cell_clusters000663.tif │ ├── A_cell_clusters000664.tif │ ├── A_cell_clusters000665.tif │ ├── A_cell_clusters000666.tif │ ├── A_cell_clusters000667.tif │ ├── A_cell_clusters000668.tif │ ├── A_cell_clusters000669.tif │ ├── A_cell_clusters000670.tif │ ├── A_cell_clusters000671.tif │ ├── A_cell_clusters000672.tif │ ├── B_keratocytes000673.tif │ ├── B_keratocytes000674.tif │ ├── B_keratocytes000675.tif │ ├── B_keratocytes000676.tif │ ├── B_keratocytes000677.tif │ ├── B_keratocytes000678.tif │ ├── B_keratocytes000679.tif │ ├── B_keratocytes000680.tif │ ├── B_keratocytes000681.tif │ ├── B_keratocytes000682.tif │ ├── B_keratocytes000683.tif │ ├── B_keratocytes000684.tif │ ├── B_keratocytes000685.tif │ ├── B_keratocytes000686.tif │ ├── B_keratocytes000687.tif │ ├── B_keratocytes000688.tif │ ├── B_keratocytes000689.tif │ ├── B_keratocytes000690.tif │ ├── B_keratocytes000691.tif │ ├── B_keratocytes000692.tif │ ├── B_keratocytes000693.tif │ ├── B_keratocytes000694.tif │ ├── B_keratocytes000695.tif │ ├── B_keratocytes000696.tif │ ├── B_keratocytes000697.tif │ ├── B_keratocytes000698.tif │ ├── B_keratocytes000699.tif │ ├── B_keratocytes000700.tif │ ├── B_keratocytes000701.tif │ ├── B_keratocytes000702.tif │ ├── B_keratocytes000703.tif │ ├── C_knizocytes000704.tif │ ├── C_knizocytes000705.tif │ ├── C_knizocytes000706.tif │ ├── C_knizocytes000707.tif │ ├── C_knizocytes000708.tif │ ├── C_knizocytes000709.tif │ ├── C_knizocytes000710.tif │ ├── C_knizocytes000711.tif │ ├── C_knizocytes000712.tif │ ├── C_knizocytes000713.tif │ ├── C_knizocytes000714.tif │ ├── C_knizocytes000715.tif │ ├── C_knizocytes000716.tif │ ├── C_knizocytes000717.tif │ ├── C_knizocytes000718.tif │ ├── C_knizocytes000719.tif │ ├── C_knizocytes000720.tif │ ├── C_knizocytes000721.tif │ ├── C_knizocytes000722.tif │ ├── C_knizocytes000723.tif │ ├── C_knizocytes000724.tif │ ├── C_knizocytes000725.tif │ ├── C_knizocytes000726.tif │ ├── D_multilobate_cells000727.tif │ ├── D_multilobate_cells000728.tif │ ├── D_multilobate_cells000729.tif │ ├── D_multilobate_cells000730.tif │ ├── D_multilobate_cells000731.tif │ ├── D_multilobate_cells000732.tif │ ├── D_multilobate_cells000733.tif │ ├── D_multilobate_cells000734.tif │ ├── D_multilobate_cells000735.tif │ ├── D_multilobate_cells000736.tif │ ├── D_multilobate_cells000737.tif │ └── D_multilobate_cells000738.tif │ ├── mask │ ├── A_cell_clusters000604.tif │ ├── A_cell_clusters000605.tif │ ├── A_cell_clusters000606.tif │ ├── A_cell_clusters000607.tif │ ├── A_cell_clusters000608.tif │ ├── A_cell_clusters000609.tif │ ├── A_cell_clusters000610.tif │ ├── A_cell_clusters000611.tif │ ├── A_cell_clusters000612.tif │ ├── A_cell_clusters000613.tif │ ├── A_cell_clusters000614.tif │ ├── A_cell_clusters000615.tif │ ├── A_cell_clusters000616.tif │ ├── A_cell_clusters000617.tif │ ├── A_cell_clusters000618.tif │ ├── A_cell_clusters000619.tif │ ├── A_cell_clusters000620.tif │ ├── A_cell_clusters000621.tif │ ├── A_cell_clusters000622.tif │ ├── A_cell_clusters000623.tif │ ├── A_cell_clusters000624.tif │ ├── A_cell_clusters000625.tif │ ├── A_cell_clusters000626.tif │ ├── A_cell_clusters000627.tif │ ├── A_cell_clusters000628.tif │ ├── A_cell_clusters000629.tif │ ├── A_cell_clusters000630.tif │ ├── A_cell_clusters000631.tif │ ├── A_cell_clusters000632.tif │ ├── A_cell_clusters000633.tif │ ├── A_cell_clusters000634.tif │ ├── A_cell_clusters000635.tif │ ├── A_cell_clusters000636.tif │ ├── A_cell_clusters000637.tif │ ├── A_cell_clusters000638.tif │ ├── A_cell_clusters000639.tif │ ├── A_cell_clusters000640.tif │ ├── A_cell_clusters000641.tif │ ├── A_cell_clusters000642.tif │ ├── A_cell_clusters000643.tif │ ├── A_cell_clusters000644.tif │ ├── A_cell_clusters000645.tif │ ├── A_cell_clusters000646.tif │ ├── A_cell_clusters000647.tif │ ├── A_cell_clusters000648.tif │ ├── A_cell_clusters000649.tif │ ├── A_cell_clusters000650.tif │ ├── A_cell_clusters000651.tif │ ├── A_cell_clusters000652.tif │ ├── A_cell_clusters000653.tif │ ├── A_cell_clusters000654.tif │ ├── A_cell_clusters000655.tif │ ├── A_cell_clusters000656.tif │ ├── A_cell_clusters000657.tif │ ├── A_cell_clusters000658.tif │ ├── A_cell_clusters000659.tif │ ├── A_cell_clusters000660.tif │ ├── A_cell_clusters000661.tif │ ├── A_cell_clusters000662.tif │ ├── A_cell_clusters000663.tif │ ├── A_cell_clusters000664.tif │ ├── A_cell_clusters000665.tif │ ├── A_cell_clusters000666.tif │ ├── A_cell_clusters000667.tif │ ├── A_cell_clusters000668.tif │ ├── A_cell_clusters000669.tif │ ├── A_cell_clusters000670.tif │ ├── A_cell_clusters000671.tif │ ├── A_cell_clusters000672.tif │ ├── B_keratocytes000673.tif │ ├── B_keratocytes000674.tif │ ├── B_keratocytes000675.tif │ ├── B_keratocytes000676.tif │ ├── B_keratocytes000677.tif │ ├── B_keratocytes000678.tif │ ├── B_keratocytes000679.tif │ ├── B_keratocytes000680.tif │ ├── B_keratocytes000681.tif │ ├── B_keratocytes000682.tif │ ├── B_keratocytes000683.tif │ ├── B_keratocytes000684.tif │ ├── B_keratocytes000685.tif │ ├── B_keratocytes000686.tif │ ├── B_keratocytes000687.tif │ ├── B_keratocytes000688.tif │ ├── B_keratocytes000689.tif │ ├── B_keratocytes000690.tif │ ├── B_keratocytes000691.tif │ ├── B_keratocytes000692.tif │ ├── B_keratocytes000693.tif │ ├── B_keratocytes000694.tif │ ├── B_keratocytes000695.tif │ ├── B_keratocytes000696.tif │ ├── B_keratocytes000697.tif │ ├── B_keratocytes000698.tif │ ├── B_keratocytes000699.tif │ ├── B_keratocytes000700.tif │ ├── B_keratocytes000701.tif │ ├── B_keratocytes000702.tif │ ├── B_keratocytes000703.tif │ ├── C_knizocytes000704.tif │ ├── C_knizocytes000705.tif │ ├── C_knizocytes000706.tif │ ├── C_knizocytes000707.tif │ ├── C_knizocytes000708.tif │ ├── C_knizocytes000709.tif │ ├── C_knizocytes000710.tif │ ├── C_knizocytes000711.tif │ ├── C_knizocytes000712.tif │ ├── C_knizocytes000713.tif │ ├── C_knizocytes000714.tif │ ├── C_knizocytes000715.tif │ ├── C_knizocytes000716.tif │ ├── C_knizocytes000717.tif │ ├── C_knizocytes000718.tif │ ├── C_knizocytes000719.tif │ ├── C_knizocytes000720.tif │ ├── C_knizocytes000721.tif │ ├── C_knizocytes000722.tif │ ├── C_knizocytes000723.tif │ ├── C_knizocytes000724.tif │ ├── C_knizocytes000725.tif │ ├── C_knizocytes000726.tif │ ├── D_multilobate_cells000727.tif │ ├── D_multilobate_cells000728.tif │ ├── D_multilobate_cells000729.tif │ ├── D_multilobate_cells000730.tif │ ├── D_multilobate_cells000731.tif │ ├── D_multilobate_cells000732.tif │ ├── D_multilobate_cells000733.tif │ ├── D_multilobate_cells000734.tif │ ├── D_multilobate_cells000735.tif │ ├── D_multilobate_cells000736.tif │ ├── D_multilobate_cells000737.tif │ └── D_multilobate_cells000738.tif │ ├── obj │ ├── A_cell_clusters000604.tif │ ├── A_cell_clusters000605.tif │ ├── A_cell_clusters000606.tif │ ├── A_cell_clusters000607.tif │ ├── A_cell_clusters000608.tif │ ├── A_cell_clusters000609.tif │ ├── A_cell_clusters000610.tif │ ├── A_cell_clusters000611.tif │ ├── A_cell_clusters000612.tif │ ├── A_cell_clusters000613.tif │ ├── A_cell_clusters000614.tif │ ├── A_cell_clusters000615.tif │ ├── A_cell_clusters000616.tif │ ├── A_cell_clusters000617.tif │ ├── A_cell_clusters000618.tif │ ├── A_cell_clusters000619.tif │ ├── A_cell_clusters000620.tif │ ├── A_cell_clusters000621.tif │ ├── A_cell_clusters000622.tif │ ├── A_cell_clusters000623.tif │ ├── A_cell_clusters000624.tif │ ├── A_cell_clusters000625.tif │ ├── A_cell_clusters000626.tif │ ├── A_cell_clusters000627.tif │ ├── A_cell_clusters000628.tif │ ├── A_cell_clusters000629.tif │ ├── A_cell_clusters000630.tif │ ├── A_cell_clusters000631.tif │ ├── A_cell_clusters000632.tif │ ├── A_cell_clusters000633.tif │ ├── A_cell_clusters000634.tif │ ├── A_cell_clusters000635.tif │ ├── A_cell_clusters000636.tif │ ├── A_cell_clusters000637.tif │ ├── A_cell_clusters000638.tif │ ├── A_cell_clusters000639.tif │ ├── A_cell_clusters000640.tif │ ├── A_cell_clusters000641.tif │ ├── A_cell_clusters000642.tif │ ├── A_cell_clusters000643.tif │ ├── A_cell_clusters000644.tif │ ├── A_cell_clusters000645.tif │ ├── A_cell_clusters000646.tif │ ├── A_cell_clusters000647.tif │ ├── A_cell_clusters000648.tif │ ├── A_cell_clusters000649.tif │ ├── A_cell_clusters000650.tif │ ├── A_cell_clusters000651.tif │ ├── A_cell_clusters000652.tif │ ├── A_cell_clusters000653.tif │ ├── A_cell_clusters000654.tif │ ├── A_cell_clusters000655.tif │ ├── A_cell_clusters000656.tif │ ├── A_cell_clusters000657.tif │ ├── A_cell_clusters000658.tif │ ├── A_cell_clusters000659.tif │ ├── A_cell_clusters000660.tif │ ├── A_cell_clusters000661.tif │ ├── A_cell_clusters000662.tif │ ├── A_cell_clusters000663.tif │ ├── A_cell_clusters000664.tif │ ├── A_cell_clusters000665.tif │ ├── A_cell_clusters000666.tif │ ├── A_cell_clusters000667.tif │ ├── A_cell_clusters000668.tif │ ├── A_cell_clusters000669.tif │ ├── A_cell_clusters000670.tif │ ├── A_cell_clusters000671.tif │ ├── A_cell_clusters000672.tif │ ├── B_keratocytes000673.tif │ ├── B_keratocytes000674.tif │ ├── B_keratocytes000675.tif │ ├── B_keratocytes000676.tif │ ├── B_keratocytes000677.tif │ ├── B_keratocytes000678.tif │ ├── B_keratocytes000679.tif │ ├── B_keratocytes000680.tif │ ├── B_keratocytes000681.tif │ ├── B_keratocytes000682.tif │ ├── B_keratocytes000683.tif │ ├── B_keratocytes000684.tif │ ├── B_keratocytes000685.tif │ ├── B_keratocytes000686.tif │ ├── B_keratocytes000687.tif │ ├── B_keratocytes000688.tif │ ├── B_keratocytes000689.tif │ ├── B_keratocytes000690.tif │ ├── B_keratocytes000691.tif │ ├── B_keratocytes000692.tif │ ├── B_keratocytes000693.tif │ ├── B_keratocytes000694.tif │ ├── B_keratocytes000695.tif │ ├── B_keratocytes000696.tif │ ├── B_keratocytes000697.tif │ ├── B_keratocytes000698.tif │ ├── B_keratocytes000699.tif │ ├── B_keratocytes000700.tif │ ├── B_keratocytes000701.tif │ ├── B_keratocytes000702.tif │ ├── B_keratocytes000703.tif │ ├── C_knizocytes000704.tif │ ├── C_knizocytes000705.tif │ ├── C_knizocytes000706.tif │ ├── C_knizocytes000707.tif │ ├── C_knizocytes000708.tif │ ├── C_knizocytes000709.tif │ ├── C_knizocytes000710.tif │ ├── C_knizocytes000711.tif │ ├── C_knizocytes000712.tif │ ├── C_knizocytes000713.tif │ ├── C_knizocytes000714.tif │ ├── C_knizocytes000715.tif │ ├── C_knizocytes000716.tif │ ├── C_knizocytes000717.tif │ ├── C_knizocytes000718.tif │ ├── C_knizocytes000719.tif │ ├── C_knizocytes000720.tif │ ├── C_knizocytes000721.tif │ ├── C_knizocytes000722.tif │ ├── C_knizocytes000723.tif │ ├── C_knizocytes000724.tif │ ├── C_knizocytes000725.tif │ ├── C_knizocytes000726.tif │ ├── D_multilobate_cells000727.tif │ ├── D_multilobate_cells000728.tif │ ├── D_multilobate_cells000729.tif │ ├── D_multilobate_cells000730.tif │ ├── D_multilobate_cells000731.tif │ ├── D_multilobate_cells000732.tif │ ├── D_multilobate_cells000733.tif │ ├── D_multilobate_cells000734.tif │ ├── D_multilobate_cells000735.tif │ ├── D_multilobate_cells000736.tif │ ├── D_multilobate_cells000737.tif │ └── D_multilobate_cells000738.tif │ └── params.json ├── figures ├── SHAPR_architecture.png ├── SHAPR_logo.png ├── SHAPR_topology.png └── youtube.png ├── pyproject.toml ├── requirements.txt ├── setup.py └── shapr ├── __init__.py ├── __pycache__ ├── __init__.cpython-38.pyc ├── _settings.cpython-38.pyc ├── data_generator.cpython-38.pyc ├── evaluate.cpython-38.pyc ├── main.cpython-38.pyc ├── metrics.cpython-38.pyc ├── model.cpython-38.pyc └── utils.cpython-38.pyc ├── _settings.py ├── config ├── 3d-cell-culture-0D.json ├── 3d-cell-culture-1D.json ├── 3d-cell-culture-2D.json ├── debug.json ├── red-blood-cell-0D.json ├── red-blood-cell-1D.json ├── red-blood-cell-2D.json ├── red-blood-cell.json ├── small-0D.json ├── small-1D.json └── small-2D.json ├── data_generator.py ├── main.py ├── metrics.py ├── model.py ├── params.json ├── run.py ├── run.sh ├── run_train_script.py ├── scripts ├── analyse_interpolation.py ├── analyse_wandb.py ├── calculate_persistence_diagrams.py ├── evaluation.py ├── evaluation │ ├── nuclei.json │ └── red-blood-cell.json ├── make_gallery.py ├── tif_to_nrrd.py ├── tif_to_x3d.py └── viewer.py ├── sweep.sh ├── sweeps ├── debug.yaml ├── red-blood-cell-baseline.yaml ├── red-blood-cell-d0.yaml ├── red-blood-cell-d1.yaml ├── red-blood-cell-d2.yaml ├── red-blood-cell.yaml ├── small.yaml ├── topology-adversarial.yaml ├── topology-all-dims.yaml ├── topology-big-lambda.yaml ├── topology-superlevel.yaml └── topology.yaml ├── tests ├── test_data │ ├── images │ │ ├── A_cell_clusters000604.tif │ │ ├── A_cell_clusters000605.tif │ │ └── A_cell_clusters000606.tif │ └── json │ │ └── settings_testing_params.json └── unit_tests │ ├── test_date_generator.py │ ├── test_metric.py │ ├── test_model.py │ ├── test_settings.py │ └── test_utils.py └── utils.py /.gitignore: -------------------------------------------------------------------------------- 1 | lightning_logs/ 2 | __pycache__/ 3 | 4 | *~ 5 | *.lock 6 | *.swp 7 | 8 | .idea/ 9 | -------------------------------------------------------------------------------- /LICENSE.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrlab/SHAPR_torch/HEAD/LICENSE.md -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrlab/SHAPR_torch/HEAD/README.md -------------------------------------------------------------------------------- /docs/jupyter notebook /Run ShapeAE from notebook.ipynb: 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