├── LICENSE ├── README.md ├── dataset ├── 3d │ └── reconstruct3d.py ├── README.md ├── classify_patches.py ├── patchify2d.py ├── patchify3d.py ├── preprocess │ ├── binvol.py │ ├── cleanup2d.py │ ├── mrc2byte.py │ └── vid2stack.py ├── scraping │ ├── crop_rois_from_volume.py │ ├── h01_download.py │ ├── ngff_datasets.csv │ └── ngff_download.py └── train_patch_classifier.py ├── environment.yml ├── evaluation ├── README.md ├── Snakefile ├── benchmark_configs │ ├── all_mito.yaml │ ├── cremi.yaml │ ├── guay.yaml │ ├── kasthuri_pp.yaml │ ├── lucchi_pp.yaml │ ├── perez_lyso.yaml │ ├── perez_mito.yaml │ ├── perez_nuclei.yaml │ ├── perez_nucleoli.yaml │ └── urocell.yaml ├── finetune.py ├── inference2d.py ├── inference3d.py ├── inference_mixed.py ├── resources │ ├── __init__.py │ ├── data.py │ ├── metrics.py │ ├── train_utils.py │ └── utils.py ├── setup_benchmarks │ ├── create_patches.py │ ├── create_slices.py │ ├── download_benchmarks.sh │ └── setup_data.py ├── snakefile_dq └── snakefile_wq ├── images ├── benchmarks.png ├── cem500k.jpg └── description.png ├── notebooks ├── _corrector.py ├── _helpers.py ├── check_benchmarks.ipynb ├── deduplication_and_filtering.ipynb ├── example_data │ ├── correlation │ │ ├── images │ │ │ ├── canalicular_channels.png │ │ │ ├── er.png │ │ │ ├── mitochondria1.png │ │ │ ├── mitochondria2.png │ │ │ ├── mitochondria3.png │ │ │ ├── mitochondria4.png │ │ │ ├── mitochondria5.png │ │ │ └── nuclei.png │ │ └── masks │ │ │ ├── canalicular_channels.png │ │ │ ├── er.png │ │ │ ├── mitochondria1.png │ │ │ ├── mitochondria2.png │ │ │ ├── mitochondria3.png │ │ │ ├── mitochondria4.png │ │ │ ├── mitochondria5.png │ │ │ └── nuclei.png │ ├── deduplication │ │ └── filter_column.tif │ └── occlusion │ │ ├── example0.tiff │ │ ├── example1.tiff │ │ ├── example2.tiff │ │ ├── example3.tiff │ │ ├── example4.tiff │ │ ├── example5.tiff │ │ ├── example6.tiff │ │ ├── example7.tiff │ │ ├── example8.tiff │ │ └── example9.tiff ├── featuremap_correlation.ipynb ├── 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