├── .editorconfig ├── .github ├── ISSUE_TEMPLATE │ ├── bug_report.md │ └── feature_request.md ├── PULL_REQUEST_TEMPLATE.md └── workflows │ ├── build-main.yml │ └── test-and-lint.yml ├── .gitignore ├── CODE_OF_CONDUCT.md ├── CONTRIBUTING.md ├── LICENSE ├── MANIFEST.in ├── Makefile ├── README.md ├── docker ├── amd64 │ ├── .dockerignore │ ├── Dockerfile │ └── run_container.sh ├── arm64 │ ├── .dockerignore │ ├── Dockerfile │ └── run_container.sh ├── cuda │ ├── .dockerignore │ ├── Dockerfile │ └── run_container.sh └── tutorial.md ├── docs ├── Makefile ├── conf.py ├── contributing.rst ├── index.rst ├── installation.rst └── make.bat ├── mmv_im2im ├── __init__.py ├── bin │ ├── __init__.py │ └── run_im2im.py ├── configs │ ├── __init__.py │ ├── config_base.py │ ├── preset_inference_labelfree_3d.yaml │ ├── preset_inference_pix2pixhd_2d.yaml │ ├── preset_train_cyclegan_2d.yaml │ ├── preset_train_cyclegan_3d.yaml │ ├── preset_train_embedseg_2d.yaml │ ├── preset_train_embedseg_3d.yaml │ ├── preset_train_labelfree_2d.yaml │ ├── preset_train_labelfree_3d.yaml │ ├── preset_train_modality_transfer_3d.yaml │ ├── preset_train_pix2pixhd_2d.yaml │ ├── preset_train_pix2pixhd_3d.yaml │ ├── preset_train_semanticseg_2d.yaml │ └── preset_train_semanticseg_3d.yaml ├── data_modules │ ├── __init__.py │ └── data_loader_basic.py ├── map_extractor.py ├── models │ ├── __init__.py │ ├── nets │ │ ├── BranchedERFNet_2d.py │ │ ├── BranchedERFNet_3d.py │ │ ├── ProbUnet.py │ │ ├── SA_2d.py │ │ ├── __init__.py │ │ ├── deeplabv3_2d.py │ │ ├── erfnet.py │ │ ├── erfnet_3d.py │ │ ├── fnet_nn_2d.py │ │ ├── fnet_nn_3d.py │ │ └── gans.py │ ├── pl_FCN.py │ ├── pl_ProbUnet.py │ ├── pl_cyclegan.py │ ├── pl_embedseg.py │ └── pl_pix2pix.py ├── postprocessing │ ├── __init__.py │ ├── basic_collection.py │ └── embedseg_cluster.py ├── preprocessing │ ├── __init__.py │ └── transforms.py ├── proj_tester.py ├── proj_trainer.py ├── tests │ ├── __init__.py │ └── test_dummy.py └── utils │ ├── __init__.py │ ├── basic_losses.py │ ├── connectivity_loss.py │ ├── elbo_loss.py │ ├── embedding_loss.py │ ├── embedseg_utils.py │ ├── for_transform.py │ ├── fourier.py │ ├── fractal_layers.py │ ├── gan_losses.py │ ├── gan_utils.py │ ├── gdl_reg.py │ ├── lovasz_losses.py │ ├── metrics.py │ ├── misc.py │ ├── model_utils.py │ ├── multi_pred.py │ ├── topological_loss.py │ ├── urcentainity_extractor.py │ └── utils.py ├── paper_configs ├── denoising_3d_inference.yaml ├── denoising_3d_train.yaml ├── instance_seg_2d_inference.yaml ├── instance_seg_2d_train.yaml ├── instance_seg_3d_inference_bf.yaml ├── instance_seg_3d_inference_fbl.yaml ├── instance_seg_3d_inference_fluo.yaml ├── instance_seg_3d_train_bf_finetune.yaml ├── instance_seg_3d_train_bf_pretrain.yaml ├── instance_seg_3d_train_fbl_finetune.yaml ├── instance_seg_3d_train_fbl_pretrain.yaml ├── instance_seg_3d_train_fluo_finetune.yaml ├── instance_seg_3d_train_fluo_pretrain.yaml ├── labelfree_2d_FCN_inference.yaml ├── labelfree_2d_FCN_train.yaml ├── labelfree_3d_FCN_inference.yaml ├── labelfree_3d_FCN_train.yaml ├── labelfree_3d_pix2pix_finetune.yaml ├── labelfree_3d_pix2pix_inference.yaml ├── labelfree_3d_pix2pix_pretrain.yaml ├── labelfree_3d_pix2pix_train.yaml ├── modality_transfer_3d_inference.yaml ├── modality_transfer_3d_train.yaml ├── multiplex_inference.yaml ├── multiplex_train.yaml ├── prepare_data │ ├── denoising.ipynb │ ├── instance_seg_2d.ipynb │ ├── instance_seg_3d.ipynb │ ├── labelfree_2d.ipynb │ ├── labelfree_3d.ipynb │ ├── modaity_transfer.ipynb │ ├── multiplex.ipynb │ ├── semantic_seg_2d.ipynb │ ├── semantic_seg_3d.ipynb │ ├── sythetic_gen_2d.ipynb │ ├── sythetic_gen_3d.ipynb │ ├── unsupervised_seg_2d.ipynb │ └── unsupervised_seg_3d.ipynb ├── semantic_seg_2d_inference.yaml ├── semantic_seg_2d_train.yaml ├── semantic_seg_3d_inference.yaml ├── semantic_seg_3d_train.yaml ├── synthetic_2d_supervised_inference.yaml ├── synthetic_2d_supervised_train.yaml ├── synthetic_2d_unsupervised_inference.yaml ├── synthetic_2d_unsupervised_train.yaml ├── synthetic_3d_supervised_inference.yaml ├── synthetic_3d_supervised_train.yaml ├── synthetic_3d_unsupervised_inference.yaml ├── synthetic_3d_unsupervised_train.yaml ├── unsupervised_seg_2d_inference.yaml ├── unsupervised_seg_2d_train.yaml ├── unsupervised_seg_3d_inference.yaml └── unsupervised_seg_3d_train.yaml ├── pyproject.toml ├── script ├── generate_synthetic_data.py └── pull_labelfree_sample_data.py ├── setup.cfg ├── tox.ini └── tutorials ├── FAQ.md ├── colab └── labelfree_2d.ipynb ├── docker ├── media │ ├── image1.png │ ├── image2.png │ ├── image3.png │ ├── image4.png │ ├── image5.png │ ├── image6.png │ └── image7.png └── mmv_im2im_docker_tutorial.md ├── example_by_use_case.md ├── how_to_understand_boilerplates.md ├── how_to_understand_config.md ├── note_embedseg.md └── quick_start.md /.editorconfig: -------------------------------------------------------------------------------- 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