├── .github ├── doc_env.yaml ├── release_config.yaml └── workflows │ ├── build_docs.yaml │ ├── build_installers.yaml │ ├── release_drafter.yaml │ └── test.yaml ├── .gitignore ├── LICENSE ├── MANIFEST.in ├── README.md ├── RELEASE_OVERVIEW.md ├── deployment ├── construct_ubuntu-latest.yaml ├── construct_windows-latest.yaml ├── env.yaml ├── post_install.bat ├── version_getter.py ├── windows_menu.json └── windows_menu_setup.py ├── development ├── .gitignore ├── README.md ├── annotator_3d_tiled.py ├── annotator_tracking_tiled.py ├── annotators_in_image_series.py ├── benchmark.py ├── check_3d_model.py ├── check_data_count.py ├── check_omero_connection.py ├── instance_segmentation.py ├── instance_segmentation_3d.py ├── promptable_segmentation.py ├── support │ └── train_cell_fluo_embl_alm.py └── tracking.py ├── doc ├── annotation_tools.md ├── band.md ├── bioimageio │ ├── em_organelles_v2.md │ ├── em_organelles_v4.md │ ├── histopathology_v1.md │ ├── inference_parameters.md │ ├── lm_v2.md │ ├── lm_v3.md │ └── lm_v4.md ├── cli_tools.md ├── contributing.md ├── data_submission.md ├── datasets │ ├── em_organelles_v2.md │ ├── em_organelles_v4.md │ ├── lm_v2.md │ ├── lm_v3.md │ └── lm_v4.md ├── deprecated │ └── development.md ├── faq.md ├── finetuned_models.md ├── images │ ├── 2d-annotator-flow.png │ ├── 2d-annotator-menu.png │ ├── 3d-annotator-menu.png │ ├── em_comparison.png │ ├── finetuning-menu.png │ ├── lm_comparison.png │ ├── model-type-selector-old.png │ ├── model-type-selector.png │ ├── napari-plugin.png │ ├── object-classifier.png │ ├── series-menu.png │ └── tracking-annotator-menu.png ├── installation.md ├── logo │ ├── logo.ico │ ├── logo.jpg │ ├── logo.png │ ├── logo_and_text.jpg │ └── logo_and_text.png ├── python_library.md └── start_page.md ├── environment.yaml ├── examples ├── README.md ├── annotator_2d.py ├── annotator_3d.py ├── annotator_tracking.py ├── automatic_segmentation.py ├── automatic_tracking.py ├── bioimageio │ ├── export_model_for_bioengine.py │ └── export_model_for_bioimageio.py ├── finetuning │ ├── .gitignore │ ├── README.md │ ├── annotator_with_finetuned_model.py │ └── finetune_hela.py ├── image_series_annotator.py ├── object_classifier.py ├── quick_start.py └── use_as_library │ └── instance_segmentation.py ├── finetuning ├── README.md ├── evaluation │ ├── .gitignore │ ├── README.md │ ├── cellpose_baseline.py │ ├── cellpose_baseline.sbatch │ ├── evaluate_amg.py │ ├── evaluate_instance_segmentation.py │ ├── experiments │ │ └── run_updated_unetr_evaluations.py │ ├── explorative_experiments.py │ ├── iterative_prompting.py │ ├── mitonet_baseline.py │ ├── precompute_embeddings.py │ ├── preprocess_datasets.py │ ├── run_all_evaluations.py │ ├── submit_all_evaluation.py │ ├── time-benchmarking.md │ └── util.py ├── generalists │ ├── README.md │ ├── outdated │ │ ├── compile_results.py │ │ ├── create_tissuenet_data.py │ │ ├── evaluate_generalist.py │ │ ├── evaluate_generalist.sbatch │ │ ├── evaluate_training_evolution.py │ │ ├── evaluate_training_evolution.sbatch │ │ ├── precompute_prompts.py │ │ └── util.py │ └── training │ │ ├── README.md │ │ ├── electron_microscopy │ │ ├── boundaries │ │ │ ├── obtain_boundaries_em_datasets.py │ │ │ └── train_boundaries_em_generalist.py │ │ └── mito_nuc │ │ │ ├── obtain_mito_nuc_em_datasets.py │ │ │ └── train_mito_nuc_em_generalist.py │ │ ├── histopathology │ │ ├── obtain_hp_datasets.py │ │ ├── train_histopathology_generalist.py │ │ └── train_model.sbatch │ │ └── light_microscopy │ │ ├── obtain_lm_datasets.py │ │ └── train_lm_generalist.py ├── livecell_evaluation.py ├── livecell_finetuning.py ├── livecell_inference.py ├── run_all_finetuning.py └── specialists │ ├── README.md │ ├── outdated │ └── livecell │ │ ├── README.md │ │ ├── evaluation │ │ ├── evaluate_amg.py │ │ ├── evaluate_amg.sbatch │ │ ├── evaluate_instance_segmentation.py │ │ ├── evaluate_instance_segmentation.sbatch │ │ ├── iterative_prompting.py │ │ ├── iterative_prompting.sbatch │ │ ├── old │ │ │ ├── evaluation.py │ │ │ ├── evaluation.sbatch │ │ │ ├── inference.py │ │ │ ├── inference.sbatch │ │ │ ├── precompute_prompts.py │ │ │ └── precompute_prompts.sbatch │ │ ├── precompute_embeddings.py │ │ ├── precompute_embeddings.sbatch │ │ ├── submit_evaluation.py │ │ ├── train_grid_search_eval.py │ │ └── util.py │ │ ├── experiments │ │ ├── README.md │ │ ├── run_experiment_evaluation.py │ │ └── submit_experiment_finetuning.py │ │ ├── joint_training │ │ ├── grid_search_train.py │ │ ├── joint_finetuning.py │ │ ├── results.md │ │ ├── run_parameter_evaluation.py │ │ └── unetr_inference.py │ │ └── partial_finetuning │ │ ├── evaluate_partially_finetuned.py │ │ ├── evaluate_partially_finetuned.sbatch │ │ └── submit_partial_finetuning.py │ ├── resource-efficient │ ├── .gitignore │ ├── README.md │ ├── check_training_times.py │ ├── covid_if_finetuning.py │ ├── plot_experiments.py │ ├── run_evaluations.py │ └── run_resource_efficient_finetuning.py │ └── training │ ├── electron_microscopy │ ├── boundaries │ │ └── cremi_finetuning.py │ └── organelles │ │ └── asem_finetuning.py │ ├── histopathology │ ├── create_dataloaders.py │ └── pannuke_finetuning.py │ └── light_microscopy │ ├── deepbacs_finetuning.py │ ├── dynamicnuclearnet_finetuning.py │ ├── livecell_multi_gpu_finetuning.py │ ├── neurips_cellseg_finetuning.py │ ├── plantseg_root_finetuning.py │ └── tissuenet_finetuning.py ├── micro_sam ├── __init__.py ├── __version__.py ├── _model_settings.py ├── _test_util.py ├── _vendored.py ├── automatic_segmentation.py ├── bioimageio │ ├── __init__.py │ ├── bioengine_export.py │ ├── model_export.py │ └── predictor_adaptor.py ├── evaluation │ ├── __init__.py │ ├── benchmark_datasets.py │ ├── evaluation.py │ ├── experiments.py │ ├── inference.py │ ├── instance_segmentation.py │ ├── livecell.py │ ├── model_comparison.py │ └── multi_dimensional_segmentation.py ├── inference.py ├── instance_segmentation.py ├── models │ ├── __init__.py │ ├── build_sam.py │ ├── peft_sam.py │ ├── sam_3d_wrapper.py │ └── simple_sam_3d_wrapper.py ├── multi_dimensional_segmentation.py ├── napari.yaml ├── object_classification.py ├── precompute_state.py ├── prompt_based_segmentation.py ├── prompt_generators.py ├── sam_annotator │ ├── __init__.py │ ├── _annotator.py │ ├── _state.py │ ├── _tooltips.py │ ├── _widgets.py │ ├── annotator_2d.py │ ├── annotator_3d.py │ ├── annotator_tracking.py │ ├── image_series_annotator.py │ ├── object_classifier.py │ ├── training_ui.py │ └── util.py ├── sample_data.py ├── training │ ├── __init__.py │ ├── joint_sam_trainer.py │ ├── sam_trainer.py │ ├── semantic_sam_trainer.py │ ├── simple_sam_trainer.py │ ├── trainable_sam.py │ ├── training.py │ └── util.py ├── util.py └── visualization.py ├── notebooks ├── README.md ├── automatic_segmentation.ipynb ├── inference_and_evaluation.ipynb ├── quick_start.ipynb └── sam_finetuning.ipynb ├── pyproject.toml ├── requirements-dev.txt ├── scripts ├── .gitignore ├── for_benchmarking_ais │ ├── common.py │ ├── submit_scripts.py │ ├── train_semanticsam.py │ ├── train_unet.py │ └── train_unetr.py ├── miscellanous │ └── 2d_ais_with_tiling.py ├── model_export │ ├── .gitignore │ ├── README.md │ ├── covers │ │ ├── cover_em.png │ │ └── cover_lm.png │ ├── export_histopathology_models.py │ ├── export_models.py │ ├── export_specialist_models.py │ ├── get_dois.py │ ├── models.py │ ├── publish_models.py │ └── stage_models.py ├── plotting │ ├── .gitignore │ ├── README.md │ ├── for_paper │ │ ├── plot_ais_ablation.py │ │ ├── plot_all_evaluation.py │ │ ├── plot_explorative_experiments.py │ │ ├── plot_fig6.py │ │ ├── plot_fig_s9.py │ │ ├── plot_inference_time.py │ │ ├── plot_limited_data_livecell.py │ │ ├── plot_livecell.py │ │ ├── plot_livecell_lora.py │ │ ├── plot_neu_inference_times.py │ │ └── plot_perf_over_epochs.py │ ├── for_release │ │ └── run_inference_for_new_benchmarking.py │ ├── outdated │ │ ├── plot_evaluation.py │ │ ├── plot_train_grid_search.py │ │ └── util.py │ └── results │ │ ├── benchmarking │ │ ├── cellpose │ │ │ ├── covid_if │ │ │ │ └── results │ │ │ │ │ ├── cellpose_cyto.csv │ │ │ │ │ └── cellpose_cyto2.csv │ │ │ └── livecell │ │ │ │ └── livecell_cellpose.csv │ │ └── mitonet │ │ │ ├── lucchi │ │ │ └── results │ │ │ │ └── mitonet.csv │ │ │ └── mitoem │ │ │ └── results │ │ │ └── mitonet.csv │ │ ├── generalists │ │ ├── em │ │ │ ├── lucchi │ │ │ │ └── mito_nuc_em_generalist_sam │ │ │ │ │ ├── with_cem │ │ │ │ │ ├── vit_b │ │ │ │ │ │ └── results │ │ │ │ │ │ │ ├── amg.csv │ │ │ │ │ │ │ ├── instance_segmentation_with_decoder.csv │ │ │ │ │ │ │ ├── iterative_prompts_start_box.csv │ │ │ │ │ │ │ └── iterative_prompts_start_point.csv │ │ │ │ │ └── vit_h │ │ │ │ │ │ └── results │ │ │ │ │ │ ├── amg.csv │ │ │ │ │ │ ├── instance_segmentation_with_decoder.csv │ │ │ │ │ │ ├── iterative_prompts_start_box.csv │ │ │ │ │ │ └── iterative_prompts_start_point.csv │ │ │ │ │ └── without_cem │ │ │ │ │ ├── vit_b │ │ │ │ │ └── results │ │ │ │ │ │ ├── amg.csv │ │ │ │ │ │ ├── instance_segmentation_with_decoder.csv │ │ │ │ │ │ ├── iterative_prompts_start_box.csv │ │ │ │ │ │ └── iterative_prompts_start_point.csv │ │ │ │ │ └── vit_h │ │ │ │ │ └── results │ │ │ │ │ ├── amg.csv │ │ │ │ │ ├── instance_segmentation_with_decoder.csv │ │ │ │ │ ├── iterative_prompts_start_box.csv │ │ │ │ │ └── iterative_prompts_start_point.csv │ │ │ ├── mitoem │ │ │ │ └── mito_nuc_em_generalist_sam │ │ │ │ │ ├── vit_b │ │ │ │ │ └── results │ │ │ │ │ │ ├── amg.csv │ │ │ │ │ │ ├── instance_segmentation_with_decoder.csv │ │ │ │ │ │ ├── iterative_prompts_start_box.csv │ │ │ │ │ │ └── iterative_prompts_start_point.csv │ │ │ │ │ └── vit_h │ │ │ │ │ └── results │ │ │ │ │ ├── amg.csv │ │ │ │ │ ├── instance_segmentation_with_decoder.csv │ │ │ │ │ ├── iterative_prompts_start_box.csv │ │ │ │ │ └── iterative_prompts_start_point.csv │ │ │ └── snemi │ │ │ │ └── boundaries_em_generalist_sam │ │ │ │ ├── vit_b │ │ │ │ └── results │ │ │ │ │ ├── amg.csv │ │ │ │ │ ├── instance_segmentation_with_decoder.csv │ │ │ │ │ ├── iterative_prompts_start_box.csv │ │ │ │ │ └── iterative_prompts_start_point.csv │ │ │ │ └── vit_h │ │ │ │ └── results │ │ │ │ ├── amg.csv │ │ │ │ ├── instance_segmentation_with_decoder.csv │ │ │ │ ├── iterative_prompts_start_box.csv │ │ │ │ └── iterative_prompts_start_point.csv │ │ └── lm │ │ │ ├── covid_if │ │ │ ├── vit_b │ │ │ │ └── results │ │ │ │ │ ├── amg.csv │ │ │ │ │ ├── instance_segmentation_with_decoder.csv │ │ │ │ │ ├── iterative_prompts_start_box.csv │ │ │ │ │ └── iterative_prompts_start_point.csv │ │ │ └── vit_h │ │ │ │ └── results │ │ │ │ ├── amg.csv │ │ │ │ ├── instance_segmentation_with_decoder.csv │ │ │ │ ├── iterative_prompts_start_box.csv │ │ │ │ └── iterative_prompts_start_point.csv │ │ │ └── livecell │ │ │ ├── vit_b │ │ │ ├── amg.csv │ │ │ ├── instance_segmentation_with_decoder.csv │ │ │ ├── iterative_prompts_start_box.csv │ │ │ └── iterative_prompts_start_point.csv │ │ │ └── vit_h │ │ │ ├── amg.csv │ │ │ ├── instance_segmentation_with_decoder.csv │ │ │ ├── iterative_prompts_start_box.csv │ │ │ └── iterative_prompts_start_point.csv │ │ ├── grid_search_train │ │ ├── instance_segmentation_with_decoder.csv │ │ ├── iterative_prompts_start_box.csv │ │ └── iterative_prompts_start_point.csv │ │ ├── specialists │ │ └── lm │ │ │ └── livecell │ │ │ ├── vit_b │ │ │ ├── amg.csv │ │ │ ├── instance_segmentation_with_decoder.csv │ │ │ ├── iterative_prompts_start_box.csv │ │ │ └── iterative_prompts_start_point.csv │ │ │ └── vit_h │ │ │ ├── amg.csv │ │ │ ├── instance_segmentation_with_decoder.csv │ │ │ ├── iterative_prompts_start_box.csv │ │ │ └── iterative_prompts_start_point.csv │ │ └── vanilla │ │ ├── em │ │ ├── lucchi │ │ │ ├── vit_b │ │ │ │ └── results │ │ │ │ │ ├── amg.csv │ │ │ │ │ ├── iterative_prompts_start_box.csv │ │ │ │ │ └── iterative_prompts_start_point.csv │ │ │ └── vit_h │ │ │ │ └── results │ │ │ │ ├── amg.csv │ │ │ │ ├── iterative_prompts_start_box.csv │ │ │ │ └── iterative_prompts_start_point.csv │ │ ├── mitoem │ │ │ ├── vit_b │ │ │ │ └── results │ │ │ │ │ ├── amg.csv │ │ │ │ │ ├── iterative_prompts_start_box.csv │ │ │ │ │ └── iterative_prompts_start_point.csv │ │ │ └── vit_h │ │ │ │ └── results │ │ │ │ ├── amg.csv │ │ │ │ ├── iterative_prompts_start_box.csv │ │ │ │ └── iterative_prompts_start_point.csv │ │ └── snemi │ │ │ ├── vit_b │ │ │ └── results │ │ │ │ ├── amg.csv │ │ │ │ ├── iterative_prompts_start_box.csv │ │ │ │ └── iterative_prompts_start_point.csv │ │ │ └── vit_h │ │ │ └── results │ │ │ ├── amg.csv │ │ │ ├── iterative_prompts_start_box.csv │ │ │ └── iterative_prompts_start_point.csv │ │ └── lm │ │ ├── covid_if │ │ ├── vit_b │ │ │ └── results │ │ │ │ ├── amg.csv │ │ │ │ ├── iterative_prompts_start_box.csv │ │ │ │ └── iterative_prompts_start_point.csv │ │ └── vit_h │ │ │ └── results │ │ │ ├── amg.csv │ │ │ ├── iterative_prompts_start_box.csv │ │ │ └── iterative_prompts_start_point.csv │ │ └── livecell │ │ ├── vit_b │ │ └── results │ │ │ ├── amg.csv │ │ │ ├── iterative_prompts_start_box.csv │ │ │ └── iterative_prompts_start_point.csv │ │ └── vit_h │ │ └── results │ │ ├── amg.csv │ │ ├── iterative_prompts_start_box.csv │ │ └── iterative_prompts_start_point.csv ├── qualitative_comparison │ ├── .gitignore │ ├── compare_benchmarks.py │ ├── compare_em.py │ ├── compare_lm.py │ ├── compare_specialists.py │ ├── get_ais_targets.py │ ├── instance_segmentation.py │ ├── interactive_segmentation.py │ └── util.py ├── training │ └── train_instance_segmentation.py ├── user_study │ ├── README.md │ ├── nuclei_em │ │ ├── evaluate_user_study.py │ │ └── finetune_model.py │ ├── organoids │ │ ├── annotate_default.sh │ │ ├── annotate_generalist.sh │ │ ├── annotation-times-organoids-baselines.xlsx │ │ ├── annotation-times-organoids-sam.xlsx │ │ ├── evaluate_user_study.py │ │ ├── finetune_local.py │ │ └── finetune_model.py │ ├── results_em_nuclei.csv │ └── results_organoids.csv └── volumetric_evaluation │ ├── .gitignore │ ├── check_volumes.py │ ├── evaluate_lucchi.py │ ├── evaluate_mitoem.py │ ├── evaluate_mouse_embryo.py │ ├── evaluate_plantseg.py │ ├── lucchi_results │ ├── results_default │ │ └── grid_search_multi_dimensional_segmentation.csv │ ├── results_v1_em_organelles │ │ └── grid_search_multi_dimensional_segmentation.csv │ └── results_v2_em_organelles │ │ └── grid_search_multi_dimensional_segmentation.csv │ ├── results.md │ ├── run_3d_segmentation.py │ ├── run_micro_sam.sh │ └── util.py ├── setup.cfg ├── test ├── __init__.py ├── test_automatic_segmentation.py ├── test_bioimageio │ └── test_model_export.py ├── test_cli.py ├── test_instance_segmentation.py ├── test_models │ ├── __init__.py │ ├── test_peft_sam.py │ ├── test_sam_3d_wrapper.py │ └── test_simple_sam_3d_wrapper.py ├── test_multi_dimensional_segmentation.py ├── test_prompt_based_segmentation.py ├── test_prompt_generators.py ├── test_sam_annotator │ ├── test_annotator_2d.py │ ├── test_annotator_3d.py │ ├── test_annotator_tracking.py │ ├── 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