├── .github ├── ISSUE_TEMPLATE │ ├── bug_report.md │ ├── example_report.md │ ├── feature_request.md │ ├── interoperability_request.md │ ├── question.md │ └── refactoring_suggestion.md ├── dependabot.yml ├── pull_request_template.md └── workflows │ ├── ci.yml │ ├── ci_lvae.yml │ └── codecov.yml ├── .gitignore ├── .pre-commit-config.yaml ├── CODE_OF_CONDUCT.md ├── LICENSE ├── README.md ├── codecov.yml ├── mypy.ini ├── pyproject.toml ├── src └── careamics │ ├── __init__.py │ ├── careamist.py │ ├── cli │ ├── __init__.py │ ├── conf.py │ ├── main.py │ └── utils.py │ ├── config │ ├── __init__.py │ ├── algorithms │ │ ├── __init__.py │ │ ├── care_algorithm_config.py │ │ ├── hdn_algorithm_config.py │ │ ├── microsplit_algorithm_config.py │ │ ├── n2n_algorithm_config.py │ │ ├── n2v_algorithm_config.py │ │ ├── pn2v_algorithm_config.py │ │ ├── unet_algorithm_config.py │ │ └── vae_algorithm_config.py │ ├── architectures │ │ ├── __init__.py │ │ ├── architecture_config.py │ │ ├── lvae_config.py │ │ └── unet_config.py │ ├── configuration.py │ ├── configuration_factories.py │ ├── data │ │ ├── __init__.py │ │ ├── data_config.py │ │ ├── inference_config.py │ │ ├── ng_data_config.py │ │ ├── patch_filter │ │ │ ├── __init__.py │ │ │ ├── filter_config.py │ │ │ ├── mask_filter_config.py │ │ │ ├── max_filter_config.py │ │ │ ├── meanstd_filter_config.py │ │ │ └── shannon_filter_config.py │ │ ├── patching_strategies │ │ │ ├── __init__.py │ │ │ ├── _overlapping_patched_config.py │ │ │ ├── _patched_config.py │ │ │ ├── random_patching_config.py │ │ │ ├── sequential_patching_config.py │ │ │ ├── tiled_patching_config.py │ │ │ └── whole_patching_config.py │ │ └── tile_information.py │ ├── lightning │ │ ├── __init__.py │ │ ├── callbacks │ │ │ ├── __init__.py │ │ │ └── callback_config.py │ │ ├── optimizer_configs.py │ │ └── training_config.py │ ├── losses │ │ ├── __init__.py │ │ └── loss_config.py │ ├── noise_model │ │ ├── __init__.py │ │ ├── likelihood_config.py │ │ └── noise_model_config.py │ ├── support │ │ ├── __init__.py │ │ ├── supported_activations.py │ │ ├── supported_algorithms.py │ │ ├── supported_architectures.py │ │ ├── supported_data.py │ │ ├── supported_filters.py │ │ ├── supported_loggers.py │ │ ├── supported_losses.py │ │ ├── supported_optimizers.py │ │ ├── supported_patching_strategies.py │ │ ├── supported_pixel_manipulations.py │ │ ├── supported_struct_axis.py │ │ └── supported_transforms.py │ ├── transformations │ │ ├── __init__.py │ │ ├── n2v_manipulate_config.py │ │ ├── normalize_config.py │ │ ├── transform_config.py │ │ ├── transform_unions.py │ │ ├── xy_flip_config.py │ │ └── xy_random_rotate90_config.py │ ├── utils │ │ ├── __init__.py │ │ └── configuration_io.py │ └── validators │ │ ├── __init__.py │ │ ├── axes_validators.py │ │ ├── model_validators.py │ │ └── patch_validators.py │ ├── conftest.py │ ├── dataset │ ├── __init__.py │ ├── dataset_utils │ │ ├── __init__.py │ │ ├── dataset_utils.py │ │ ├── file_utils.py │ │ ├── iterate_over_files.py │ │ └── running_stats.py │ ├── in_memory_dataset.py │ ├── in_memory_pred_dataset.py │ ├── in_memory_tiled_pred_dataset.py │ ├── iterable_dataset.py │ ├── iterable_pred_dataset.py │ ├── iterable_tiled_pred_dataset.py │ ├── patching │ │ ├── __init__.py │ │ ├── patching.py │ │ ├── random_patching.py │ │ ├── sequential_patching.py │ │ └── validate_patch_dimension.py │ └── tiling │ │ ├── __init__.py │ │ ├── collate_tiles.py │ │ ├── lvae_tiled_patching.py │ │ └── tiled_patching.py │ ├── dataset_ng │ ├── README.md │ ├── __init__.py │ ├── dataset.py │ ├── demos │ │ ├── bsd68_demo.ipynb │ │ ├── bsd68_zarr_demo.ipynb │ │ ├── care_U2OS_demo.ipynb │ │ ├── demo_custom_image_stack.ipynb │ │ ├── demo_datamodule.ipynb │ │ ├── demo_dataset.ipynb │ │ ├── demo_patch_extractor.py │ │ └── mouse_nuclei_demo.ipynb │ ├── factory.py │ ├── grouped_index_sampler.py │ ├── image_stack │ │ ├── __init__.py │ │ ├── czi_image_stack.py │ │ ├── file_image_stack.py │ │ ├── image_stack_protocol.py │ │ ├── image_utils │ │ │ ├── __init__.py │ │ │ └── image_stack_utils.py │ │ ├── in_memory_image_stack.py │ │ └── zarr_image_stack.py │ ├── image_stack_loader │ │ ├── __init__.py │ │ ├── image_stack_loader_protocol.py │ │ ├── image_stack_loaders.py │ │ └── zarr_utils.py │ ├── legacy_interoperability.py │ ├── microsplit_input_synth.py │ ├── patch_extractor │ │ ├── __init__.py │ │ ├── limit_file_extractor.py │ │ ├── patch_construction.py │ │ └── patch_extractor.py │ ├── patch_filter │ │ ├── __init__.py │ │ ├── coordinate_filter_protocol.py │ │ ├── filter_factory.py │ │ ├── mask_filter.py │ │ ├── max_filter.py │ │ ├── mean_std_filter.py │ │ ├── patch_filter_protocol.py │ │ └── shannon_filter.py │ └── patching_strategies │ │ ├── __init__.py │ │ ├── patching_strategy_factory.py │ │ ├── patching_strategy_protocol.py │ │ ├── random_patching.py │ │ ├── sequential_patching.py │ │ ├── tiling_strategy.py │ │ └── whole_sample.py │ ├── file_io │ ├── __init__.py │ ├── read │ │ ├── __init__.py │ │ ├── get_func.py │ │ └── tiff.py │ └── write │ │ ├── __init__.py │ │ ├── get_func.py │ │ └── tiff.py │ ├── lightning │ ├── __init__.py │ ├── callbacks │ │ ├── __init__.py │ │ ├── data_stats_callback.py │ │ ├── hyperparameters_callback.py │ │ ├── prediction_writer_callback │ │ │ ├── __init__.py │ │ │ ├── file_path_utils.py │ │ │ ├── prediction_writer_callback.py │ │ │ ├── write_strategy.py │ │ │ └── write_strategy_factory.py │ │ └── progress_bar_callback.py │ ├── dataset_ng │ │ ├── __init__.py │ │ ├── callbacks │ │ │ ├── __init__.py │ │ │ └── prediction_writer │ │ │ │ ├── __init__.py │ │ │ │ ├── cached_tiles_strategy.py │ │ │ │ ├── file_path_utils.py │ │ │ │ ├── prediction_writer_callback.py │ │ │ │ ├── write_image_strategy.py │ │ │ │ ├── write_strategy.py │ │ │ │ ├── write_strategy_factory.py │ │ │ │ └── write_tiles_zarr_strategy.py │ │ ├── data_module.py │ │ ├── data_module_utils.py │ │ ├── lightning_modules │ │ │ ├── __init__.py │ │ │ ├── care_module.py │ │ │ ├── n2v_module.py │ │ │ └── unet_module.py │ │ └── prediction │ │ │ ├── __init__.py │ │ │ ├── convert_prediction.py │ │ │ └── stitch_prediction.py │ ├── lightning_module.py │ ├── microsplit_data_module.py │ ├── predict_data_module.py │ └── train_data_module.py │ ├── losses │ ├── __init__.py │ ├── fcn │ │ ├── __init__.py │ │ └── losses.py │ ├── loss_factory.py │ └── lvae │ │ ├── __init__.py │ │ ├── loss_utils.py │ │ └── losses.py │ ├── lvae_training │ ├── __init__.py │ ├── calibration.py │ ├── dataset │ │ ├── __init__.py │ │ ├── config.py │ │ ├── lc_dataset.py │ │ ├── ms_dataset_ref.py │ │ ├── multich_dataset.py │ │ ├── multicrop_dset.py │ │ ├── multifile_dataset.py │ │ ├── types.py │ │ └── utils │ │ │ ├── __init__.py │ │ │ ├── data_utils.py │ │ │ ├── empty_patch_fetcher.py │ │ │ ├── index_manager.py │ │ │ └── index_switcher.py │ ├── eval_utils.py │ ├── get_config.py │ ├── lightning_module.py │ ├── metrics.py │ ├── train_lvae.py │ └── train_utils.py │ ├── model_io │ ├── __init__.py │ ├── bioimage │ │ ├── __init__.py │ │ ├── _readme_factory.py │ │ ├── bioimage_utils.py │ │ ├── cover_factory.py │ │ └── model_description.py │ ├── bmz_io.py │ └── model_io_utils.py │ ├── models │ ├── __init__.py │ ├── activation.py │ ├── layers.py │ ├── lvae │ │ ├── __init__.py │ │ ├── layers.py │ │ ├── likelihoods.py │ │ ├── lvae.py │ │ ├── noise_models.py │ │ ├── stochastic.py │ │ └── utils.py │ ├── model_factory.py │ └── unet.py │ ├── nm_training_placeholder.py │ ├── prediction_utils │ ├── __init__.py │ ├── lvae_prediction.py │ ├── lvae_tiling_manager.py │ ├── prediction_outputs.py │ └── stitch_prediction.py │ ├── py.typed │ ├── transforms │ ├── __init__.py │ ├── compose.py │ ├── n2v_manipulate.py │ ├── n2v_manipulate_torch.py │ ├── normalize.py │ ├── pixel_manipulation.py │ ├── pixel_manipulation_torch.py │ ├── struct_mask_parameters.py │ ├── transform.py │ ├── tta.py │ ├── xy_flip.py │ └── xy_random_rotate90.py │ └── utils │ ├── __init__.py │ ├── autocorrelation.py │ ├── base_enum.py │ ├── context.py │ ├── deprecation.py │ ├── lightning_utils.py │ ├── logging.py │ ├── metrics.py │ ├── path_utils.py │ ├── plotting.py │ ├── ram.py │ ├── receptive_field.py │ ├── serializers.py │ ├── torch_utils.py │ └── version.py ├── tests ├── cli │ ├── __init__.py │ ├── test_conf.py │ └── test_main.py ├── config │ ├── algorithms │ │ ├── test_care_algorithm_config.py │ │ ├── test_n2n_algorithm_config.py │ │ ├── test_n2v_algorithm_config.py │ │ ├── test_n2v_preprocessing.py │ │ ├── test_pn2v_algorithm_config.py │ │ ├── test_unet_algorithm_config.py │ │ └── test_vae_algorithm_config.py │ ├── architectures │ │ ├── test_architecture_config.py │ │ ├── test_lvae_config.py │ │ └── test_unet_config.py │ ├── data │ │ ├── patching_strategies │ │ │ └── test_strategies.py │ │ ├── test_data_config.py │ │ ├── test_inference_config.py │ │ ├── test_ng_data_config.py │ │ └── test_tile_information.py │ ├── lightning │ │ ├── callbacks │ │ │ └── test_callback_config.py │ │ └── test_optimizer_configs.py │ ├── support │ │ ├── test_supported_data.py │ │ └── test_supported_optimizers.py │ ├── test_configuration.py │ ├── test_configuration_factories.py │ ├── transformations │ │ ├── test_n2v_manipulate_config.py │ │ ├── test_normalize_config.py │ │ ├── test_xy_flip_config.py │ │ └── test_xy_random_rotate90_config.py │ ├── utils │ │ └── test_configuration_io.py │ └── validators │ │ ├── test_axes_validators.py │ │ ├── test_model_validators.py │ │ └── test_validator_utils.py ├── conftest.py ├── dataset │ ├── dataset_utils │ │ ├── test_compute_normalization_stats.py │ │ └── test_list_files.py │ ├── patching │ │ ├── test_patching_utils.py │ │ ├── test_random_patching.py │ │ └── test_sequential_patching.py │ ├── test_in_memory_dataset.py │ ├── test_in_memory_pred_dataset.py │ ├── test_in_memory_tiled_pred_dataset.py │ ├── test_iterable_dataset.py │ ├── test_iterable_pred_dataset.py │ ├── test_iterable_tiled_pred_dataset.py │ └── tiling │ │ ├── test_collate_tiles.py │ │ ├── test_lvae_tiled_patching.py │ │ └── test_tiled_patching.py ├── dataset_ng │ ├── dataset │ │ └── test_dataset.py │ ├── image_stack │ │ ├── czi │ │ │ ├── test_czi_image_stack.py │ │ │ └── test_import_czi_image_stack.py │ │ ├── test_file_image_stack.py │ │ ├── test_image_stack_utils.py │ │ ├── test_in_memory_image_stack.py │ │ └── zarr │ │ │ ├── conftest.py │ │ │ ├── test_zarr_image_stack.py │ │ │ └── test_zarr_utils.py │ ├── image_stack_loader │ │ └── test_czi_image_stack_loader.py │ ├── patch_extractor │ │ ├── test_lateral_context_construction.py │ │ └── test_limit_files_extractor.py │ ├── patch_filter │ │ ├── test_mask_filter.py │ │ ├── test_max_filter.py │ │ ├── test_mean_std_patch_filter.py │ │ └── test_shannon_entropy_filter.py │ ├── patching_strategies │ │ ├── test_all_strategies.py │ │ ├── test_patching_strategy_factory.py │ │ ├── test_random_patching_ng.py │ │ ├── test_sequential_patching_ng.py │ │ └── test_tiling_strategy.py │ └── test_grouped_index_sampler.py ├── file_io │ ├── read │ │ ├── test_get_read_func.py │ │ └── test_read_tiff.py │ └── write │ │ ├── test_get_write_func.py │ │ └── test_write_tiff.py ├── lightning │ ├── callbacks │ │ └── prediction_writer_callback │ │ │ ├── test_cache_tiles_write_strategy.py │ │ │ ├── test_file_path_utils.py │ │ │ ├── test_prediction_writer_callback.py │ │ │ ├── test_write_image_write_strategy.py │ │ │ └── test_write_strategy_factory.py │ ├── dataset_ng │ │ ├── callbacks │ │ │ └── prediction_writer_callbacks │ │ │ │ ├── test_ng_cache_tiles_write_strategy.py │ │ │ │ ├── test_ng_file_path_utils.py │ │ │ │ ├── test_ng_prediction_writer_callback.py │ │ │ │ ├── test_ng_write_image_write_strategy.py │ │ │ │ ├── test_ng_write_strategy_factory.py │ │ │ │ └── test_write_tile_zarr_strategy.py │ │ ├── conftest.py │ │ ├── prediction │ │ │ ├── test_ng_convert_prediction.py │ │ │ └── test_ng_stitch_prediction.py │ │ ├── test_data_module_utils.py │ │ ├── test_data_module_zarr.py │ │ └── test_datamodule.py │ ├── test_LVAE_lightning_module.py │ ├── test_lightning_api.py │ ├── test_lightning_module.py │ ├── test_lightning_module_onnx_exportability.py │ ├── test_microsplit_train_datamodule.py │ ├── test_predict_data_module.py │ └── test_train_data_module.py ├── likelihood_modules │ └── test_likelihoods.py ├── losses │ ├── test_lvae_losses.py │ └── test_pn2v_loss.py ├── model_io │ └── test_bmz_io.py ├── models │ ├── lvae │ │ ├── test_lvae_architecture.py │ │ ├── test_noise_model.py │ │ └── test_utils.py │ ├── test_model_factory.py │ └── test_unet.py ├── prediction_utils │ ├── test_lvae_prediction.py │ ├── test_prediction_outputs.py │ └── test_stitch_prediction.py ├── smoke_test.py ├── test_careamist.py ├── test_conftest.py ├── transforms │ ├── test_compose.py │ ├── test_manipulate_n2v.py │ ├── test_normalize.py │ ├── test_pixel_manipulation.py │ ├── test_tta.py │ ├── test_xy_flip.py │ └── test_xy_random_rotate90.py └── utils │ ├── test_autocorrelation.py │ ├── test_base_enum.py │ ├── test_context.py │ ├── test_lightning_utils.py │ ├── test_logging.py │ ├── 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