.gitignore
LICENSE
Makefile
README.md
pyproject.toml
version.toml
working_req.txt
.github/workflows/create_publish_pr.yaml
.github/workflows/publish.yaml
.github/workflows/publish_tag_to_pypi.yaml
.github/workflows/publish_to_artifactory.yaml
.github/workflows/publish_to_pypi.yaml
.github/workflows/test_lint.yml
.github/workflows/test_lint_pr.yaml
.github/workflows/test_lint_push.yml
docs/dev.md
docs/pub-sub-design.md
docs/supported-environments.md
docs/test-guidelines.md
docs/resources/Segmenter ML pub-sub.drawio.png
docs/resources/progress-thread-diagram.jpeg
src/allencell_ml_segmenter/__init__.py
src/allencell_ml_segmenter/_style.py
src/allencell_ml_segmenter/napari.yaml
src/allencell_ml_segmenter/_tests/__init__.py
src/allencell_ml_segmenter/_tests/test_style.py
src/allencell_ml_segmenter/_tests/config/test_user_settings.py
src/allencell_ml_segmenter/_tests/core/__init__.py
src/allencell_ml_segmenter/_tests/core/test_channel_extraction.py
src/allencell_ml_segmenter/_tests/core/test_dialog_box.py
src/allencell_ml_segmenter/_tests/core/test_directories.py
src/allencell_ml_segmenter/_tests/core/test_progress_tracker.py
src/allencell_ml_segmenter/_tests/core/test_publisher.py
src/allencell_ml_segmenter/_tests/curation/__init__.py
src/allencell_ml_segmenter/_tests/curation/test_curation_input_view.py
src/allencell_ml_segmenter/_tests/curation/test_curation_main.py
src/allencell_ml_segmenter/_tests/curation/test_curation_model.py
src/allencell_ml_segmenter/_tests/curation/test_curation_service.py
src/allencell_ml_segmenter/_tests/curation/test_curation_widget.py
src/allencell_ml_segmenter/_tests/curation/curation_tests/file1.ome.tiff
src/allencell_ml_segmenter/_tests/curation/curation_tests/file_test.ome.tiff
src/allencell_ml_segmenter/_tests/fakes/__init__.py
src/allencell_ml_segmenter/_tests/fakes/fake_channel_extraction.py
src/allencell_ml_segmenter/_tests/fakes/fake_experiments_model.py
src/allencell_ml_segmenter/_tests/fakes/fake_qsettings.py
src/allencell_ml_segmenter/_tests/fakes/fake_subscriber.py
src/allencell_ml_segmenter/_tests/fakes/fake_user_settings.py
src/allencell_ml_segmenter/_tests/fakes/fake_viewer.py
src/allencell_ml_segmenter/_tests/main/__init__.py
src/allencell_ml_segmenter/_tests/main/test_experiments_model.py
src/allencell_ml_segmenter/_tests/main/test_main_model.py
src/allencell_ml_segmenter/_tests/main/test_main_service.py
src/allencell_ml_segmenter/_tests/main/test_main_widget.py
src/allencell_ml_segmenter/_tests/main/experiments_home/0_exp/0.ckpt
src/allencell_ml_segmenter/_tests/main/experiments_home/0_exp/train_config.yaml
src/allencell_ml_segmenter/_tests/main/experiments_home/1_exp/checkpoints/foo.bar
src/allencell_ml_segmenter/_tests/main/experiments_home/1_exp/csv/version_0/test_metrics_csv_empty.csv
src/allencell_ml_segmenter/_tests/main/experiments_home/1_exp/csv/version_1/test_metrics_csv_3_epochs.csv
src/allencell_ml_segmenter/_tests/main/experiments_home/2_exp/checkpoints/0.ckpt
src/allencell_ml_segmenter/_tests/main/experiments_home/2_exp/checkpoints/1.ckpt
src/allencell_ml_segmenter/_tests/main/experiments_home/a_exp/foo
src/allencell_ml_segmenter/_tests/main/experiments_home/m_exp/foo
src/allencell_ml_segmenter/_tests/main/experiments_home/one_ckpt_exp/checkpoints/epoch_000.ckpt
src/allencell_ml_segmenter/_tests/main/experiments_home/z_exp/foo
src/allencell_ml_segmenter/_tests/main/experiments_home/z_exp/data/train.csv
src/allencell_ml_segmenter/_tests/prediction/__init__.py
src/allencell_ml_segmenter/_tests/prediction/test_file_input_widget.py
src/allencell_ml_segmenter/_tests/prediction/test_model.py
src/allencell_ml_segmenter/_tests/prediction/test_model_input_widget.py
src/allencell_ml_segmenter/_tests/prediction/test_prediction_folder_event_handler.py
src/allencell_ml_segmenter/_tests/prediction/test_view.py
src/allencell_ml_segmenter/_tests/sample/__init__.py
src/allencell_ml_segmenter/_tests/sample/test_sample_state_widget.py
src/allencell_ml_segmenter/_tests/services/__init__.py
src/allencell_ml_segmenter/_tests/services/test_prediction_service.py
src/allencell_ml_segmenter/_tests/services/test_training_service.py
src/allencell_ml_segmenter/_tests/test_files/channel_selection_json/valid_0.json
src/allencell_ml_segmenter/_tests/test_files/channel_selection_json/valid_mixed.json
src/allencell_ml_segmenter/_tests/test_files/csv/metrics.csv
src/allencell_ml_segmenter/_tests/test_files/csv/metrics_empty_loss.csv
src/allencell_ml_segmenter/_tests/test_files/csv/test_csv.csv
src/allencell_ml_segmenter/_tests/test_files/images/test_3_channels.tiff
src/allencell_ml_segmenter/_tests/test_files/img_folder/t1.tiff
src/allencell_ml_segmenter/_tests/test_files/img_folder/t2.tiff
src/allencell_ml_segmenter/_tests/test_files/img_folder/t3.tiff
src/allencell_ml_segmenter/_tests/test_files/img_folder/t4.tiff
src/allencell_ml_segmenter/_tests/test_files/img_folder/t5.tiff
src/allencell_ml_segmenter/_tests/test_files/img_folder_with_hidden_files/.hidden
src/allencell_ml_segmenter/_tests/test_files/img_folder_with_hidden_files/t1.tiff
src/allencell_ml_segmenter/_tests/test_files/img_folder_with_hidden_files/test_subdirectory/do_not_include.tiff
src/allencell_ml_segmenter/_tests/test_files/multiple_csv/test.csv
src/allencell_ml_segmenter/_tests/test_files/multiple_csv/train.csv
src/allencell_ml_segmenter/_tests/test_files/multiple_csv/val.csv
src/allencell_ml_segmenter/_tests/test_files/output_test_folder/target/output_1.tiff
src/allencell_ml_segmenter/_tests/test_files/output_test_folder/target/output_2.tiff
src/allencell_ml_segmenter/_tests/test_files/output_test_folder_extra/target/output_1.tiff
src/allencell_ml_segmenter/_tests/test_files/output_test_folder_extra/target/output_2.tiff
src/allencell_ml_segmenter/_tests/test_files/output_test_folder_extra/target/output_3.tiff
src/allencell_ml_segmenter/_tests/test_files/output_test_folder_extra/target/output_4.tiff
src/allencell_ml_segmenter/_tests/test_files/zip_files/test_zip.zip
src/allencell_ml_segmenter/_tests/test_files/zip_files/test_zip/testmodel
src/allencell_ml_segmenter/_tests/training/__init__.py
src/allencell_ml_segmenter/_tests/training/test_image_selection_widget.py
src/allencell_ml_segmenter/_tests/training/test_metrics_csv_event_handler.py
src/allencell_ml_segmenter/_tests/training/test_model.py
src/allencell_ml_segmenter/_tests/training/test_model_selection_widget.py
src/allencell_ml_segmenter/_tests/training/test_patch_size_validator.py
src/allencell_ml_segmenter/_tests/training/test_view.py
src/allencell_ml_segmenter/_tests/utils/__init__.py
src/allencell_ml_segmenter/_tests/utils/test_cyto_overrides_manager.py
src/allencell_ml_segmenter/_tests/utils/test_file_utils.py
src/allencell_ml_segmenter/_tests/utils/test_image_processing.py
src/allencell_ml_segmenter/_tests/utils/s3/__init__.py
src/allencell_ml_segmenter/_tests/utils/s3/s3_response_fixtures.py
src/allencell_ml_segmenter/_tests/utils/s3/test_available_model.py
src/allencell_ml_segmenter/_tests/utils/s3/test_s3_model_bucket.py
src/allencell_ml_segmenter/_tests/utils/zip_file/__init__.py
src/allencell_ml_segmenter/_tests/utils/zip_file/test_zip_file_manager.py
src/allencell_ml_segmenter/_tests/widgets/__init__.py
src/allencell_ml_segmenter/_tests/widgets/test_check_box_list_widget.py
src/allencell_ml_segmenter/_tests/widgets/test_directory_or_csv_file_dialog.py
src/allencell_ml_segmenter/_tests/widgets/test_input_button_widget.py
src/allencell_ml_segmenter/_tests/widgets/test_label_with_hint_widget.py
src/allencell_ml_segmenter/_tests/widgets/test_model_download_dialog.py
src/allencell_ml_segmenter/assets/loading.gif
src/allencell_ml_segmenter/assets/icons/question-circle.svg
src/allencell_ml_segmenter/config/i_user_settings.py
src/allencell_ml_segmenter/config/user_settings.py
src/allencell_ml_segmenter/core/__init__.py
src/allencell_ml_segmenter/core/aics_widget.py
src/allencell_ml_segmenter/core/channel_extraction.py
src/allencell_ml_segmenter/core/dialog_box.py
src/allencell_ml_segmenter/core/directories.py
src/allencell_ml_segmenter/core/event.py
src/allencell_ml_segmenter/core/extractor_factory.py
src/allencell_ml_segmenter/core/i_extractor_factory.py
src/allencell_ml_segmenter/core/info_dialog_box.py
src/allencell_ml_segmenter/core/progress_tracker.py
src/allencell_ml_segmenter/core/publisher.py
src/allencell_ml_segmenter/core/subscriber.py
src/allencell_ml_segmenter/core/view.py
src/allencell_ml_segmenter/core/image_data_extractor/__init__.py
src/allencell_ml_segmenter/core/image_data_extractor/aics_image_data_extractor.py
src/allencell_ml_segmenter/core/image_data_extractor/fake_image_data_extractor.py
src/allencell_ml_segmenter/core/image_data_extractor/i_image_data_extractor.py
src/allencell_ml_segmenter/core/image_data_extractor/image_data.py
src/allencell_ml_segmenter/core/q_runnable_manager/__init__.py
src/allencell_ml_segmenter/core/q_runnable_manager/global_q_runnable_manager.py
src/allencell_ml_segmenter/core/q_runnable_manager/i_q_runnable_manager.py
src/allencell_ml_segmenter/core/q_runnable_manager/synchro_q_runnable_manager.py
src/allencell_ml_segmenter/core/task_executor/__init__.py
src/allencell_ml_segmenter/core/task_executor/i_task_executor.py
src/allencell_ml_segmenter/core/task_executor/napari_thread_task_executor.py
src/allencell_ml_segmenter/core/task_executor/synchro_task_executor.py
src/allencell_ml_segmenter/curation/__init__.py
src/allencell_ml_segmenter/curation/curation_data_class.py
src/allencell_ml_segmenter/curation/curation_model.py
src/allencell_ml_segmenter/curation/curation_service.py
src/allencell_ml_segmenter/curation/curation_widget.py
src/allencell_ml_segmenter/curation/input_view.py
src/allencell_ml_segmenter/curation/main_view.py
src/allencell_ml_segmenter/curation/stacked_spinner.py
src/allencell_ml_segmenter/main/__init__.py
src/allencell_ml_segmenter/main/experiments_model.py
src/allencell_ml_segmenter/main/i_experiments_model.py
src/allencell_ml_segmenter/main/i_viewer.py
src/allencell_ml_segmenter/main/main_model.py
src/allencell_ml_segmenter/main/main_service.py
src/allencell_ml_segmenter/main/main_widget.py
src/allencell_ml_segmenter/main/segmenter_layer.py
src/allencell_ml_segmenter/main/viewer.py
src/allencell_ml_segmenter/napari/__init__.py
src/allencell_ml_segmenter/napari/napari_reader.py
src/allencell_ml_segmenter/napari/napari_writer.py
src/allencell_ml_segmenter/napari/sample_data.py
src/allencell_ml_segmenter/prediction/__init__.py
src/allencell_ml_segmenter/prediction/file_input_widget.py
src/allencell_ml_segmenter/prediction/model.py
src/allencell_ml_segmenter/prediction/model_input_widget.py
src/allencell_ml_segmenter/prediction/prediction_folder_event_handler.py
src/allencell_ml_segmenter/prediction/prediction_folder_progress_tracker.py
src/allencell_ml_segmenter/prediction/service.py
src/allencell_ml_segmenter/prediction/view.py
src/allencell_ml_segmenter/sample/README.md
src/allencell_ml_segmenter/sample/__init__.py
src/allencell_ml_segmenter/sample/sample_model.py
src/allencell_ml_segmenter/sample/sample_results_list_widget.py
src/allencell_ml_segmenter/sample/sample_select_files_widget.py
src/allencell_ml_segmenter/sample/sample_state_widget.py
src/allencell_ml_segmenter/sample/sample_view.py
src/allencell_ml_segmenter/sample/process/__init__.py
src/allencell_ml_segmenter/sample/process/progress_widget.py
src/allencell_ml_segmenter/sample/process/service.py
src/allencell_ml_segmenter/sample/resources/Segmenter ML pub-sub.drawio.png
src/allencell_ml_segmenter/scripts/bumpver_handler.py
src/allencell_ml_segmenter/scripts/tag_with_current_version.py
src/allencell_ml_segmenter/services/__init__.py
src/allencell_ml_segmenter/services/prediction_service.py
src/allencell_ml_segmenter/services/training_service.py
src/allencell_ml_segmenter/styles/core.qss
src/allencell_ml_segmenter/styles/curation_main.qss
src/allencell_ml_segmenter/styles/input_button_widget.qss
src/allencell_ml_segmenter/styles/prediction_view.qss
src/allencell_ml_segmenter/styles/training_view.qss
src/allencell_ml_segmenter/training/__init__.py
src/allencell_ml_segmenter/training/cache_dir_event_handler.py
src/allencell_ml_segmenter/training/image_selection_widget.py
src/allencell_ml_segmenter/training/metrics_csv_event_handler.py
src/allencell_ml_segmenter/training/model_selection_widget.py
src/allencell_ml_segmenter/training/patch_size_validator.py
src/allencell_ml_segmenter/training/training_model.py
src/allencell_ml_segmenter/training/training_progress_tracker.py
src/allencell_ml_segmenter/training/view.py
src/allencell_ml_segmenter/utils/__init__.py
src/allencell_ml_segmenter/utils/cuda_util.py
src/allencell_ml_segmenter/utils/cyto_overrides_manager.py
src/allencell_ml_segmenter/utils/file_utils.py
src/allencell_ml_segmenter/utils/image_processing.py
src/allencell_ml_segmenter/utils/file_writer/__init__.py
src/allencell_ml_segmenter/utils/file_writer/fake_file_writer.py
src/allencell_ml_segmenter/utils/file_writer/file_writer.py
src/allencell_ml_segmenter/utils/file_writer/i_file_writer.py
src/allencell_ml_segmenter/utils/s3/__init__.py
src/allencell_ml_segmenter/utils/s3/s3_available_model.py
src/allencell_ml_segmenter/utils/s3/s3_bucket_constants.py
src/allencell_ml_segmenter/utils/s3/s3_model_bucket.py
src/allencell_ml_segmenter/utils/s3/s3_request_exception.py
src/allencell_ml_segmenter/utils/zip_file/__init__.py
src/allencell_ml_segmenter/utils/zip_file/fake_zip_file_manager.py
src/allencell_ml_segmenter/utils/zip_file/i_zip_file_manager.py
src/allencell_ml_segmenter/utils/zip_file/zip_file_manager.py
src/allencell_ml_segmenter/widgets/__init__.py
src/allencell_ml_segmenter/widgets/check_box_list_widget.py
src/allencell_ml_segmenter/widgets/directory_or_csv_file_dialog.py
src/allencell_ml_segmenter/widgets/input_button_widget.py
src/allencell_ml_segmenter/widgets/label_with_hint_widget.py
src/allencell_ml_segmenter/widgets/model_download_dialog.py
src/allencell_segmenter_ml.egg-info/PKG-INFO
src/allencell_segmenter_ml.egg-info/SOURCES.txt
src/allencell_segmenter_ml.egg-info/dependency_links.txt
src/allencell_segmenter_ml.egg-info/entry_points.txt
src/allencell_segmenter_ml.egg-info/requires.txt
src/allencell_segmenter_ml.egg-info/top_level.txt