README.md
pyproject.toml
setup.py
openhcs/__init__.py
openhcs.egg-info/PKG-INFO
openhcs.egg-info/SOURCES.txt
openhcs.egg-info/dependency_links.txt
openhcs.egg-info/entry_points.txt
openhcs.egg-info/not-zip-safe
openhcs.egg-info/requires.txt
openhcs.egg-info/top_level.txt
openhcs/build_utils/__init__.py
openhcs/build_utils/zeroc_ice_installer.py
openhcs/components/__init__.py
openhcs/components/framework.py
openhcs/config_framework/__init__.py
openhcs/constants/__init__.py
openhcs/constants/constants.py
openhcs/constants/input_source.py
openhcs/core/__init__.py
openhcs/core/config.py
openhcs/core/config_cache.py
openhcs/core/lazy_gpu_imports.py
openhcs/core/lazy_placeholder.py
openhcs/core/lazy_placeholder_simplified.py
openhcs/core/log_utils.py
openhcs/core/metadata_cache.py
openhcs/core/path_cache.py
openhcs/core/streaming_config_factory.py
openhcs/core/utils.py
openhcs/core/xdg_paths.py
openhcs/core/components/__init__.py
openhcs/core/components/metaprogramming.py
openhcs/core/components/multiprocessing.py
openhcs/core/components/parser_metaprogramming.py
openhcs/core/components/validation.py
openhcs/core/context/__init__.py
openhcs/core/context/processing_context.py
openhcs/core/memory/__init__.py
openhcs/core/memory/exceptions.py
openhcs/core/orchestrator/__init__.py
openhcs/core/orchestrator/execution_result.py
openhcs/core/orchestrator/gpu_scheduler.py
openhcs/core/orchestrator/orchestrator.py
openhcs/core/pipeline/__init__.py
openhcs/core/pipeline/compiler.py
openhcs/core/pipeline/funcstep_contract_validator.py
openhcs/core/pipeline/function_contracts.py
openhcs/core/pipeline/gpu_memory_validator.py
openhcs/core/pipeline/materialization_flag_planner.py
openhcs/core/pipeline/path_planner.py
openhcs/core/pipeline/step_attribute_stripper.py
openhcs/core/progress/__init__.py
openhcs/core/progress/emitters.py
openhcs/core/progress/exceptions.py
openhcs/core/progress/projection.py
openhcs/core/progress/registry.py
openhcs/core/progress/types.py
openhcs/core/steps/__init__.py
openhcs/core/steps/abstract.py
openhcs/core/steps/function_step.py
openhcs/debug/__init__.py
openhcs/debug/example_export.py
openhcs/debug/example_export_clean.py
openhcs/debug/export.py
openhcs/debug/pickle_converter.py
openhcs/formats/experimental_analysis.py
openhcs/formats/func_arg_prep.py
openhcs/formats/metaxpress.py
openhcs/formats/pattern/__init__.py
openhcs/formats/pattern/pattern_discovery.py
openhcs/formats/pattern/pattern_resolver.py
openhcs/introspection/__init__.py
openhcs/introspection/lazy_dataclass_utils.py
openhcs/microscopes/__init__.py
openhcs/microscopes/handler_registry_service.py
openhcs/microscopes/imagexpress.py
openhcs/microscopes/microscope_base.py
openhcs/microscopes/microscope_interfaces.py
openhcs/microscopes/omero.py
openhcs/microscopes/openhcs.py
openhcs/microscopes/opera_phenix.py
openhcs/microscopes/opera_phenix_xml_parser.py
openhcs/omero/docker-compose.openhcs.yml
openhcs/omero/docker-compose.yml
openhcs/processing/__init__.py
openhcs/processing/func_registry.py
openhcs/processing/backends/__init__.py
openhcs/processing/backends/analysis/__init__.py
openhcs/processing/backends/analysis/cache_utils.py
openhcs/processing/backends/analysis/cell_counting_cpu.py
openhcs/processing/backends/analysis/cell_counting_cupy.py
openhcs/processing/backends/analysis/cell_counting_pyclesperanto.py
openhcs/processing/backends/analysis/cell_counting_pyclesperanto_simple.py
openhcs/processing/backends/analysis/consolidate_analysis_results.py
openhcs/processing/backends/analysis/consolidate_special_outputs.py
openhcs/processing/backends/analysis/cx5_format.py
openhcs/processing/backends/analysis/dxf_mask_pipeline.py
openhcs/processing/backends/analysis/focus_analyzer.py
openhcs/processing/backends/analysis/hmm_axon.py
openhcs/processing/backends/analysis/hmm_axon_torbi.py
openhcs/processing/backends/analysis/multi_template_matching.py
openhcs/processing/backends/analysis/self_supervised_segmentation_3d.py
openhcs/processing/backends/analysis/skan_axon_analysis.py
openhcs/processing/backends/analysis/straighten_object_3d.py
openhcs/processing/backends/analysis/test_simple_implementation.py
openhcs/processing/backends/assemblers/__init__.py
openhcs/processing/backends/assemblers/assemble_stack_cpu.py
openhcs/processing/backends/assemblers/assemble_stack_cupy.py
openhcs/processing/backends/assemblers/self_supervised_stitcher.py
openhcs/processing/backends/enhance/__init__.py
openhcs/processing/backends/enhance/basic_processor_cupy.py
openhcs/processing/backends/enhance/basic_processor_jax.py
openhcs/processing/backends/enhance/basic_processor_numpy.py
openhcs/processing/backends/enhance/cupy_clahe.py
openhcs/processing/backends/enhance/dl_edof_unsupervised.py
openhcs/processing/backends/enhance/focus_torch.py
openhcs/processing/backends/enhance/jax_nlm_processor.py
openhcs/processing/backends/enhance/n2v2_processor_torch.py
openhcs/processing/backends/enhance/self_supervised_2d_deconvolution.py
openhcs/processing/backends/enhance/self_supervised_3d_deconvolution.py
openhcs/processing/backends/enhance/torch_nlm_processor.py
openhcs/processing/backends/experimental_analysis/__init__.py
openhcs/processing/backends/experimental_analysis/cx5_registry.py
openhcs/processing/backends/experimental_analysis/format_registry.py
openhcs/processing/backends/experimental_analysis/format_registry_service.py
openhcs/processing/backends/experimental_analysis/metaxpress_registry.py
openhcs/processing/backends/experimental_analysis/unified_analysis_engine.py
openhcs/processing/backends/lib_registry/cupy_registry.py
openhcs/processing/backends/lib_registry/openhcs_registry.py
openhcs/processing/backends/lib_registry/pyclesperanto_registry.py
openhcs/processing/backends/lib_registry/registry_service.py
openhcs/processing/backends/lib_registry/scikit_image_registry.py
openhcs/processing/backends/lib_registry/unified_registry.py
openhcs/processing/backends/pos_gen/__init__.py
openhcs/processing/backends/pos_gen/ashlar_main_cpu.py
openhcs/processing/backends/pos_gen/ashlar_main_gpu.py
openhcs/processing/backends/pos_gen/mist_processor_cupy.py
openhcs/processing/backends/pos_gen/mist/__init__.py
openhcs/processing/backends/pos_gen/mist/boruvka_mst.py
openhcs/processing/backends/pos_gen/mist/gpu_kernels.py
openhcs/processing/backends/pos_gen/mist/mist_main.py
openhcs/processing/backends/pos_gen/mist/phase_correlation.py
openhcs/processing/backends/pos_gen/mist/position_reconstruction.py
openhcs/processing/backends/pos_gen/mist/quality_metrics.py
openhcs/processing/backends/processors/__init__.py
openhcs/processing/backends/processors/cupy_processor.py
openhcs/processing/backends/processors/jax_processor.py
openhcs/processing/backends/processors/numpy_processor.py
openhcs/processing/backends/processors/percentile_utils.py
openhcs/processing/backends/processors/pyclesperanto_processor.py
openhcs/processing/backends/processors/tensorflow_processor.py
openhcs/processing/backends/processors/torch_processor.py
openhcs/processing/custom_functions/__init__.py
openhcs/processing/custom_functions/manager.py
openhcs/processing/custom_functions/signals.py
openhcs/processing/custom_functions/templates.py
openhcs/processing/custom_functions/validation.py
openhcs/processing/materialization/__init__.py
openhcs/processing/materialization/constants.py
openhcs/processing/materialization/core.py
openhcs/processing/materialization/options.py
openhcs/processing/materialization/presets.py
openhcs/processing/materialization/utils.py
openhcs/processing/presets/__init__.py
openhcs/processing/presets/pipelines/10x_mfd_crop_analyze.py
openhcs/processing/presets/pipelines/10x_mfd_crop_analyze_dapi-fitc-cy5.py
openhcs/processing/presets/pipelines/10x_mfd_stitch_ashlar_cpu.py
openhcs/processing/presets/pipelines/10x_mfd_stitch_gpu.py
openhcs/processing/presets/pipelines/cy5_axon_cell_body_crop_analysis.py
openhcs/processing/presets/pipelines/cy5_ctb_cell_count.py
openhcs/processing/presets/pipelines/imx_96_well_neurite_outgrowth_pipeline_cpu.py
openhcs/processing/presets/pipelines/imx_96_well_neurite_outgrowth_pipeline_gpu.py
openhcs/processing/presets/pipelines/test.py
openhcs/pyqt_gui/__init__.py
openhcs/pyqt_gui/__main__.py
openhcs/pyqt_gui/app.py
openhcs/pyqt_gui/config.py
openhcs/pyqt_gui/launch.py
openhcs/pyqt_gui/main.py
openhcs/pyqt_gui/dialogs/custom_function_manager_dialog.py
openhcs/pyqt_gui/dialogs/function_selector_dialog.py
openhcs/pyqt_gui/dialogs/metadata_viewer_dialog.py
openhcs/pyqt_gui/services/__init__.py
openhcs/pyqt_gui/services/async_service_bridge.py
openhcs/pyqt_gui/services/config_cache_adapter.py
openhcs/pyqt_gui/services/llm_pipeline_service.py
openhcs/pyqt_gui/services/reactor_providers.py
openhcs/pyqt_gui/services/service_adapter.py
openhcs/pyqt_gui/services/shortcut_manager.py
openhcs/pyqt_gui/services/window_config.py
openhcs/pyqt_gui/services/window_handlers.py
openhcs/pyqt_gui/shared/__init__.py
openhcs/pyqt_gui/shared/config_validator.py
openhcs/pyqt_gui/testing/__init__.py
openhcs/pyqt_gui/testing/event_recorder.py
openhcs/pyqt_gui/testing/test_validator.py
openhcs/pyqt_gui/utils/__init__.py
openhcs/pyqt_gui/utils/log_detection_utils.py
openhcs/pyqt_gui/widgets/__init__.py
openhcs/pyqt_gui/widgets/config_preview_formatters.py
openhcs/pyqt_gui/widgets/image_browser.py
openhcs/pyqt_gui/widgets/pipeline_editor.py
openhcs/pyqt_gui/widgets/plate_manager.py
openhcs/pyqt_gui/widgets/step_parameter_editor.py
openhcs/pyqt_gui/widgets/shared/__init__.py
openhcs/pyqt_gui/widgets/shared/plate_view_widget.py
openhcs/pyqt_gui/widgets/shared/time_travel_widget.py
openhcs/pyqt_gui/widgets/shared/well_selector_dialog.py
openhcs/pyqt_gui/widgets/shared/zmq_server_manager.py
openhcs/pyqt_gui/widgets/shared/server_browser/__init__.py
openhcs/pyqt_gui/widgets/shared/server_browser/presentation_models.py
openhcs/pyqt_gui/widgets/shared/server_browser/progress_tree_builder.py
openhcs/pyqt_gui/widgets/shared/server_browser/server_kill_service.py
openhcs/pyqt_gui/widgets/shared/server_browser/server_tree_population.py
openhcs/pyqt_gui/widgets/shared/services/batch_workflow_service.py
openhcs/pyqt_gui/widgets/shared/services/execution_server_status_presenter.py
openhcs/pyqt_gui/widgets/shared/services/plate_config_resolver.py
openhcs/pyqt_gui/widgets/shared/services/progress_batch_reset.py
openhcs/pyqt_gui/widgets/shared/services/zmq_client_service.py
openhcs/pyqt_gui/windows/__init__.py
openhcs/pyqt_gui/windows/config_window.py
openhcs/pyqt_gui/windows/dual_editor_window.py
openhcs/pyqt_gui/windows/file_browser_window.py
openhcs/pyqt_gui/windows/help_window.py
openhcs/pyqt_gui/windows/help_windows.py
openhcs/pyqt_gui/windows/managed_windows.py
openhcs/pyqt_gui/windows/plate_viewer_window.py
openhcs/pyqt_gui/windows/snapshot_browser_window.py
openhcs/pyqt_gui/windows/synthetic_plate_generator_window.py
openhcs/runtime/fiji_stream_visualizer.py
openhcs/runtime/fiji_viewer_server.py
openhcs/runtime/napari_stream_visualizer.py
openhcs/runtime/napari_viewer_server.py
openhcs/runtime/omero_instance_manager.py
openhcs/runtime/remote_orchestrator.py
openhcs/runtime/zmq_config.py
openhcs/runtime/zmq_execution_client.py
openhcs/runtime/zmq_execution_server.py
openhcs/runtime/zmq_execution_server_launcher.py
openhcs/serialization/__init__.py
openhcs/serialization/pycodify_formatters.py
openhcs/tests/__init__.py
openhcs/tests/basic_pipeline.py
openhcs/tests/test_pipeline.py
openhcs/tests/test_pipeline_old.py
openhcs/tests/generators/__init__.py
openhcs/tests/generators/generate_synthetic_data.py
openhcs/textual_tui/styles.css
openhcs/ui/shared/__init__.py
openhcs/ui/shared/code_editor_form_updater.py
openhcs/ui/shared/parameter_form_config_factory.py
openhcs/ui/shared/parameter_form_constants.py
openhcs/ui/shared/pattern_data_manager.py
openhcs/ui/shared/pattern_file_service.py
openhcs/ui/shared/search_service.py
openhcs/ui/shared/streaming_service.py
openhcs/ui/shared/system_monitor_core.py
openhcs/ui/shared/ui_utils.py
openhcs/utils/display_config_factory.py
openhcs/utils/enum_factory.py
openhcs/utils/environment.py
openhcs/utils/import_utils.py
openhcs/utils/performance_monitor.py
openhcs/utils/pipeline_migration.py
openhcs/utils/recache_function_registry.py
openhcs/utils/string_case.py
openhcs/validation/__init__.py
openhcs/validation/ast_validator.py
openhcs/validation/validate.py