README.md
pyproject.toml
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/components/__init__.py
openhcs/components/framework.py
openhcs/config_framework/__init__.py
openhcs/config_framework/cache_warming.py
openhcs/config_framework/config.py
openhcs/config_framework/context_manager.py
openhcs/config_framework/dual_axis_resolver.py
openhcs/config_framework/global_config.py
openhcs/config_framework/lazy_factory.py
openhcs/config_framework/placeholder.py
openhcs/constants/__init__.py
openhcs/constants/constants.py
openhcs/constants/input_source.py
openhcs/constants/streaming.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/registry_discovery.py
openhcs/core/roi.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/conversion_helpers.py
openhcs/core/memory/converters.py
openhcs/core/memory/decorators.py
openhcs/core/memory/dtype_scaling.py
openhcs/core/memory/exceptions.py
openhcs/core/memory/framework_config.py
openhcs/core/memory/framework_ops.py
openhcs/core/memory/gpu_cleanup.py
openhcs/core/memory/oom_recovery.py
openhcs/core/memory/slice_processing.py
openhcs/core/memory/stack_utils.py
openhcs/core/memory/utils.py
openhcs/core/orchestrator/__init__.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/pipeline_utils.py
openhcs/core/pipeline/step_attribute_stripper.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_to_python.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/signature_analyzer.py
openhcs/introspection/unified_parameter_analyzer.py
openhcs/io/__init__.py
openhcs/io/async_init.py
openhcs/io/atomic.py
openhcs/io/backend_registry.py
openhcs/io/base.py
openhcs/io/disk.py
openhcs/io/exceptions.py
openhcs/io/fiji_stream.py
openhcs/io/filemanager.py
openhcs/io/memory.py
openhcs/io/metadata_migration.py
openhcs/io/metadata_writer.py
openhcs/io/napari_stream.py
openhcs/io/omero_local.py
openhcs/io/pipeline_migration.py
openhcs/io/streaming.py
openhcs/io/virtual_workspace.py
openhcs/io/zarr.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/__init__.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/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/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/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/function_selector_dialog.py
openhcs/pyqt_gui/dialogs/group_by_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/persistent_system_monitor.py
openhcs/pyqt_gui/services/service_adapter.py
openhcs/pyqt_gui/services/simple_code_editor.py
openhcs/pyqt_gui/shared/__init__.py
openhcs/pyqt_gui/shared/color_scheme.py
openhcs/pyqt_gui/shared/config_validator.py
openhcs/pyqt_gui/shared/palette_manager.py
openhcs/pyqt_gui/shared/style_generator.py
openhcs/pyqt_gui/utils/__init__.py
openhcs/pyqt_gui/utils/log_detection_utils.py
openhcs/pyqt_gui/utils/process_tracker.py
openhcs/pyqt_gui/utils/window_utils.py
openhcs/pyqt_gui/widgets/__init__.py
openhcs/pyqt_gui/widgets/enhanced_path_widget.py
openhcs/pyqt_gui/widgets/function_list_editor.py
openhcs/pyqt_gui/widgets/function_pane.py
openhcs/pyqt_gui/widgets/image_browser.py
openhcs/pyqt_gui/widgets/log_viewer.py
openhcs/pyqt_gui/widgets/pipeline_editor.py
openhcs/pyqt_gui/widgets/plate_manager.py
openhcs/pyqt_gui/widgets/status_bar.py
openhcs/pyqt_gui/widgets/step_parameter_editor.py
openhcs/pyqt_gui/widgets/system_monitor.py
openhcs/pyqt_gui/widgets/mixins/__init__.py
openhcs/pyqt_gui/widgets/mixins/selection_preservation_mixin.py
openhcs/pyqt_gui/widgets/shared/__init__.py
openhcs/pyqt_gui/widgets/shared/clickable_help_components.py
openhcs/pyqt_gui/widgets/shared/column_filter_widget.py
openhcs/pyqt_gui/widgets/shared/layout_constants.py
openhcs/pyqt_gui/widgets/shared/no_scroll_spinbox.py
openhcs/pyqt_gui/widgets/shared/parameter_form_manager.py
openhcs/pyqt_gui/widgets/shared/plate_view_widget.py
openhcs/pyqt_gui/widgets/shared/widget_strategies.py
openhcs/pyqt_gui/widgets/shared/zmq_server_manager.py
openhcs/pyqt_gui/windows/__init__.py
openhcs/pyqt_gui/windows/base_form_dialog.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/plate_viewer_window.py
openhcs/pyqt_gui/windows/synthetic_plate_generator_window.py
openhcs/runtime/execution_server.py
openhcs/runtime/fiji_stream_visualizer.py
openhcs/runtime/fiji_viewer_server.py
openhcs/runtime/napari_stream_visualizer.py
openhcs/runtime/omero_instance_manager.py
openhcs/runtime/queue_tracker.py
openhcs/runtime/remote_orchestrator.py
openhcs/runtime/roi_converters.py
openhcs/runtime/zmq_base.py
openhcs/runtime/zmq_execution_client.py
openhcs/runtime/zmq_execution_server.py
openhcs/runtime/zmq_execution_server_launcher.py
openhcs/runtime/zmq_messages.py
openhcs/tests/__init__.py
openhcs/tests/basic_pipeline.py
openhcs/tests/test_pipeline.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/parameter_form_base.py
openhcs/ui/shared/parameter_form_config_factory.py
openhcs/ui/shared/parameter_form_constants.py
openhcs/ui/shared/parameter_form_service.py
openhcs/ui/shared/parameter_type_utils.py
openhcs/ui/shared/pattern_data_manager.py
openhcs/ui/shared/pattern_file_service.py
openhcs/ui/shared/search_service.py
openhcs/ui/shared/system_monitor_core.py
openhcs/ui/shared/ui_utils.py
openhcs/ui/shared/widget_creation_registry.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/recache_function_registry.py
openhcs/validation/__init__.py
openhcs/validation/ast_validator.py
openhcs/validation/validate.py