LICENSE
MANIFEST.in
README.md
pyproject.toml
setup.py
THIRD_PARTY_LICENSES/napari-roi-manager-LICENSE
openhcs/__init__.py
openhcs/_source_dependencies.py
openhcs/cli.py
openhcs/napari.yaml
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/agent/__init__.py
openhcs/agent/authoring_contexts.py
openhcs/agent/capabilities.py
openhcs/agent/exceptions.py
openhcs/agent/knowledge_manifest.py
openhcs/agent/knowledge_manifest_schema.py
openhcs/agent/path_policy.py
openhcs/agent/runtime_platform.py
openhcs/agent/ui_bridge_actions.py
openhcs/agent/ui_bridge_identities.py
openhcs/agent/dto/__init__.py
openhcs/agent/dto/architecture.py
openhcs/agent/dto/authoring.py
openhcs/agent/dto/common.py
openhcs/agent/dto/config.py
openhcs/agent/dto/execution.py
openhcs/agent/dto/functions.py
openhcs/agent/dto/knowledge.py
openhcs/agent/dto/mcp.py
openhcs/agent/dto/pipeline.py
openhcs/agent/dto/plate.py
openhcs/agent/dto/ui_bridge.py
openhcs/agent/dto/viewer.py
openhcs/agent/resources/__init__.py
openhcs/agent/services/__init__.py
openhcs/agent/services/architecture_projection_service.py
openhcs/agent/services/config_service.py
openhcs/agent/services/execution_session_service.py
openhcs/agent/services/function_catalog_service.py
openhcs/agent/services/knowledge_base_service.py
openhcs/agent/services/llm_context_service.py
openhcs/agent/services/llm_prompt_resources.py
openhcs/agent/services/object_state_field_help_service.py
openhcs/agent/services/object_state_field_projection.py
openhcs/agent/services/pipeline_authoring_service.py
openhcs/agent/services/plate_inspection_service.py
openhcs/agent/services/plate_streaming_service.py
openhcs/agent/services/runtime_server_service.py
openhcs/agent/services/selected_plate_service.py
openhcs/agent/services/stdio.py
openhcs/agent/services/synthetic_plate_service.py
openhcs/agent/services/ui_bridge_service.py
openhcs/agent/services/ui_bridge_transport.py
openhcs/agent/services/viewer_window_service.py
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/alias_property.py
openhcs/core/aligned_image_payload.py
openhcs/core/artifact_inspection.py
openhcs/core/artifact_key_selection.py
openhcs/core/artifact_observability.py
openhcs/core/artifacts.py
openhcs/core/autoregister_preparation.py
openhcs/core/axis_filter.py
openhcs/core/callable_contract.py
openhcs/core/compiled_execution.py
openhcs/core/compiled_step_plan.py
openhcs/core/component_group_scope.py
openhcs/core/component_set.py
openhcs/core/config.py
openhcs/core/config_cache.py
openhcs/core/config_document.py
openhcs/core/debug.py
openhcs/core/debug_session_projection.py
openhcs/core/debug_views.py
openhcs/core/enum_utils.py
openhcs/core/execution_state.py
openhcs/core/function_contract_metadata.py
openhcs/core/function_patterns.py
openhcs/core/function_reference.py
openhcs/core/function_step_document.py
openhcs/core/function_step_transport.py
openhcs/core/image_file_serialization.py
openhcs/core/image_shapes.py
openhcs/core/input_workspace.py
openhcs/core/invocation_artifacts.py
openhcs/core/lazy_gpu_imports.py
openhcs/core/lazy_placeholder.py
openhcs/core/log_utils.py
openhcs/core/measurement_feature_queries.py
openhcs/core/measurement_image_alignment.py
openhcs/core/measurement_lookup_dialect.py
openhcs/core/measurement_row_materialization.py
openhcs/core/metadata_cache.py
openhcs/core/native_threading.py
openhcs/core/path_cache.py
openhcs/core/path_pattern_matching.py
openhcs/core/pipeline_document.py
openhcs/core/pipeline_document_fields.py
openhcs/core/plate_file_inventory.py
openhcs/core/plate_image_inventory.py
openhcs/core/process_local_cache.py
openhcs/core/public_api.py
openhcs/core/python_source_literal.py
openhcs/core/registry_strategies.py
openhcs/core/runtime_adapters.py
openhcs/core/runtime_array_values.py
openhcs/core/runtime_artifact_queries.py
openhcs/core/runtime_artifact_values.py
openhcs/core/runtime_batch_contracts.py
openhcs/core/runtime_equivalence.py
openhcs/core/runtime_execution_validation.py
openhcs/core/runtime_exports.py
openhcs/core/runtime_identifier.py
openhcs/core/runtime_image_loading.py
openhcs/core/runtime_image_values.py
openhcs/core/runtime_measurements.py
openhcs/core/runtime_object_label_aggregation.py
openhcs/core/runtime_object_label_building.py
openhcs/core/runtime_object_label_domains.py
openhcs/core/runtime_object_labels.py
openhcs/core/runtime_output_matching.py
openhcs/core/runtime_pattern_cache.py
openhcs/core/runtime_plane_projection.py
openhcs/core/runtime_profile.py
openhcs/core/runtime_relationships.py
openhcs/core/runtime_slice_alignment.py
openhcs/core/runtime_slice_projection.py
openhcs/core/runtime_source_binding_cache.py
openhcs/core/runtime_sparse_labels.py
openhcs/core/runtime_spatial_graph.py
openhcs/core/runtime_spatial_grid.py
openhcs/core/runtime_stack_cache.py
openhcs/core/runtime_stores.py
openhcs/core/runtime_tabular_values.py
openhcs/core/selection.py
openhcs/core/source_binding_context.py
openhcs/core/source_binding_selection.py
openhcs/core/source_binding_workspace.py
openhcs/core/source_bindings.py
openhcs/core/source_bindings_view.py
openhcs/core/source_image_provenance.py
openhcs/core/source_image_semantics.py
openhcs/core/source_load_plan.py
openhcs/core/source_matching.py
openhcs/core/source_metadata.py
openhcs/core/source_path_identity.py
openhcs/core/source_plane_alignment.py
openhcs/core/source_projection.py
openhcs/core/source_spatial_domain.py
openhcs/core/source_workspace_projection.py
openhcs/core/step_dependencies.py
openhcs/core/streaming_config_declarations.py
openhcs/core/streaming_config_factory.py
openhcs/core/synthetic_plate_generation.py
openhcs/core/utils.py
openhcs/core/variable_component_stack_requirement.py
openhcs/core/vfs_protocol.py
openhcs/core/viewer_streaming_service.py
openhcs/core/virtual_workspace_metadata.py
openhcs/core/worker_start_policy.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/equivalence/__init__.py
openhcs/core/equivalence/arrays.py
openhcs/core/equivalence/cells.py
openhcs/core/equivalence/comparison.py
openhcs/core/equivalence/images.py
openhcs/core/equivalence/keys.py
openhcs/core/equivalence/measurement_facts.py
openhcs/core/equivalence/measurement_features.py
openhcs/core/equivalence/measurement_requirements.py
openhcs/core/equivalence/measurement_rows.py
openhcs/core/equivalence/object_label_measurements.py
openhcs/core/equivalence/outputs.py
openhcs/core/equivalence/policy.py
openhcs/core/equivalence/relationships.py
openhcs/core/equivalence/report.py
openhcs/core/equivalence/tables.py
openhcs/core/memory/__init__.py
openhcs/core/memory/decorators.py
openhcs/core/orchestrator/__init__.py
openhcs/core/orchestrator/analysis_consolidation.py
openhcs/core/orchestrator/compiled_plate_execution.py
openhcs/core/orchestrator/execution_result.py
openhcs/core/orchestrator/gpu_scheduler.py
openhcs/core/orchestrator/orchestrator.py
openhcs/core/orchestrator/worker_execution.py
openhcs/core/orchestrator/worker_lanes.py
openhcs/core/orchestrator/worker_profiling.py
openhcs/core/pipeline/__init__.py
openhcs/core/pipeline/artifact_planning.py
openhcs/core/pipeline/compilation_session.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/pipeline/step_snapshot.py
openhcs/core/progress/__init__.py
openhcs/core/progress/debug_projection.py
openhcs/core/progress/emitters.py
openhcs/core/progress/exceptions.py
openhcs/core/progress/live_measurements.py
openhcs/core/progress/projection.py
openhcs/core/progress/registry.py
openhcs/core/progress/runtime_artifacts.py
openhcs/core/progress/runtime_tree.py
openhcs/core/progress/types.py
openhcs/core/steps/__init__.py
openhcs/core/steps/abstract.py
openhcs/core/steps/function_artifact_materialization.py
openhcs/core/steps/function_execution.py
openhcs/core/steps/function_io.py
openhcs/core/steps/function_output_identity.py
openhcs/core/steps/function_output_manifest.py
openhcs/core/steps/function_outputs.py
openhcs/core/steps/function_runtime.py
openhcs/core/steps/function_step.py
openhcs/core/steps/stream_component_semantics.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/experimental_layout_rows.py
openhcs/formats/metaxpress.py
openhcs/formats/pattern/__init__.py
openhcs/formats/pattern/pattern_discovery.py
openhcs/formats/pattern/pattern_resolver.py
openhcs/interop/__init__.py
openhcs/interop/cellprofiler_setting_normalization.py
openhcs/interop/cellprofiler/__init__.py
openhcs/interop/cellprofiler/analyst_export.py
openhcs/interop/cellprofiler/cellprofiler_literals.py
openhcs/interop/cellprofiler/compile_time_contracts.py
openhcs/interop/cellprofiler/database_column_dialect.py
openhcs/interop/cellprofiler/image_normalization.py
openhcs/interop/cellprofiler/image_set_numbering.py
openhcs/interop/cellprofiler/measurement_dialect.py
openhcs/interop/cellprofiler/measurement_lookup.py
openhcs/interop/cellprofiler/measurement_scope.py
openhcs/interop/cellprofiler/measurement_semantic_profiles.py
openhcs/interop/cellprofiler/module_artifact_contracts.py
openhcs/interop/cellprofiler/module_artifact_declarations.py
openhcs/interop/cellprofiler/module_callable_abi.py
openhcs/interop/cellprofiler/module_declarations.py
openhcs/interop/cellprofiler/module_measurement_features.py
openhcs/interop/cellprofiler/module_settings.py
openhcs/interop/cellprofiler/module_structuring_element_settings.py
openhcs/interop/cellprofiler/parser.py
openhcs/interop/cellprofiler/pipeline_import.py
openhcs/interop/cellprofiler/plate_workspace.py
openhcs/interop/cellprofiler/setting_names.py
openhcs/interop/cellprofiler/settings_binder.py
openhcs/interop/cellprofiler/source_metadata.py
openhcs/interop/cellprofiler/worm_measurements.py
openhcs/interop/cellprofiler/runtime/__init__.py
openhcs/interop/cellprofiler/runtime/adapter.py
openhcs/interop/cellprofiler/runtime/artifact_binding.py
openhcs/interop/cellprofiler/runtime/function_contract_execution.py
openhcs/interop/cellprofiler/runtime/invocation.py
openhcs/interop/cellprofiler/runtime/main_flow.py
openhcs/interop/cellprofiler/runtime/measurement_execution_support.py
openhcs/interop/cellprofiler/runtime/measurement_recording.py
openhcs/interop/cellprofiler/runtime/measurement_rows.py
openhcs/interop/cellprofiler/runtime/measurement_source_names.py
openhcs/interop/cellprofiler/runtime/module_execution.py
openhcs/interop/cellprofiler/runtime/object_input_policies.py
openhcs/interop/cellprofiler/runtime/object_label_measurements.py
openhcs/interop/cellprofiler/runtime/object_measurement_execution.py
openhcs/interop/cellprofiler/runtime/object_measurement_row_completion.py
openhcs/interop/cellprofiler/runtime/object_measurement_row_policies.py
openhcs/interop/cellprofiler/runtime/object_measurement_tables.py
openhcs/interop/cellprofiler/runtime/object_measurement_vectors.py
openhcs/interop/cellprofiler/runtime/output_contexts.py
openhcs/interop/cellprofiler/runtime/output_record_request.py
openhcs/interop/cellprofiler/runtime/output_recording.py
openhcs/interop/cellprofiler/runtime/primary_image_input_policies.py
openhcs/interop/cellprofiler/runtime/profile_fields.py
openhcs/interop/cellprofiler/runtime/relationship_measurement_rows.py
openhcs/interop/cellprofiler/runtime/runtime_profile.py
openhcs/introspection/__init__.py
openhcs/introspection/lazy_dataclass_utils.py
openhcs/mcp/__init__.py
openhcs/mcp/__main__.py
openhcs/mcp/bootstrap.py
openhcs/mcp/context.py
openhcs/mcp/control_timeout.py
openhcs/mcp/dev_client.py
openhcs/mcp/dev_client_commanding.py
openhcs/mcp/dev_client_core.py
openhcs/mcp/dev_client_rendering.py
openhcs/mcp/http.py
openhcs/mcp/http_auth.py
openhcs/mcp/installed_demo.py
openhcs/mcp/server.py
openhcs/mcp/dev_client_commands/__init__.py
openhcs/mcp/dev_client_commands/knowledge_pipeline.py
openhcs/mcp/dev_client_commands/plate.py
openhcs/mcp/dev_client_commands/ui.py
openhcs/mcp/dev_client_commands/viewer.py
openhcs/mcp/dev_client_renderers/__init__.py
openhcs/mcp/dev_client_renderers/config.py
openhcs/mcp/dev_client_renderers/knowledge.py
openhcs/mcp/dev_client_renderers/object_state.py
openhcs/mcp/dev_client_renderers/pipeline.py
openhcs/mcp/dev_client_renderers/plate.py
openhcs/mcp/dev_client_renderers/ui_bridge.py
openhcs/mcp/dev_client_renderers/viewer.py
openhcs/microscopes/__init__.py
openhcs/microscopes/bbbc.py
openhcs/microscopes/bioformats.py
openhcs/microscopes/bioformats_adapter.py
openhcs/microscopes/bioformats_well_key.py
openhcs/microscopes/exceptions.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/microscopes/source_bindings_handler.py
openhcs/microscopes/source_schema.py
openhcs/microscopes/tiff_metadata_mixin.py
openhcs/napari_roi_manager/__init__.py
openhcs/napari_roi_manager/_dataclasses.py
openhcs/napari_roi_manager/ij/__init__.py
openhcs/napari_roi_manager/ij/_convert.py
openhcs/napari_roi_manager/widgets/__init__.py
openhcs/napari_roi_manager/widgets/_dialogs.py
openhcs/napari_roi_manager/widgets/_roi_manager.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/numpy_runtime.py
openhcs/processing/backends/analysis/__init__.py
openhcs/processing/backends/analysis/cache_utils.py
openhcs/processing/backends/analysis/cell_counting_common.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/count_cells_simple.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/metaxpress_utils.py
openhcs/processing/backends/analysis/multi_template_matching.py
openhcs/processing/backends/analysis/neurite_outgrowth.py
openhcs/processing/backends/analysis/region_properties.py
openhcs/processing/backends/analysis/self_supervised_segmentation_3d.py
openhcs/processing/backends/analysis/skan_axon_analysis.py
openhcs/processing/backends/analysis/skeletonize_and_save.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/cellprofiler/__init__.py
openhcs/processing/backends/cellprofiler/_backend.py
openhcs/processing/backends/cellprofiler/alignment.py
openhcs/processing/backends/cellprofiler/alignment_mutual_information_offset.py
openhcs/processing/backends/cellprofiler/area_occupied.py
openhcs/processing/backends/cellprofiler/calculate_statistics.py
openhcs/processing/backends/cellprofiler/classification.py
openhcs/processing/backends/cellprofiler/colocalization.py
openhcs/processing/backends/cellprofiler/colocalization_costes.py
openhcs/processing/backends/cellprofiler/colocalization_costes_prefix.py
openhcs/processing/backends/cellprofiler/colocalization_costes_prefix_numba_pearson.py
openhcs/processing/backends/cellprofiler/color.py
openhcs/processing/backends/cellprofiler/contracts.json
openhcs/processing/backends/cellprofiler/crop.py
openhcs/processing/backends/cellprofiler/display_modules.py
openhcs/processing/backends/cellprofiler/distance_propagation_numba.py
openhcs/processing/backends/cellprofiler/edge.py
openhcs/processing/backends/cellprofiler/edit_objects.py
openhcs/processing/backends/cellprofiler/enum_attributes.py
openhcs/processing/backends/cellprofiler/export_to_database.py
openhcs/processing/backends/cellprofiler/feature_enhancement.py
openhcs/processing/backends/cellprofiler/flagging.py
openhcs/processing/backends/cellprofiler/gaussian_filter.py
openhcs/processing/backends/cellprofiler/granularity.py
openhcs/processing/backends/cellprofiler/grid.py
openhcs/processing/backends/cellprofiler/illumination.py
openhcs/processing/backends/cellprofiler/image_geometry.py
openhcs/processing/backends/cellprofiler/image_math.py
openhcs/processing/backends/cellprofiler/image_quality.py
openhcs/processing/backends/cellprofiler/imagej_macro.py
openhcs/processing/backends/cellprofiler/infrastructure.py
openhcs/processing/backends/cellprofiler/intensity.py
openhcs/processing/backends/cellprofiler/intensity_distribution.py
openhcs/processing/backends/cellprofiler/intensity_object_quantiles_numba.py
openhcs/processing/backends/cellprofiler/label_geometry.py
openhcs/processing/backends/cellprofiler/manual_objects.py
openhcs/processing/backends/cellprofiler/maxima.py
openhcs/processing/backends/cellprofiler/measurement_math.py
openhcs/processing/backends/cellprofiler/medial_axis.py
openhcs/processing/backends/cellprofiler/median_filter.py
openhcs/processing/backends/cellprofiler/morphology.py
openhcs/processing/backends/cellprofiler/neighbors.py
openhcs/processing/backends/cellprofiler/object_filtering.py
openhcs/processing/backends/cellprofiler/object_images.py
openhcs/processing/backends/cellprofiler/object_measurement_columnar_rows.py
openhcs/processing/backends/cellprofiler/object_overlap.py
openhcs/processing/backends/cellprofiler/outlines.py
openhcs/processing/backends/cellprofiler/perf_fixtures.py
openhcs/processing/backends/cellprofiler/primary_objects.py
openhcs/processing/backends/cellprofiler/projection.py
openhcs/processing/backends/cellprofiler/relationships.py
openhcs/processing/backends/cellprofiler/save_images.py
openhcs/processing/backends/cellprofiler/secondary.py
openhcs/processing/backends/cellprofiler/shape.py
openhcs/processing/backends/cellprofiler/skeleton.py
openhcs/processing/backends/cellprofiler/smoothing.py
openhcs/processing/backends/cellprofiler/spreadsheet_export.py
openhcs/processing/backends/cellprofiler/structuring_elements.py
openhcs/processing/backends/cellprofiler/texture.py
openhcs/processing/backends/cellprofiler/thresholding.py
openhcs/processing/backends/cellprofiler/thresholding_threshold_numba_diagnostics.py
openhcs/processing/backends/cellprofiler/thresholding_threshold_numba_diagnostics_quantized.py
openhcs/processing/backends/cellprofiler/thresholding_threshold_numba_otsu.py
openhcs/processing/backends/cellprofiler/thresholding_threshold_numba_otsu_histogram_multiotsu.py
openhcs/processing/backends/cellprofiler/thresholding_threshold_numba_otsu_weighted.py
openhcs/processing/backends/cellprofiler/tracking.py
openhcs/processing/backends/cellprofiler/watershed.py
openhcs/processing/backends/cellprofiler/worm_geometry.py
openhcs/processing/backends/cellprofiler/worms.py
openhcs/processing/backends/cellprofiler/zernike.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_config.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/method_axes.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/presets/__init__.py
openhcs/processing/presets/demo_contribution.py
openhcs/processing/presets/mfd_specs.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/czi_brain_axon_cellbody.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/loose_operaphenix_neurite_outgrowth.py
openhcs/processing/presets/pipelines/loose_operaphenix_neurite_outgrowth_metaxpress.py
openhcs/processing/presets/pipelines/neuroncyto_ii_crossover_neurite_outgrowth.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/embedded_code_documents.py
openhcs/pyqt_gui/services/function_step_code_document.py
openhcs/pyqt_gui/services/llm_pipeline_service.py
openhcs/pyqt_gui/services/main_window_workflows.py
openhcs/pyqt_gui/services/pipeline_object_state_binding.py
openhcs/pyqt_gui/services/plate_manager_batch_workflow.py
openhcs/pyqt_gui/services/plate_manager_root_state.py
openhcs/pyqt_gui/services/plate_manager_row.py
openhcs/pyqt_gui/services/plate_manager_state_projection.py
openhcs/pyqt_gui/services/pycodified_window_code_document.py
openhcs/pyqt_gui/services/reactor_providers.py
openhcs/pyqt_gui/services/service_adapter.py
openhcs/pyqt_gui/services/step_scope_identity.py
openhcs/pyqt_gui/services/time_travel_navigation.py
openhcs/pyqt_gui/services/ui_agent_bridge.py
openhcs/pyqt_gui/services/ui_bridge_composition.py
openhcs/pyqt_gui/services/ui_bridge_contracts.py
openhcs/pyqt_gui/services/ui_bridge_live_overview.py
openhcs/pyqt_gui/services/ui_bridge_object_state.py
openhcs/pyqt_gui/services/ui_bridge_object_state_scope_policy.py
openhcs/pyqt_gui/services/ui_bridge_pipeline_editor.py
openhcs/pyqt_gui/services/ui_bridge_plate_manager.py
openhcs/pyqt_gui/services/ui_bridge_registry.py
openhcs/pyqt_gui/services/ui_bridge_server.py
openhcs/pyqt_gui/services/ui_bridge_windows.py
openhcs/pyqt_gui/services/ui_thread_dispatch.py
openhcs/pyqt_gui/services/ui_window_ids.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/widgets/__init__.py
openhcs/pyqt_gui/widgets/artifact_plan_view.py
openhcs/pyqt_gui/widgets/config_preview_formatters.py
openhcs/pyqt_gui/widgets/debug_toolbar.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/source_bindings_editor.py
openhcs/pyqt_gui/widgets/step_parameter_editor.py
openhcs/pyqt_gui/widgets/shared/__init__.py
openhcs/pyqt_gui/widgets/shared/geometry_tracking.py
openhcs/pyqt_gui/widgets/shared/openhcs_manager_mixins.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/live_tree_sync.py
openhcs/pyqt_gui/widgets/shared/server_browser/presentation_models.py
openhcs/pyqt_gui/widgets/shared/server_browser/progress_projection.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_context.py
openhcs/pyqt_gui/widgets/shared/services/batch_workflow_components.py
openhcs/pyqt_gui/widgets/shared/services/compile_batch_workflow_service.py
openhcs/pyqt_gui/widgets/shared/services/compile_workflow_service.py
openhcs/pyqt_gui/widgets/shared/services/debug_progress_service.py
openhcs/pyqt_gui/widgets/shared/services/debug_session_projection.py
openhcs/pyqt_gui/widgets/shared/services/debug_workflow_service.py
openhcs/pyqt_gui/widgets/shared/services/execution_control_service.py
openhcs/pyqt_gui/widgets/shared/services/execution_server_status_presenter.py
openhcs/pyqt_gui/widgets/shared/services/execution_state.py
openhcs/pyqt_gui/widgets/shared/services/execution_submission_service.py
openhcs/pyqt_gui/widgets/shared/services/gui_event_bus_broadcast.py
openhcs/pyqt_gui/widgets/shared/services/live_measurement_progress_service.py
openhcs/pyqt_gui/widgets/shared/services/pipeline_debug_actions.py
openhcs/pyqt_gui/widgets/shared/services/pipeline_editor_workflows.py
openhcs/pyqt_gui/widgets/shared/services/plate_config_resolver.py
openhcs/pyqt_gui/widgets/shared/services/plate_manager_workflows.py
openhcs/pyqt_gui/widgets/shared/services/plate_pipeline_request_builder.py
openhcs/pyqt_gui/widgets/shared/services/plate_status_presenter.py
openhcs/pyqt_gui/widgets/shared/services/progress_batch_reset.py
openhcs/pyqt_gui/widgets/shared/services/progress_workflow_service.py
openhcs/pyqt_gui/widgets/shared/services/qt_widget_edit_commit.py
openhcs/pyqt_gui/widgets/shared/services/runtime_artifact_progress_service.py
openhcs/pyqt_gui/widgets/shared/services/terminal_result_builder.py
openhcs/pyqt_gui/widgets/shared/services/widget_action_dispatch.py
openhcs/pyqt_gui/widgets/shared/services/zmq_client_service.py
openhcs/pyqt_gui/windows/__init__.py
openhcs/pyqt_gui/windows/config_edit_session.py
openhcs/pyqt_gui/windows/config_window.py
openhcs/pyqt_gui/windows/debug_inspector_window.py
openhcs/pyqt_gui/windows/dual_editor_session.py
openhcs/pyqt_gui/windows/dual_editor_tab_builder.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/live_measurements_window.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_macro_runtime.py
openhcs/runtime/fiji_stream_visualizer.py
openhcs/runtime/fiji_viewer_server.py
openhcs/runtime/napari_stream_visualizer.py
openhcs/runtime/napari_streaming_handlers.py
openhcs/runtime/napari_swc_reader.py
openhcs/runtime/napari_viewer_server.py
openhcs/runtime/omero_instance_manager.py
openhcs/runtime/qt_window_snapshot.py
openhcs/runtime/viewer_component_system.py
openhcs/runtime/viewer_controls.py
openhcs/runtime/viewer_protocol.py
openhcs/runtime/window_snapshot.py
openhcs/runtime/zmq_compilation.py
openhcs/runtime/zmq_config.py
openhcs/runtime/zmq_control.py
openhcs/runtime/zmq_execution_client.py
openhcs/runtime/zmq_execution_observation.py
openhcs/runtime/zmq_execution_server.py
openhcs/runtime/zmq_execution_server_launcher.py
openhcs/runtime/zmq_execution_signature.py
openhcs/runtime/zmq_orchestrator_environment.py
openhcs/runtime/zmq_progress.py
openhcs/runtime/zmq_server_hooks.py
openhcs/runtime/zmq_worker_execution.py
openhcs/serialization/__init__.py
openhcs/serialization/json.py
openhcs/serialization/pycodify_formatters.py
openhcs/serialization/source_path_factoring.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/plate_manager_code_document.py
openhcs/ui/shared/plate_scope_identity.py
openhcs/ui/shared/search_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/validation/__init__.py
openhcs/validation/ast_validator.py
openhcs/validation/validate.py
scripts/build_mcp_knowledge_assets.py
scripts/smoke_installed_mcp.py