{
  "schema_version": "openhcs.agent-workflow-validation.v1",
  "run": {
    "run_id": "candidate-20260804-13",
    "thread_id": "019fcec9-0355-7fd3-8fc1-6d305f67687b",
    "started_at_utc": "2026-08-04T21:58:29.363988900Z",
    "ended_at_utc": "2026-08-04T22:08:38.429664911Z",
    "agent_wall_time_seconds": 609.065676,
    "uncut_video_seconds": 647.2,
    "verdict": "passed",
    "operation_mode": "unattended",
    "failure": null,
    "blocker": null
  },
  "client": {
    "name": "OpenAI Codex",
    "version": "0.146.0",
    "model": "gpt-5.6-sol",
    "provider": "OpenAI",
    "registration_target_id": null,
    "host_platform": "Linux 7.0.12-zen1-1-zen x86_64",
    "authentication_mode": "existing Codex account session",
    "approval_policy": "dangerously-bypass-approvals-and-sandbox",
    "invocation_flags": [
      "exec",
      "--json",
      "--ephemeral",
      "--ignore-user-config",
      "--skip-git-repo-check",
      "--dangerously-bypass-approvals-and-sandbox"
    ]
  },
  "openhcs": {
    "version": "0.7.13",
    "commit": "f1c1d9b670181d712419d5d8d4d07c199ebcf01d",
    "polystore_commit": "2ce7ad051282ee95a6f1bd1c05751d4ed52a675f",
    "pyqt_reactive_commit": "e49d44e88339aad9341a65fc7ba1dc6e0ded3011",
    "installation_kind": "source checkout virtual environment",
    "mcp_transport": "stdio",
    "surface_profile": "desktop",
    "exposed_tool_count": 66,
    "packaged_resource_count": 42,
    "server_health": "ok",
    "server_source_changed_since_import": false
  },
  "fixture": {
    "kind": "public NeuronCyto II crossover neurite-outgrowth assay field 1",
    "source_publication": "NeuronCyto II: An automatic and quantitative solution for crossover neural cells in high throughput screening",
    "source_publication_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC5089663/",
    "plate_root": "/home/ts/code/projects/openhcs/mcp_outputs/website-agent-demo/candidate-20260804-13/plate",
    "output_root": "/home/ts/code/projects/openhcs/mcp_outputs/website-agent-demo/candidate-20260804-13/outputs",
    "biological_projection": {
      "well": "1",
      "site": "1",
      "z_index": "1",
      "timepoint": "1",
      "channels": {
        "1_w1.tif": "1 / W1_neuron_neurite",
        "1_w2.tif": "2 / W2_soma_nuclear"
      }
    },
    "file_manifest": [
      {
        "path": "1_w1.tif",
        "shape": [800, 800],
        "dtype": "uint8",
        "sha256": "2fdef90d08c132fb8de02a03071b03caed38cdd8d41cd048371dc17592b574e7"
      },
      {
        "path": "1_w2.tif",
        "shape": [800, 800],
        "dtype": "uint8",
        "sha256": "ddd9f8a9edd0837275d6967fd746bdd424bb7a642139073e443a07eca0271847"
      },
      {
        "path": "openhcs_metadata.json",
        "sha256": "06e3df8150322731012af5be86c4e8312914c72622bdda0611517e9b5aa5425f"
      }
    ],
    "exact_file_set_verified_before_run": true
  },
  "protocol": {
    "acceptance_gate_version": "agent-workflow-validation.v1",
    "prompt_sha256": "18e732a9607e58423b852debb9a74c9fcfa6207e1b088b713db03fc34a5b82da",
    "prompt": "The folder /home/ts/code/projects/openhcs/mcp_outputs/website-agent-demo/candidate-20260804-13/plate contains field 1 from the public NeuronCyto II crossover neurite-outgrowth assay. The W1 plane is the neuronal cell-and-neurite signal, and the W2 plane is the soma/nuclear signal. Treat both planes as biological well/image id 1.\n\nUsing only the OpenHCS MCP and the connected OpenHCS desktop, build a compact but biologically meaningful pipeline that normalizes the raw channels, enhances dim neurites, segments nuclei and neuronal cell bodies, assigns neurite outgrowth to individual neurons, and measures per-neuron morphology and topology. Save reviewable images, object ROIs, spatial-graph paths, SWC morphology, and measurement tables under /home/ts/code/projects/openhcs/mcp_outputs/website-agent-demo/candidate-20260804-13/outputs, and open the results in Napari on port 5613.\n\nStart by inspecting the folder and confirming its axes and channel identities. These exported TIFF containers each expose their own native channel coordinate, so declare the authoritative Source Bindings projection from the start: keep both planes in biological well/image id 1 and preserve their physical filename provenance, while projecting W1 and W2 as distinct biological channels 1 and 2. Use registered OpenHCS functions or presets, not repository/source inspection or a new custom function. Leave the finished workflow visible and editable in the desktop UI. Keep the ZMQ Server Manager and its granular execution progress visible while the pipeline runs. Validate and compile before running, inspect the structured measurements and persistent outputs, and verify the settled Napari viewer state.\n\nMake the final viewer scientifically legible rather than showing every intermediate mask at once: retain an enhanced neuronal signal as context, show the unified neuron labels in which each cell body and its assigned neurites share one identity, show the spatial-graph path layer, hide redundant intermediate label layers, select the graph layer, and expose its feature table so branch identity, neuron assignment, distance, and tortuosity can be inspected. Return the editable generated Python plus a concise evidence summary. If validation, execution, or presentation fails, diagnose and repair it through MCP.\n\nThis prompt authorizes writes under the stated output directory, changes to this isolated OpenHCS desktop session, pipeline execution, and launching Napari. Do not use shell commands or inspect repository files.",
    "granted_write_roots": [
      "/home/ts/code/projects/openhcs/mcp_outputs"
    ],
    "authorized_side_effects": [
      "mutate the isolated OpenHCS desktop session",
      "write beneath the stated output root",
      "execute the pipeline",
      "launch Napari on port 5613"
    ],
    "prohibited_tool_classes": [
      "shell",
      "repository inspection",
      "browser",
      "non-OpenHCS filesystem tools"
    ]
  },
  "trace": {
    "event_log_path": "cold-start-workflow-events.jsonl",
    "event_log_sha256": "de8342948e39a9a9a8dc487770bdb32012f683799d4479a1ebeb5d125a563749",
    "transcript_path": "cold-start-workflow-transcript.txt",
    "transcript_sha256": "0a1242f902d8fdb76137edf6f5d37055ff3f43650b3691f54fc77a8c333a9e50",
    "final_response_path": "cold-start-workflow-final.md",
    "final_response_sha256": "145a0231f59bc359d88e0213a401912aeaf4921ab951e11451278e9535bed503",
    "ordered_mcp_call_count": 140,
    "completed_mcp_call_count": 139,
    "failed_mcp_call_count": 1,
    "result_error_count": 30,
    "failed_or_error_call_ids": [
      "item_41",
      "item_42",
      "item_44",
      "item_45",
      "item_46",
      "item_54",
      "item_55",
      "item_56",
      "item_57",
      "item_58",
      "item_64",
      "item_65",
      "item_66",
      "item_67",
      "item_68",
      "item_69",
      "item_70",
      "item_71",
      "item_73",
      "item_77",
      "item_78",
      "item_79",
      "item_80",
      "item_85",
      "item_92",
      "item_96",
      "item_118",
      "item_119",
      "item_120",
      "item_130",
      "item_133"
    ],
    "non_mcp_calls": [],
    "human_interventions": [],
    "approval_events": [],
    "model_repair_attempts": [
      "projected the two exported TIFFs through Source Bindings into one biological image with two channels",
      "moved from an unavailable preset contribution shape to the same registered functions in an authored pipeline",
      "corrected lazy configuration and enum values through validation feedback",
      "corrected the selected-plate workflow enum from init to init_plate",
      "corrected output targeting and the aggregate code-document route"
    ]
  },
  "evidence": {
    "typed_plate_inspection_call": "item_11",
    "pipeline_validation_call": "item_81",
    "pipeline_apply_call": "item_88",
    "initialization_call": "item_94",
    "compilation_call": "item_100",
    "execution_call": "item_106",
    "terminal_state_call": "item_113",
    "viewer_state_call": "item_122",
    "viewer_presentation_calls": [
      "item_124",
      "item_125"
    ],
    "viewer_validation_call": "item_126",
    "viewer_snapshot_call": "item_128",
    "pipeline_source_call": "item_138",
    "pipeline_source_path": "cold-start-workflow-pipeline.py",
    "pipeline_source_sha256": "48b6e4f9dbc54932df8a95c405f4b832c1ca35856d866a261faf15fa3c14b754",
    "terminal_state": "complete",
    "execution_time_seconds": 16.5,
    "result_summary": {
      "neurons": 9,
      "nuclei": 10,
      "total_outgrowth_pixels": 1982,
      "processes": 47,
      "branches": 8,
      "mean_outgrowth_per_neuron_pixels": 220.22,
      "mean_straightness": 0.901,
      "significant_growth_percent": 100.0,
      "spatial_graph_path_count": 25
    },
    "output_inventory": {
      "review_tiff_count": 2,
      "roi_zip_count": 5,
      "swc_count": 1,
      "detail_csv_count": 2,
      "consolidated_csv_count": 1,
      "summary_text_count": 4,
      "metadata_json_count": 1,
      "napari_screenshot_count": 1,
      "total_persistent_output_count_excluding_screenshot": 16
    },
    "viewer": {
      "port": 5613,
      "mounted_layer_count": 7,
      "visible_layer_count": 3,
      "selected_graph_feature_row": 0,
      "nonzero_payloads": 9,
      "expected_payloads": 9,
      "missing_coordinates": 0,
      "duplicate_coordinates": 0,
      "pending_updates": 0
    },
    "post_run_finding": {
      "description": "The SWC file was materialized but the 0.7.13 result inventory did not classify the .swc suffix.",
      "release_fix_commit": "973c51fd0425af52db58d16ab283bcae4dd864fe",
      "fix_boundary": "FileFormat.TEXT suffix ownership",
      "verification": "30 focused and adjacent tests passed; the exact output directory then returned the SWC record through the ordinary result query."
    },
    "post_qa_corrected_recapture": {
      "reason": "Visual review of the unattended result exposed one clustered neurite crossover that the tracing algorithm had classified as branches.",
      "relationship_to_unattended_run": "The first 38 seconds of the edited video retain the original unattended desktop construction and execution. The final Napari interaction is a post-fix recapture against the same public field; the original uncut run, transcript, event log, report, and generated pipeline remain unchanged.",
      "execution_mode": "Direct OpenHCS MCP execution followed by native Napari feature-table capture",
      "openhcs_version": "0.7.14",
      "release_fix_commit": "0eb5f77c02bb17ae612ad262d8d514f4690b59ee",
      "fix_boundary": "Registered neurite graph extraction strategy",
      "pipeline_source_sha256": "f1e91832e1791e5addd1ebcb99afbe3294109a78eabffa16ac8f2480a92943cf",
      "execution_record_sha256": "1c2527067c751fcb91dce4cc6675e9a11f5c06e8b9f9eb9cc7d12ca952018bfd",
      "viewer_state_sha256": "c3dd75c00a3077686400843f6308fd45f46216a5551d37c84df96f188016adb0",
      "row_selection_capture_sha256": "42ed55fb6cceeb62444f7b600616a1aeedc62867a415468a3ae7506625e9d200",
      "result_summary": {
        "neurons": 9,
        "nuclei": 10,
        "total_outgrowth_pixels": 1865,
        "processes": 47,
        "branches": 6,
        "resolved_crossovers": 1,
        "mean_outgrowth_per_neuron_pixels": 207.22222222222223,
        "mean_straightness": 0.901054,
        "significant_growth_percent": 100.0,
        "spatial_graph_path_count": 24
      }
    },
    "media": {
      "uncut_video_path": "cold-start-workflow-uncut.mp4",
      "uncut_video_sha256": "e3c71086fbe6ea85bfb8ae557d3cc129c6a745779fcfa6c0c0b5388e13956c58",
      "retired_composite": {
        "reason": "Mixed the unattended run with a later human QA recapture",
        "video_sha256": "26c3a8b110c14598504f2403f7b4ba35441799122fa53a17fcca05df6a13b588",
        "video_seconds": 42.6,
        "poster_sha256": "bd78ee088005a005e88a49b5968a5941c0738b5f0f37e4ad505ab536057e0758"
      }
    }
  },
  "acceptance": {
    "typed_plate_inspection": true,
    "editable_validated_compiled_pipeline": true,
    "materialized_images_rois_spatial_graph_swc_measurements": true,
    "settled_viewer_without_coordinate_defects": true,
    "no_repository_or_non_mcp_workflow_tools": true,
    "no_domain_intervention_after_prompt": true
  }
}