Evidence session: 019fcec9-0355-7fd3-8fc1-6d305f67687b Agent working... I’ll use the OpenHCS MCP as the sole control and inspection surface. I’ll first inspect the TIFF metadata and desktop state, then build the Source Bindings-aware workflow, validate/compile it, run with granular progress visible, inspect outputs, and finish the Napari presentation on port 5613. -> OpenHCS: health check OK health check -> OpenHCS: get authoring context OK get authoring context -> OpenHCS: get authoring context OK get authoring context -> OpenHCS: search capabilities OK search capabilities -> OpenHCS: ui list bridges OK ui list bridges -> OpenHCS: ui list state surfaces OK ui list state surfaces -> OpenHCS: ui list code documents OK ui list code documents -> OpenHCS: ui get state surface OK ui get state surface -> OpenHCS: ui get code document OK ui get code document -> OpenHCS: ui get code document OK ui get code document -> OpenHCS: inspect plate path OK inspect plate path -> OpenHCS: query plate files OK query plate files -> OpenHCS: sample plate image OK sample plate image -> OpenHCS: sample plate image OK sample plate image The source model is confirmed: two 800×800 uint8 Bio-Formats planes, each with native channel 1 and separate filename-derived wells (`1_w1.tif`, `1_w2.tif`). I’ll preserve Bio-Formats ingestion and apply Source Bindings only as the semantic projection so both map to biological well/image 1 while W1→channel 1 and W2→channel 2, retaining both physical source paths. -> OpenHCS: search knowledge OK search knowledge -> OpenHCS: search functions OK search functions -> OpenHCS: search functions OK search functions -> OpenHCS: search functions OK search functions -> OpenHCS: search functions OK search functions -> OpenHCS: search functions OK search functions -> OpenHCS: search functions OK search functions -> OpenHCS: get knowledge document OK get knowledge document -> OpenHCS: get knowledge document OK get knowledge document -> OpenHCS: get knowledge document OK get knowledge document -> OpenHCS: search knowledge OK search knowledge -> OpenHCS: search functions OK search functions -> OpenHCS: ui list actions OK ui list actions -> OpenHCS: search capabilities OK search capabilities -> OpenHCS: search capabilities OK search capabilities -> OpenHCS: search capabilities OK search capabilities -> OpenHCS: search capabilities OK search capabilities -> OpenHCS: search functions OK search functions -> OpenHCS: search functions OK search functions -> OpenHCS: search functions OK search functions -> OpenHCS: search functions OK search functions -> OpenHCS: describe function OK describe function -> OpenHCS: describe function OK describe function -> OpenHCS: search functions OK search functions -> OpenHCS: describe config schema OK describe config schema -> OpenHCS: describe config schema OK describe config schema -> OpenHCS: describe config schema OK describe config schema -> OpenHCS: describe config schema OK describe config schema -> OpenHCS: describe config schema OK describe config schema -> OpenHCS: describe config schema OK describe config schema -> OpenHCS: describe config schema OK describe config schema -> OpenHCS: describe config schema OK describe config schema -> OpenHCS: describe config schema OK describe config schema -> OpenHCS: describe config schema OK describe config schema -> OpenHCS: describe config schema OK describe config schema -> OpenHCS: describe config schema OK describe config schema -> OpenHCS: get knowledge document OK get knowledge document -> OpenHCS: search functions OK search functions -> OpenHCS: ui validate code document OK ui validate code document -> OpenHCS: ui validate code document OK ui validate code document -> OpenHCS: ui validate code document OK ui validate code document -> OpenHCS: ui validate code document OK ui validate code document -> OpenHCS: ui validate code document OK ui validate code document -> OpenHCS: search knowledge OK search knowledge -> OpenHCS: search knowledge OK search knowledge -> OpenHCS: search knowledge OK search knowledge -> OpenHCS: search knowledge OK search knowledge -> OpenHCS: search knowledge OK search knowledge -> OpenHCS: ui validate code document OK ui validate code document -> OpenHCS: ui validate code document OK ui validate code document -> OpenHCS: ui validate code document OK ui validate code document -> OpenHCS: ui validate code document OK ui validate code document -> OpenHCS: ui validate code document OK ui validate code document -> OpenHCS: ui validate code document OK ui validate code document -> OpenHCS: ui validate code document OK ui validate code document -> OpenHCS: ui validate code document OK ui validate code document -> OpenHCS: get knowledge document OK get knowledge document -> OpenHCS: describe internal symbol OK describe internal symbol -> OpenHCS: describe function OK describe function -> OpenHCS: get knowledge document OK get knowledge document -> OpenHCS: search knowledge OK search knowledge -> OpenHCS: ui validate code document OK ui validate code document -> OpenHCS: ui validate code document OK ui validate code document -> OpenHCS: ui validate code document OK ui validate code document -> OpenHCS: ui validate code document OK ui validate code document -> OpenHCS: ui validate code document OK ui validate code document The compact workflow now validates as a typed desktop document: exact Source Bindings, per-plane percentile normalization (the W1 context layer is deliberately named “Enhanced neuronal signal”), followed by the registered MetaXpress neurite engine. That engine segments nuclei and cell bodies, assigns outgrowth to neuron identities, emits per-image/per-neuron measurements, four label artifacts, and a rooted spatial graph whose materializers provide ROI paths and SWC. I’m applying it to the live Plate Manager now, then I’ll initialize and inspect the projected axes before compile/run. -> OpenHCS: ui get code document OK ui get code document -> OpenHCS: ui apply code document OK ui apply code document -> OpenHCS: ui wait for operation receipt OK ui wait for operation receipt -> OpenHCS: ui get state surface OK ui get state surface -> OpenHCS: ui get code document OK ui get code document -> OpenHCS: ui apply code document OK ui apply code document -> OpenHCS: ui wait for operation receipt OK ui wait for operation receipt -> OpenHCS: ui get state surface OK ui get state surface -> OpenHCS: ui list actions OK ui list actions -> OpenHCS: ui selected plate workflow ERROR ui selected plate workflow -> OpenHCS: ui list actions OK ui list actions -> OpenHCS: ui selected plate workflow OK ui selected plate workflow -> OpenHCS: ui wait for operation receipt OK ui wait for operation receipt -> OpenHCS: ui get state surface OK ui get state surface -> OpenHCS: ui get state surface OK ui get state surface -> OpenHCS: ui inspect selected plate images OK ui inspect selected plate images -> OpenHCS: ui list actions OK ui list actions -> OpenHCS: ui selected plate workflow OK ui selected plate workflow -> OpenHCS: ui wait for operation receipt OK ui wait for operation receipt -> OpenHCS: ui get state surface OK ui get state surface -> OpenHCS: ui get state surface OK ui get state surface -> OpenHCS: ui get state surface OK ui get state surface -> OpenHCS: ui list actions OK ui list actions -> OpenHCS: ui selected plate workflow OK ui selected plate workflow -> OpenHCS: ui wait for operation receipt OK ui wait for operation receipt -> OpenHCS: ui get state surface OK ui get state surface -> OpenHCS: ui get state surface OK ui get state surface -> OpenHCS: ui get state surface OK ui get state surface -> OpenHCS: ui get state surface OK ui get state surface -> OpenHCS: ui get state surface OK ui get state surface -> OpenHCS: ui query selected plate files OK ui query selected plate files -> OpenHCS: ui query selected plate files OK ui query selected plate files -> OpenHCS: ui query selected plate files OK ui query selected plate files -> OpenHCS: ui query selected plate files OK ui query selected plate files The pipeline has completed successfully with nine neurons quantified. I’m tightening the persistent-artifact inventory and settling the Napari presentation now—specifically the unified neuron identities, graph paths, and graph feature table. -> OpenHCS: ui query selected plate files OK ui query selected plate files -> OpenHCS: ui query selected plate files OK ui query selected plate files -> OpenHCS: ui query selected plate files OK ui query selected plate files -> OpenHCS: probe viewer window OK probe viewer window -> OpenHCS: get viewer window state OK get viewer window state Napari is live on 5613 with seven mounted layers. The graph artifact contains 25 feature-bearing paths; I’m reducing the display to the W1 enhanced context, unified neuron ROIs, and those paths, then selecting a graph row so its feature table is active. -> OpenHCS: isolate viewer window layers OK isolate viewer window layers -> OpenHCS: navigate viewer window OK navigate viewer window -> OpenHCS: validate viewer window state OK validate viewer window state The settled viewer now has exactly the intended three visible layers, W1 selected on the channel axis, and graph path 0 selected; all nine mounted payloads validate as nonzero with no missing or duplicate coordinates. I’m capturing the final window and retrieving the live editable Python plus the results action. -> OpenHCS: viewer snapshot window OK viewer snapshot window -> OpenHCS: ui list actions -> OpenHCS: ui get code document -> OpenHCS: get viewer window payloads OK ui list actions OK ui get code document OK get viewer window payloads -> OpenHCS: ui invoke action OK ui invoke action -> OpenHCS: ui invoke action OK ui invoke action -> OpenHCS: ui list code documents OK ui list code documents -> OpenHCS: ui list actions OK ui list actions -> OpenHCS: ui invoke action OK ui invoke action -> OpenHCS: ui get code document -> OpenHCS: ui get code document OK ui get code document OK ui get code document -> OpenHCS: ui query selected plate files OK ui query selected plate files -> OpenHCS: ui query selected plate files OK ui query selected plate files -> OpenHCS: ui query selected plate files OK ui query selected plate files -> OpenHCS: ui query selected plate files OK ui query selected plate files One artifact check found a gap: the spatial graph ROI is persistent, but the output index has no SWC file. I’m diagnosing that through the registered OpenHCS function catalog and will repair the workflow if a graph-to-SWC materializer is available. -> OpenHCS: search functions OK search functions -> OpenHCS: search functions OK search functions -> OpenHCS: search functions OK search functions Completed successfully in the connected OpenHCS desktop. - Source Bindings preserve `1_w1.tif` and `1_w2.tif` provenance while projecting both to well/image 1 as biological channels 1 and 2. - Pipeline validated, compiled, and completed through the visible ZMQ execution server. - Editable generated Python remains open in the Pipeline Editor and Plate Manager code-mode window. - Detected 9 neurons and 10 nuclei. - Total assigned neurite outgrowth: 1,982 px; 47 processes; 8 branches. - Mean outgrowth per neuron: 220.22 px; mean straightness: 0.901. - Graph layer contains 25 paths with inspectable `edge_id`, `neuron_label`, branch distance, soma distance, branch type, and tortuosity. - Napari remains active on port `5613`, showing only enhanced W1 context, unified neuron ROIs, and spatial-graph paths. The graph layer and feature row 0 are selected; redundant masks are hidden. - Viewer validation passed: all nine payloads nonzero, with no missing or duplicate coordinates. Key outputs: - [Final Napari snapshot](/home/ts/code/projects/openhcs/mcp_outputs/website-agent-demo/candidate-20260804-13/outputs/20260804T220728118912Z_napari_5613_OpenHCS_Napari_Visualization.png) - [Per-neuron measurements](/home/ts/code/projects/openhcs/mcp_outputs/website-agent-demo/candidate-20260804-13/outputs/plate_openhcs/images_results/1_site-1_z_index-1_timepoint-1_neurite_outgrowth_cells_step1_details.csv) - [Summary measurements](/home/ts/code/projects/openhcs/mcp_outputs/website-agent-demo/candidate-20260804-13/outputs/plate_openhcs/images_results/1_site-1_z_index-1_timepoint-1_neurite_outgrowth_summary_step1_details.csv) - [Unified neuron ROIs](/home/ts/code/projects/openhcs/mcp_outputs/website-agent-demo/candidate-20260804-13/outputs/plate_openhcs/images_results/1_s001_w1_z001_t001_neurons_step1_rois.roi.zip) - [Spatial-graph paths](/home/ts/code/projects/openhcs/mcp_outputs/website-agent-demo/candidate-20260804-13/outputs/plate_openhcs/images_results/1_s001_w1_z001_t001_neurite_morphology_step1.graph.roi.zip) The registered spatial-graph output was materialized and exposed in Napari, but the OpenHCS output index did not expose a separate `.swc` record despite the function’s SWC-capable artifact contract. No unregistered exporter or custom function was substituted. Run complete.