Runs and reproducibility
Every analysis step is a versioned pipeline run suitable for methods sections and audit trails.
Finding runs
| Location | What you see |
|---|---|
| Study home — Run history | All pipeline runs for the study |
| Slide detail — pipeline buttons | Latest completed run per pipeline type |
| Slide detail — QC panels | Summary statistics from latest runs |
Run record
Each run stores:
- Pipeline type (
tile_slide,tissue_detect,segment_cells,spatial_quantification,multiplex_phenotype,color_deconvolution,train_object_classifier,tma_dearray,export_ome_tiff,spatial_align,cohort_compare,interpret,batch, …) - Status, timestamps, and
run_id - Parameter JSON and pipeline version
- Result summary (cell count, tissue fraction, density, etc.)
- Artifact paths for masks, overlays, and export files
Provenance chains
Common chains:
spatial_quantification → segment_cells → tile_slide → slide upload
segment_cells → tile_slide → slide upload
tissue_detect → tile_slide → slide upload
Segmentation requires tiles. Spatial quantification requires completed segmentation.
Artifacts
Pipeline outputs — masks, overlays, and export files (JSON, CSV) — are downloadable from the slide detail page's export links.
Failed runs
Failed runs show an error message on the slide detail page. Common causes:
- Tiles not generated before segmentation
- Unsupported or corrupt image format
- Segmentation not complete before spatial quantification
- A whole-slide format that isn't supported yet
Fix the underlying issue and re-run from the slide detail page.
Versioning
Every run records a pipeline version. Include run IDs and versions in methods sections for reproducibility.
Re-running pipelines
Launch the same pipeline again from the slide detail page. A new run is created; the UI displays results from the latest completed run per pipeline type.