Review QC overlays¶
| For | Researchers reviewing image alignment after a completed sample |
| Hands-on steps | Open overview, annotated zoom, composite, summary, and audit |
| Prerequisites | At least one completed real-inference sample |
| Download/storage | No download; images and PDF already exist in the result |
| Writes to | Nothing unless report is rerun |
Open the generated images¶
For each completed sample, the current worker writes:
| File | Review |
|---|---|
overlays/overview_with_zoom_box.png |
Whole-slide orientation and the selected zoom box |
overlays/zoom_overlay_celltypes.png |
High-resolution cell annotations |
overlays/celltypes_overview_and_zoom.png |
Combined overview and annotated zoom |
overlays/celltypes_overview_and_zoom.pdf |
Vector/text-friendly version of the combined figure |
The repository output name is celltypes_overview_and_zoom.png—not a guessed
singular or alternate overlay name.
Compare the images with summary/summary.json. Confirm the slide ID, source
MPP, target MPP, processed percentage, random seed, and zoom coordinates. Then
check aggregated_celltypes/sample_aggregation_audit.csv for inclusion.
Visual review should consider tissue orientation, focus/stain artifacts, tissue selection, registration, cell-mark alignment, implausible dense/sparse regions, and whether the displayed zoom is representative. It does not turn model predictions into pathologist ground truth.
Rebuild the navigator¶
tumorquantai report /data/results
Expected output is a self-contained START_HERE.html with relative links only
to files that exist.
Stop and clean up¶
Image review does not modify results. Press Ctrl+C if report generation is interrupted and rerun. Do not delete overlays while retaining derived tables for a reproducible analysis.
Next: learn counts versus fractions.