docs: link Histology Databank Explorer from data management plan, fix stale README numbers - #2481
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sr320 wants to merge 2 commits into
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docs: link Histology Databank Explorer from data management plan, fix stale README numbers#2481sr320 wants to merge 2 commits into
sr320 wants to merge 2 commits into
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The Histology Data Management Plan described filling out the databank sheet and storing images on owl, but never pointed at the Explorer that joins the two. Add that pointer after the owl storage convention, noting the "Unmatched images" backfill view and that the Explorer is a rebuilt snapshot rather than a live read of the sheet. Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
The README claimed 56 of the 100 imaged samples had a browser-viewable image, but data/qc_report.json from the last build reports 100. The gap was the JPEG derivative run: build/derivatives_manifest.csv has 352 rows, and every imaged sample in data/samples.json now resolves to a viewable image, 44 of them via generated derivatives. Update the coverage figures and add the matched-image count so the 918/651 split accounts for all indexed files. Also reword the .tif note, which was stale in the same way -- it implied archival sets like O_angasi still render as "TIF only" placeholders, when that state now only applies to a .tif with no derivative. Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
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What changed
1. Link the Explorer from the Histology Data Management Plan (
docs/Data-Management.md)The Explorer was already integrated in three places (mkdocs nav under Databases and Catalogs,
docs/index.md, anddocs/Lab-Inventory.md). The one place that discussed the databank without pointing at the portal was the Histology Data Management Plan — which is where someone actually working with histology lands. Added a pointer right after the owl storage convention, so the page flows from "where images go" to "where you look them up." It calls out the "Unmatched images" backfill view and notes the Explorer is a rebuilt snapshot, not a live read of the sheet.2. Fix stale numbers in the Explorer README (
docs/histology-explorer/README.md)The README claimed 56 of the 100 imaged samples had a browser-viewable image;
data/qc_report.jsonfrom the last build says 100.The
.tifnote was stale from the same cause and mattered more than the number — it said a.tif-only sample shows a "TIF only" card, implying archival sets likeO_angasiare still placeholders. Reworded to describe the no-derivative case it now actually is.Verification
Checked against the shipped data, not just the QC report:
build/derivatives_manifest.csv— 352 rowsdata/samples.json— all 100 imaged samples resolve to a viewable image, 44 via generated derivatives, zero in the TIF-only stateThat 56 → 100 jump is the derivative run, which is why both stale spots trace to one event.
Notes for reviewers
histology-explorer/index.htmlform (matchingLab-Inventory.md) rather than the../form the Bivalve Histology Tutorial link on the same page uses. Both render correctly on the live site — I checked the deployed HTML — but mkdocs rewrites the former to../histology-explorer/itself, without the outside-docs-dir warning the../form triggers.docs/histology-explorer/README.mdis not in the mkdocs nav; it's the maintainer doc the rebuild workflow points at.🤖 Generated with Claude Code