Skip to content

docs: link Histology Databank Explorer from data management plan, fix stale README numbers #2481

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
sr320 wants to merge 2 commits into
base: master
Choose a base branch
from
+10 −5
Open

docs: link Histology Databank Explorer from data management plan, fix stale README numbers #2481

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
0bfa7c1
docs: link Histology Databank Explorer from data management plan
sr320 Aug 6, 2026
57f0fe4
docs: correct stale coverage numbers in explorer README
sr320 Aug 6, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 2 additions & 0 deletions docs/Data-Management.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -319,6 +319,8 @@ _Taxa Representation in Nightingales_

All images should be stored in the proper species directory at http://owl.fish.washington.edu/hesperornis/

To browse what has already been catalogued, use the [Histology Databank Explorer](histology-explorer/index.html) — it joins the databank sheet to the images on owl so you can search samples by species, project, year, tissue, and researcher, and view the slides. Its "Unmatched images" view lists specimens imaged on owl that have no databank row yet. The Explorer is a snapshot rebuilt from a CSV export of the sheet, so new entries appear only after the next [rebuild](https://github.com/RobertsLab/resources/blob/master/docs/histology-explorer/README.md).



---
Expand Down
13 changes: 8 additions & 5 deletions docs/histology-explorer/README.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -43,8 +43,10 @@ histology-explorer/

Many images (all of `O_angasi`, the 2026 geoduck gonad set) are archival **`.tif`** files,
which browsers cannot display. The explorer shows browser-viewable `.jpg`/`.png` inline and
offers `.tif` as a download link. A sample with only `.tif` images shows a "TIF only" card.
To give those real thumbnails, generate `.jpg` derivatives (see next section).
offers the `.tif` as a download link. For `.tif` files with a generated `.jpg` derivative, the
derivative is displayed and the original stays downloadable — 44 of the 100 imaged samples
currently display this way. A `.tif` with no derivative shows a "TIF only" card; to give those
real thumbnails, generate derivatives (see next section).

## Generating JPEG derivatives for `.tif` images

Expand Down Expand Up @@ -76,9 +78,10 @@ updates `build/derivatives_manifest.csv`. Then:
## Current coverage (from the last build)

- 1,308 sheet rows → **940 unique samples**
- **100 samples** have at least one image; **56** have a browser-viewable image
- **918 image files** indexed; ~651 are "orphans" — imaged on owl but **not yet entered in the sheet**
(e.g. `O_angasi` 45–146, `O_lurida` 241–386, the Larken clam set). See `data/qc_report.md`.
- **100 samples** have at least one image, all of them browser-viewable
- **918 image files** indexed; **267** matched to a sample and **651** are "orphans" — imaged on owl
but **not yet entered in the sheet** (e.g. `O_angasi` 45–146, `O_lurida` 241–386, the Larken clam
set). See `data/qc_report.md`.

## Viewing locally

Expand Down