einarolafsson/community_toxoplasma_plaque_figures

Community Toxoplasma plaque-assay figures

Figure pages from plaque-assay papers, each with a box drawn by a spaCR user around every plaque well on the page. Contributions come from spaCR's Plaque Assay (Figure mode, "Contribute training data..."): spaCR proposes the wells its own detector finds, and the contributor corrects, deletes and adds boxes until every well is boxed.

Purpose

This is training data for spaCR's YOLO well detector (einarolafsson/toxoplasma-plaque-well-detector-yolo26, trained on einarolafsson/toxoplasma-plaque-well-detector-dataset). Accepted contributions are folded into the next detector release.

Licence

Everything here is shared under CC BY 4.0. By uploading, a contributor confirms that they have the right to share the page (for a published figure: the paper's licence permits redistribution, e.g. an open-access CC BY article) and agrees that it is redistributed under CC BY 4.0, with the source paper cited in the page's metadata.

File layout

Each upload is one folder:

contributions/<contribution-id>/
  contribution.json        spaCR version, date, licence agreed, consent, counts
  images/<page>.png        the figure page exactly as the boxes were drawn on it
  labels/<page>.txt        YOLO format, one line per well: `0 cx cy w h` (normalised 0-1)
  meta/<page>.json         source DOI / citation / PMCID when known, original file name,
                           image size, the boxes in pixels, and which of spaCR's
                           proposed boxes the contributor kept, moved or deleted

Class 0 is "plaque well" (a well, dish or spot image in which plaques are counted). A page is only accepted with at least one box; spaCR refuses to upload a page without annotations.

Review

Contributions arrive as pull requests and are reviewed by the maintainer before they are merged. Boxes that miss wells, or boxes around things that are not wells, are corrected or the contribution is declined. Careful boxes make the next detector better and let it ship sooner.

spaCR: https://github.com/EinarOlafsson/spacr