einarolafsson/community_toxoplasma_plaques

Community Toxoplasma plaques

Plaque-assay images, each with every plaque drawn as a label mask by a spaCR user. Contributions come from spaCR's Plaque Assay (Plaque mode, "Contribute training data..."): spaCR proposes the plaques its own segmentation model finds, and the contributor paints, erases and adds plaques until every plaque is outlined.

Purpose

This is training data for spaCR's next plaque segmentation model (the current one is einarolafsson/toxoplasma-plaque-segmentation-cpsam-r5, trained on einarolafsson/toxoplasma-plaque-dataset). Accepted contributions are folded into the next model release.

Licence

Everything here is shared under CC BY 4.0. By uploading, a contributor confirms that they have the right to share the images (they took them, or their source permits redistribution) and agrees that they are redistributed under CC BY 4.0.

File layout

Each upload is one folder:

contributions/<contribution-id>/
  contribution.json        spaCR version, date, licence agreed, consent, counts
  images/<stem>.<ext>      the original image file, unchanged
  masks/<stem>.tif         uint16 label mask, 0 = background, 1..N = one plaque each,
                           same height and width as the image
  meta/<stem>.json         original file name, image size, plaque count, and which of
                           spaCR's proposed plaques the contributor kept, edited or removed

An image is only accepted with at least one plaque mask; spaCR refuses to upload an image without annotations.

Review

Contributions arrive as pull requests and are reviewed by the maintainer before they are merged. Loose, missing or merged outlines are corrected or the contribution is declined. Careful masks make the next plaque model better and let it ship sooner.

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