---
license: cc-by-4.0
pretty_name: Community Toxoplasma plaques (plaque masks)
tags: [image-segmentation, cellpose, plaque-assay, toxoplasma, spacr, community]
task_categories: [image-segmentation]
---
# 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](https://huggingface.co/einarolafsson/toxoplasma-plaque-segmentation-cpsam-r5),
trained on [einarolafsson/toxoplasma-plaque-dataset](https://huggingface.co/datasets/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