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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
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