| --- |
| 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 |
|
|
