https://github.com/qupath/qupath-extension-stardist
QuPath extension to run StarDist nucleus detection
https://github.com/qupath/qupath-extension-stardist
Last synced: 7 days ago
JSON representation
QuPath extension to run StarDist nucleus detection
- Host: GitHub
- URL: https://github.com/qupath/qupath-extension-stardist
- Owner: qupath
- License: apache-2.0
- Created: 2021-08-06T16:27:20.000Z (over 3 years ago)
- Default Branch: main
- Last Pushed: 2025-02-06T19:10:48.000Z (2 months ago)
- Last Synced: 2025-03-23T06:41:25.357Z (23 days ago)
- Language: Java
- Size: 278 KB
- Stars: 39
- Watchers: 6
- Forks: 7
- Open Issues: 2
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Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- License: LICENSE
Awesome Lists containing this project
- awesome-scientific-image-analysis - qupath-extension-stardist - StarDist. (🧬 QuPath / Extensions)
README
[](https://qupath.readthedocs.io/en/stable/docs/deep/stardist.html)
[](https://forum.image.sc/tag/qupath)
[](https://github.com/qupath/qupath-extension-stardist/releases/latest)
[](https://github.com/qupath/qupath-extension-stardist/releases)# QuPath StarDist extension
Welcome to the StarDist extension for [QuPath](http://qupath.github.io)!
This adds support for running the 2D version of StarDist nucleus detection developed by Uwe Schmidt and Martin Weigert.
The current version is written for QuPath v0.5.0 - the documentation is [here](https://qupath.readthedocs.io/en/0.5/docs/deep/stardist.html).
See what's new in the [changelog](CHANGELOG.md);
## Installing
**Better extension support in QuPath v0.5!**
See [readthedocs](https://qupath.readthedocs.io/en/0.5/docs/intro/extensions.html) for details.To install the StarDist extension, download the latest `qupath-extension-stardist-[version].jar` file from [releases](https://github.com/qupath/qupath-extension-stardist/releases) and drag it onto the main QuPath window.
If you haven't installed any extensions before, you'll be prompted to select a QuPath user directory.
The extension will then be copied to a location inside that directory.You might then need to restart QuPath (but not your computer).
## Citing
If you use this extension, you should cite the original StarDist publication
- Uwe Schmidt, Martin Weigert, Coleman Broaddus, and Gene Myers.
[*Cell Detection with Star-convex Polygons*](https://arxiv.org/abs/1806.03535).
International Conference on Medical Image Computing and Computer-Assisted Intervention (MICCAI), Granada, Spain, September 2018.You should also cite the QuPath publication, as described [here](https://qupath.readthedocs.io/en/stable/docs/intro/citing.html).
## Building
You can build the QuPath StarDist extension from source with
```bash
gradlew clean build
```The output will be under `build/libs`.
* `clean` removes anything old
* `build` builds the QuPath extension as a *.jar* file and adds it to `libs`