https://github.com/qupath/qupath-extension-stardist

QuPath extension to run StarDist nucleus detection
https://github.com/qupath/qupath-extension-stardist

Last synced: 2 months ago
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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: 2024-08-07T09:49:19.000Z (5 months ago)
• Last Synced: 2024-08-07T13:26:04.608Z (5 months ago)
• Language: Java
• Size: 248 KB
• Stars: 33
• Watchers: 6
• Forks: 6
• Open Issues: 3
• Metadata Files:
  • Readme: README.md
  • Changelog: CHANGELOG.md
  • License: LICENSE

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README

        
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# 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`