petebankhead/qupath-extension-stardist

QuPath extension to run StarDist nucleus detection

QuPath StarDist extension

Welcome to the StarDist extension for QuPath!

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.

See what's new in the changelog;

Installing

Better extension support in QuPath v0.5! See readthedocs for details.

To install the StarDist extension, download the latest qupath-extension-stardist-[version].jar file from 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.
  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.

Building

You can build the QuPath StarDist extension from source with

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