stardist-napari 2021.10.25

Object Detection with Star-convex Shapes

StarDist Napari Plugin

This project provides the napari plugin for StarDist, a deep learning based 2D and 3D object detection method with star-convex shapes. StarDist has originally been developed (see papers) for the segmentation of densely packed cell nuclei in challenging images with low signal-to-noise ratios. The plugin allows to apply pretrained and custom trained models from within napari.

Installation & Usage

Install the plugin with pip install stardist-napari or from within napari via Plugins > Install/Uninstall Package(s)…. If you want GPU-accelerated prediction, please read the more detailed installation instructions for StarDist.

You can activate the plugin in napari via Plugins > StarDist: StarDist. Example images for testing are provided via File > Open Sample > StarDist.

For a more detailed demonstration of the plugin, please watch this short video.

There's no dedicated documentation yet, but the most important parameters are identical to those of our StarDist ImageJ/Fiji plugin, which are documented here.

If you use this plugin for your research, please cite us.

Troubleshooting & Support

• The image.sc forum is the best place to start getting help and support. Make sure to use the tag stardist, since we are monitoring all questions with this tag.
• For general questions about StarDist, it's worth taking a look at the frequently asked questions (FAQ).
• If you have technical questions or found a bug, feel free to open an issue.