• Version:

    • 2021.6.28
  • Release date:

    • 28 June 2021
  • First released:

    • 01 June 2021
  • Development status:

    • 4 - Beta
  • License:

    • BSD-3-Clause

Github Activity

  • Stars: 13
  • Forks: 3
  • Issues + PRs: 1
  • Python versions supported:

    • >=3.7
  • Operating system:

    • OS Independent
  • Requirements:

    • stardist (>=0.7.0)
    • tensorflow
    • napari (>=0.4.8)
    • magicgui (>=0.2.9)

stardist-napari

Object Detection with Star-convex Shapes

PyPI version Image.sc forum

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.

Screenshot

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.
  • Version:

    • 2021.6.28
  • Release date:

    • 28 June 2021
  • First released:

    • 01 June 2021
  • Development status:

    • 4 - Beta
  • License:

    • BSD-3-Clause

Github Activity

  • Stars: 13
  • Forks: 3
  • Issues + PRs: 1
  • Python versions supported:

    • >=3.7
  • Operating system:

    • OS Independent
  • Requirements:

    • stardist (>=0.7.0)
    • tensorflow
    • napari (>=0.4.8)
    • magicgui (>=0.2.9)

Sign up to receive updates