stardist / stardist-imagej

StarDist plugin for ImageJ

StarDist ImageJ/Fiji Plugin

This is the ImageJ/Fiji plugin for StarDist, which can be used to apply already trained models to new images.
Note: The plugin (currently) only supports 2D image and time lapse data.

See the main repository for links to our publications and the full-featured Python package that can also be used to train new models.

Installation

The StarDist plugin can be installed in Fiji by selecting both update sites CSBDeep and StarDist.
Concretely, you can follow these steps:

1. Start Fiji (or download and install it from here first).
2. Select Help > Update... from the menu bar.
3. Click on the button Manage update sites.
4. Scroll down the list and tick the checkboxes for update sites CSBDeep and StarDist, then click the Close button.
   (If StarDist is missing, click Update URLs to refresh the list of update sites.)
5. Click on Apply changes to install the plugin.
6. Restart Fiji.

Usage

See the wiki page for more information.