Cellpose - Appose Fiji plugin

This is a plugin to install and run cellpose on 2D/3D in Fiji. Two version of cellpose is available:

• Cellpose (v3)
• Cellpose-SAM (v4)

This plugin is based on Appose, that automatically install python environment and allows python script execution with shared objects with Fiji.

Plugin Installation

You can install the plugin for the unliste update site Appose-Playground: in Fiji, go to Help>Update... then to Manage Update Sites in the window that opens. Click Add unliste update site, name it Appose-Playground and write its address https://sites.imagej.net/Appose-Playground.

Select the Appose-Cellpose .jar file to install only this plugin, or keep all proposed plugins. Press Apply changes and restart Fiji when it's done.

Important

You should have a recent version of Fiji, based on Java 21 or more. Download a new version if you're current installation is too old.

Usage

From Fiji

• Open the image that you want to process.
• Launch one of the cellpose version available in the plugin:
  • Plugins>Segmentation>Cellpose-Appose>Cellpose...
  • Plugins>Segmentation>Cellpose-Appose>Cellpose-SAM...
• Configure your Cellpose run through the Graphic Interface
• Press "Ok" and Enjoy!

Note

The python environment will be automatically installed in your home .local\shared\appose directory and activated from the plugin when needed.

Development

To build the repository from source you will need both Maven and Java SDK 21 install on your system and available in your PATH.

At the root of the repo, run:

mvn clean install

You can also directly install the .jar in a Fiji via the option -Dscijava.app.directory=<path/to/your/Fiji>