Running Cellpose in Fiji
Cellpose is a very efficient framework to segment cell or nucleus. It can run on a large variety of dataset or be retrained for specific dataset.
While Cellpose is a python package, several options exists in Fiji to run it:
- Fiji-Cellpose: handles
Cellposethanks to Appose. Appose creates and activates python virtual environment automatically, without any action from the user.
In addition of the online documentation, this youtube tutorial shows how to use this plugin.
- TrackMate-Cellpose allows to both run Cellpose to segment objects and track them in time.
In the current version, the user has to install a virtual environment with
Cellposeto be able to use it but in coming versions, it will be automatically handled also thanks to Appose.
In addition of the online documentation, this tutorial guide you through the installation and usage of TrackMate-Cellpose, including creation of the python environment.
- BioP offers the possibility to run several deep learning algorithms, including
Cellposefrom Fiji. It also requires the user to install a virtual environment before to be able to use it.
You can find several resources to help you install the BioP plugin along with the virtual environment. This youtube tutorial shows you how to install a virtual environment, the BIOP plugin and run it. This tutorial guide you for a full installation in Windows operating system. This repository provides macro to use the plugin and match labels from cell and nuclei.
- More generally, this page https://imagej.net/scripting/python indicates how to run python programs, as Cellpose, from Fiji.
