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Image Analysis Group

We are the Image Analysis Group at the Francis Crick Institute.

How to install Cellpose on OnDemand

Cellpose is a general model for cell and nuclear segmentation. The following is a simple, step-by-step guide to installing Cellpose on OnDemand.

More detailed information on installing Cellpose can be found here if needed.

⚠️ BEWARE – the FIJI wrapper only works for cellpose version 3.0 (and below). If you have a newer version, you will have to create a new cellpose environment for FIJI to access an older version of it (see instructions below).

Step 1: Open xterm

When your GPU OnDemand Desktop session starts, right click and select xterm to open a terminal:

image

Step 2: Load Anaconda

You need to set up a conda environment, which will contain your Cellpose installation. To do this, you first need to load Anaconda. Type the following in your terminal window and press Enter:

ml Anaconda3

Step 3: Create Cellpose environment

You then need to create the environment that will contain the Cellpose installation, using the following command:

conda create --name cellpose-fiji python=3.11

In this example, the environment has been named cellpose-fiji, but you can call it whatever you want. The terminal will produce output similar to the following, where user_name will be replaced with whatever your user name is:

Retrieving notices: ...working... done
Collecting package metadata (current_repodata.json): done
Solving environment: done
 
## Package Plan ##
 
environment location: /camp/home/user_name/.conda/envs/cellpose-env

Proceed ([y]/n)?

Press y and Enter to proceed.

Step 4: Activate environment

Activate your new Cellpose environment with the following command:

conda activate cellpose-fiji

Step 5: Install Cellpose

At this point, it is important to note that you have merely created what is essentially an empty environment called cellpose-fiji. To actually install Cellpose within this environment, run the following series of commands:

pip install cellpose==3.0

The terminal will produce a large amount of output as the necessary packages are installed. Press y and Enter to proceed.

Step 6: Verify installation

To test whether the installation was successful, run the following:

cellpose --help

If the installation was successful, this should produce a list of all the parameters that can be used when running Cellpose.

Step 7: Deactivate environment

You can now deactivate your Cellpose environment by running the following:

conda deactivate

Step 8 (Optional): Run Cellpose as a GUI

To run the cellpose GUI you need to load VirtualGL before activating the conda environment for Cellpose. To load VirtualGL enter the following commands in the command line:

ml VirtualGL
conda activate cellpose-fiji
cellpose

Each step will take a few seconds

Step 9 (Optional): Run Cellpose from FIJI

It is possible to run Cellpose directly from FIJI. Instructions for installing the necessary FIJI Plugin can be found here. To run from FIJI on OnDemand, you have to activate the environment before launching FIJI. For example:

conda activate cellpose-fiji

When the conda environment is activated, it’s name will show up in parentheses in the command line, so, launching FIJI will look like this:

(cellpose-fiji) ./ImageJ-linux64

Step 10: Cite!

If you use Cellpose in your work, be sure to cite the relevant paper: