Stable release

To install the Cell Maps Pipeline, run this command in your terminal:

$ pip install cellmaps_pipeline

This is the preferred method to install Cell Maps Pipeline, as it will always install the most recent stable release.

If you don’t have pip installed, this Python installation guide can guide you through the process.

From sources

The sources for Cell Maps Pipeline can be downloaded from the Github repo.

You can either clone the public repository:

$ git clone git://

Or download the tarball:

$ curl  -OL

Once you have a copy of the source, you can install it with:

$ python install


Due to the large number of dependent packages, we suggest a virtual environment like Anaconda set to Python 3.8 like so: conda create -n cellmaps_env python=3.8