camaralab/cajal repository overview

CAJAL is a Python library for multi-modal cell morphology analyses using Gromov-Wasserstein (GW) distance. The source is available at https://github.com/CamaraLab/CAJAL⁠.

We provide a Docker image which contains CAJAL and its dependencies, cajal:latest is built on top of the Docker image jupyter/base-notebook and contains numerous data science tools for further analysis of the output of CAJAL. Running the following command will launch a Jupyter notebook server on localhost with CAJAL and its dependencies installed:

docker run -it -p 8888:8888 -v C:\Users\myusername\Documents\myfolder:/home/jovyan/work camaralab/cajal:latest

The -p flag controls the port number on local host. For example, writing -p 4264:8888 will let you access the Jupyter server from 127.0.0.1:4264. The -v "bind mount" flag allows one to mount a local directory on the host machine to a folder inside the container so that you can read and write files on the host machine from within the Docker image. Here one must mount the folder on the host machine as /home/jovyan/work or /home/jovyan/some_other_folder as the primary user "jovyan" in the Docker image only has access to that directory and to the /opt/conda folder. See the Jupyter docker image documentation⁠ for more information.