CellBaum

Installation

To create a local environment with every (Python) package you need, run:

{conda,mamba} env create --prefix ./cenv --file env.yml

e.g. if you have Conda installed, use:

conda env create --prefix ./cenv --file env.yml

This will create a local environment within whatever directory you ran the command. If you'd instead like to make a (user-global) named environment, you can use the -n flag and name the environment instead of specifying its prefix:

{conda,mamba} env create --name cenv_name --file env.yml

You will need to install CellProfiler and Fiji (with the MIST plugin) for CellBaum to work. Normally, you'll want to do this outside of the environment, as both tools are useful as GUI tools.

Afterwards, you can activate the local environment with:

{conda,mamba} activate ./cenv

Note that you must use a relative or absolute path (e.g. include the ./), this is how Conda identifies locally installed environments versus named, global environments.

Using Micromamba

After getting the latest version of micromamba and unpacking it into your PATH:

https://micromamba.snakepit.net/api/micromamba/win-64/latest
https://micromamba.snakepit.net/api/micromamba/osx-64/latest
https://micromamba.snakepit.net/api/micromamba/linux-64/latest

you can create the main environment with:

micromamba create -p ./cenv --file env.yml

If you need the 'extras' (e.g. for installing on a cluster), you can do:

micromamba update -p ./cenv --file cp_addons.yml

To activate the environment, you can use

micromamba activate ./cenv

Cluster/headless/Linux install

If you need to install CellProfiler within Conda (e.g. on a cluster), you should update the environment with the CellProfiler addons:

{conda,mamba} env update --prefix ./cenv --file cp_addons.yml

if you are using a named/user-global environment, specify the name instead of the prefix:

{conda,mamba} env update --name --file cp_addons.yml

Fiji is technically available through Conda, but the version it installs is very old (2017). It is recommended that you download the latest Fiji installation for your operating system, then install MIST. If you are running on a headless system (a cluster), you can install MIST through the command line with:

./path/to/ImageJ-YOUR_OS --update add-update-site MIST https://sites.imagej.net/NIST-ISG-MIST/
./path/to/ImageJ-YOUR_OS --update update

For example, on Linux, the first command could be

wherever/you/put/Fiji.app/ImageJ-linux64 --update add-update-site MIST https://sites.imagej.net/NIST-ISG-MIST/