brainglobe-workflows is a collection of common data analysis pipelines that utilise a combination of BrainGlobe tools. It currently provides:

You can find more information on each of these tools by visiting the links below:


brainglobe-workflows can be installed into your Python environment using pip:

pip install brainglobe-workflows


If you are using macOS, and you require 3D registration functionality (e.g. in brainmapper), please also run conda install -c conda-forge niftyreg

Doing so will make all of the command-line tools that brainglobe-workflows provides visible whilst working inside your environment.

Installing with cellfinder versions older than v1.0.0#

The cellfinder package, command-line tool, and workflow have undergone significant changes in the move to version 1. You can find a case-by-case breakdown of what you will need to do if you want to upgrade/install brainglobe-workflows whilst retaining the functionality of old cellfinder installs (and the command-line tool) in the corresponding changelog.

However, the simplest option is to create a fresh Python environment and install brainglobe-workflows:

pip install brainglobe-workflows

This will fetch the latest version of brainglobe-workflows, providing you with the brainmapper command-line tool / workflow which is functionally equivalent to the old “cellfinder” command-line tool. It will also provide you with the updated cellfinder package (at least v1.0.0) whose API and package structure matches that described in the documentation.