brainglobe-workflows

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

• brainmapper: Whole-brain cell detection and classification. Read more about the command line interface here. This workflow was previously called cellfinder.

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

• brainmapper command line tool

Installation

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

pip install brainglobe-workflows

Note

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.