Documentation#

Installing BrainGlobe#

We always recommend that you install BrainGlobe tools into a virtual environment (managed by software such as conda or venv). Your environment should run Python 3.10, 3.11 or 3.12. To specify the Python version for new conda environment, add it as a parameter on creation:

conda create -n brainglobe-env python=3.11

Once you have created and activated your desired environment, you can install all BrainGlobe tools using pip:

pip install brainglobe

This will fetch all BrainGlobe tools, their Python APIs, and napari plugins if they possess one. It will also install napari into your environment so that you can make use of the plugins.

If you also want to install our analysis workflows (such as brainmapper, previously the cellfinder CLI), you will also need to install the brainglobe-workflows package. This package builds on top of the brainglobe tools, and provides you with some commonly-used data analysis pipelines to save you from having to write your own scripts for standard workflows. You can read about the workflows that are provided on the documentation page. To install brainglobe-workflows, run

pip install brainglobe-workflows>=1.0.0

in your environment. If you didn’t previously install brainglobe into this environment, brainglobe-workflows will do so when you run the command above. Otherwise, it will use the version of brainglobe that you already have installed.

Updating#

You can update your BrainGlobe tools by running

pip install brainglobe --upgrade

in your virtual environment.

Installing Individual Tools#

We recommend installing BrainGlobe in the manner detailed above, however each of the tools in the suite can be individually installed if you so wish. This can be done by following the install instructions for the particular tool in question.

Please note that, if you choose to install the tools individually, we cannot guarantee that you will have a consistent and interoperable set of BrainGlobe tools - you may encounter version conflicts or dependency issues. If you’re not confident in resolving these yourself, we recommend installing BrainGlobe in the manner above, and updating your BrainGlobe tools by updating the overarching brainglobe package.

Individual Tool Documentation#

Once you have installed brainglobe, or installed an individual tool if you choose to go that route, you can lookup how to use it by following the links below.

Developers may also wish to review the documentation for the brainglobe package itself.