We always recommend that you install BrainGlobe tools into a virtual environment (managed by software such as
Your environment should run Python 3.9 or 3.10. To specify the Python version for new conda environment, add it as a parameter on creation:
conda create -n brainglobe-env python=3.10
Once you have created and activated your desired environment, you can install all BrainGlobe tools using
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
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.
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.
You can update your BrainGlobe tools by running
pip install brainglobe --update
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
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.