BrainGlobe version 1 overview

BrainGlobe version 1 provides users with the brainglobe “meta”-package: a single package that will fetch all the tools in the BrainGlobe suite and install them onto your machine, ready for use. It also provides the brainglobe-workflows package, which builds on top of brainglobe and provides some common analysis pipelines to users, as well as a benchmarking suite for developers working on code performance improvements.

If you want to know more about the under-the-hood workings of the brainglobe “meta”-package, you can head to the developer documentation.

Updating to version 1

Our recommendation for updating to BrainGlobe version 1 is to follow the installation instructions on the main documentation page in a clean virtual environment, and delete or archive your old environment. This will ensure that when you install brainglobe, the tools are fetched in a consistent manner and do not pick up any manually installed BrainGlobe tools that might be in your environment or python path. Likewise, it also avoids potential issues when tools have been installed from both conda-forge and PyPI.

If you don’t want to install the entire BrainGlobe suite and are happy to manage the tooling interdependencies yourself, you can still manually install the individual BrainGlobe tools that you wish to use.

Can I install from conda-forge?

We are working on providing a conda-forge install for BrainGlobe version 1, as an alternative to the pip install brainglobe command that we currently recommend. However for the time being, there is no one-line installation possible using conda.

There are no problems with pip install brainglobe-ing into a conda environment, we just need some time to setup all of the individual BrainGlobe tools on conda-forge before we can provide an all-in-one install through conda!

Changes at-a-glance

Below is a high-level overview of the changes to the brainglobe suite of tools that we offer. You can follow the links provided for more information; including a listing of relocated and/or renamed tools.

Change
brainreg and brainreg-napari have been merged into a single package	Further info
brainreg-segment has been renamed to brainglobe-segmentation	Further info
The cellfinder command-line-interface has been moved into brainglobe-workflows	Further info
The cellfinder package is deprecated - it will later be recycled to merge some backend functionality	Further info
The cellfinder Docker image is discontinued	Further info
cellfinder-core and cellfinder-napari merged into “new cellfinder”	Further info
The cellfinder command-line tool has been replaced with brainmapper	Further info
brainrender and brainrender-napari are now available through the brainglobe meta-package	Further info

• Version 1: changes to registration and segmentation tools
• Version 1: Cellfinder migration and brainglobe-workflows
• Version 1: changes to the cellfinder backend and plugin

Full Changelog

• Recommended BrainGlobe install is via pip, into a clean environment.

  • pip install brainglobe to install BrainGlobe tools. Recommended even if you only want to use one or two tools.

  • pip install brainglobe-workflows if you also want to use the example analysis workflows that we provide.

• brainreg-napari is now shipped with brainreg

  • brainreg functionality is now available in a submodule, brainreg.core. If you previously used the Python API provided in brainreg, you will need to change your from brainreg import X statements to from brainreg.core import X.

  • The brainreg-napari plugin is now just called brainreg when using napari. The plugin’s backend is in the submodule brainreg.napari rather than brainreg-napari.

  • The new brainreg.core and brainreg.napari submodules retain the old internal structure of the respective deprecated packages.

• brainreg-segment has been renamed brainglobe-segmentation.

  • Beyond the name change, package internals have not changed.

• cellfinder command-line-interface (CLI) has been renamed and moved.

  • The command-line interface is now provided by brainglobe-workflows.

  • The command-line tool is now called brainmapper.

  • The name “cellfinder” is now reserved for the merged cellfinder-core and cellfinder-napari packages.

• cellfinder-core and cellfinder-napari have been merged into a single package, called cellfinder.

  • The cellfinder package should not be confused with the old cellfinder command-line tool, described above. Going forward, “cellfinder” will refer exclusively to this new, merged package created from cellfinder-core and cellfinder-napari which only performs cell detection. The command-line tool will use the name brainmapper.

  • The core and napari features are now available as submodules of the cellfinder package. If you previously used from cellfinder_core import X, you’ll have to use from cellfinder.core import X instead.

  • Internal function names and locations have otherwise not changed, beyond their conversion into the core and napari submodules.

  • The napari plugin is now referred to as the cellfinder plugin, and shows up with the name cellfinder when viewed in napari (as opposed to the old cellfinder-napari name it used to have).

• brainglobe-workflows has been released.

  • This package provides some exemplar data analysis workflows for users to modify or customise to suit their needs.

  • It will also provide command-line interfaces for particularly common workflows. Currently it provides brainmapper, the successor to the old cellfinder command-line tool.

• pip install brainglobe is now the recommended way to install all BrainGlobe tools.

  • This will fetch the brainglobe meta-package, which includes the latest stable versions of all BrainGlobe tools and napari plugins.

  • All tools will be accessible in the install environment as if they had been pip-installed directly.

  • If you are updating to brainglobe version 1 having previously installed BrainGlobe tools individually, we recommend you create a clean Python environment and install brainglobe into this fresh environment to avoid potential package conflicts.

  • brainglobe package now ships the fixed brainrender, as well as brainrender-napari which we plan to transition to in the future.