BrainGlobe version 1 is here! Head over to the blog to find out more

bg-atlasapi and bg-atlasgen have merged under a new name#

bg-atlasapi and bg-atlasgen have merged into a single package, now called brainglobe-atlasapi. brainglobe-atlasapi now provides the same API that bg-atlasapi provided, in exactly the same way - all that needs to happen is a name change in your scripts.

bg-atlasgen used to provide the developer code for adding a new atlas to the collection of BrainGlobe atlases that are available for download. This code was exclusively used by developers, however it hinges on the functionality of bg-atlasapi to complete the generation and upload process. As such, it has now been moved into a submodule, brainglobe_atlasapi.atlas_generation, but again the way one interacts with this submodule is the same as they would have with bg-atlasgen.

What do I need to do?#

If you are using an install of bg-atlasapi that you got through pip install brainglobe, then all you need to do is update brainglobe to the latest version with

pip install --update brainglobe

This will remove the old packages from your environment, install brainglobe-atlasapi, and also update all your other BrainGlobe tools to use the new package rather than the old bg-atlasapi.

If you were previously using a standalone install of bg-atlasapi, to continue receiving updates you should perform the following changes to your environment:

  • Uninstall bg-atlasapi (and bg-atlasgen if you have it).

  • Install the latest version of brainglobe-atlasapi.

  • Update all of the following BrainGlobe tools that you also have in your environment:

    • brainrender-napari

    • brainglobe-utils

    • brainglobe-segmentation

    • brainreg

    • brainglobe-napari-io

    • cellfinder

    • morphapi

    • brainrender

    • brainglobe-heatmap