Version 1 of brainreg and brainglobe-segmentation released#

The restructuring of BrainGlobe is underway, beginning with the release of version 1 of brainreg and brainglobe-segmentation (previously known as brainreg-segment). Previously, there were three tools with the prefix brainreg (“brain registration”) that were split across three packages:

  • brainreg was the core Python package that contained the functional code for performing registration of an atlas to a sample image (sequence).

  • brainreg-napari provided a plugin to perform the registration steps interactively through napari. It depended on brainreg for the core functionality.

  • brainreg-segment was a companion to brainreg that allowed for segmentation of regions/objects within the brain. However it was not necessarily involved with the registration process itself.

This release sees brainreg come bundled with its napari plugin as an optional package extra, rather than requiring users to install the two packages separately. Consequently, brainreg-napari has been retired; we recommend you uninstall this package from your environments when you update. The “combined” brainreg is now tagged as brainreg v1.0.0 and should be considered a stable first release of this tool.

brainglobe-segmentation is the new name of the brainreg-segment tool. With the forthcoming release of BrainGlobe version 1 and the development of brainglobe-registration, the decision was made to disambiguate the role of the segmentation functionality and combine the napari plugin with the core functionality.

What do I need to do?#

If you were previously using any of the affected tools; you don’t need to do anything right now if you want to wait for the full release of BrainGlobe version 1, which will take care of these dependencies for you. In the time between now and then, the tools as installed will still work but be aware that they will no longer receive updates due to the restructuring.

If you would like to update your packages now, or would like to know how this will affect your scripts or workflows, see the full changelog which covers API changes and the installation process.

Full changelog#

You can find the full changelog on the releases page.

BrainGlobe is being restructured, version 1 is on it’s way!   cellfinder has moved: version 1 of brainglobe-workflows released