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

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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.

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imio will be merging into brainglobe-utils

The imio package will be absorbed into brainglobe-utils as a submodule, so will no longer be receiving standalone updates. This decision was made because:

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bg-space has been renamed

The “bg” prefix that a number of BrainGlobe tools carry is not very distinctive nor informative, so we are rolling out minor name changes to a lot of our packages that contain this prefix. We are also taking this opportunity to bring these tools into line with our developer guidelines for automatic deployment, tooling, and testing.

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BrainGlobe version 1 is here!

Following our series of incremental updates to a number of BrainGlobe tools, we are pleased to announce that BrainGlobe version 1 has been released today! Users can now enjoy:

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cellfinder-core and cellfinder-napari have merged

BrainGlobe version 1 is almost ready, and the next stage of its release journey is the merging of the “backend” cellfinder-core and cellfinder-napari packages into one. We had previously migrated the cellfinder data analysis workflow into the new brainglobe-workflows package, as part of our efforts to separate “backend” BrainGlobe tools from common analysis pipelines. This means that there is no longer any need to keep the “backend” package (cellfinder-core) and nor the visualisation plugin (cellfinder-napari) stored in separate, lower-level packages. As such;

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Plans for brainrender

Recent maintenance work means brainrender now works with more recent versions of Python and more recent versions of key dependencies (such as vedo). It should also be straightforward to install on all operating systems. We take this opportunity to set out the next steps for this tool.

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cellfinder has moved: version 1 of brainglobe-workflows released

Continuing the restructuring of BrainGlobe, the cellfinder command-line tool has moved to a new home, brainglobe-workflows. Please note that we will no longer be providing Docker images for cellfinder’s command-line functionality either - if you were previously using the Docker image, please see the advice in the full changelog.

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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:

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BrainGlobe is being restructured, version 1 is on it’s way!

BrainGlobe provides and maintains a number of open-source tools, each of which are provided as Python-based software packages. A number of these tools also come with a graphical user-interface provided by a napari plugin that can be installed on top of the Python package. Whilst there is an advantage to the modularity provided by maintaining separate tools, the same modularity can present challenges and unnecessary difficulties when running an analysis that relies on multiple BrainGlobe tools. Particular pinch points include:

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