BrainGlobe

@brainglobe

We build open source computational neuroanatomy software that works across species. Posts by @adamltyson.com

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BrainGlobe@brainglobe· 3d

A Tawny Dragon brain atlas has been added to BrainGlobe! This lizard has shown great promise for neuroevolutionary research and we hope inclusion of the atlas within BrainGlobe will help researchers understand its brain structure. Read more in the blog: brainglobe.info/blog/tawny-d...

BrainGlobe@brainglobe· 4d

BrainGlobe Atlas API V3 is out! After 6 years, this is the first major change in how BrainGlobe works. Each atlas component is fetched independently, meaning all BrainGlobe tools will work faster, and more reliably. Read more at: brainglobe.info/blog/braingl...

A figure illustrating the use of the new BrainGlobe Atlas API. Lazy fetching of components for analysis. To draw the hippocampus inside a transparent brain, V2 pulled a 7.4 GB archive containing every image and every mesh in the atlas. V3 fetches the two meshes the render actually uses, 2.3 MB

BrainGlobe@brainglobe· 10d

All BrainGlobe atlases now have Neuroglancer links so that you can explore atlases in the browser without needing to download them first! All links here: brainglobe.info/documentatio... Here you can view our Eurasian Blackcap atlas: neuroglancer-demo.appspot.com#!https://bra...

Screenshot of the Neuroglancer preview of the BrainGlobe Eurasian Blackcap atlas.

BrainGlobe@brainglobe· 26d

Do you use the BrainGlobe Atlas API directly in your work? Have you built a tool on top of BrainGlobe? We will soon release V3 of the API, which changes how brain atlas data is stored and accessed. A release candidate is available for testing, please see our blog: brainglobe.info/blog/atlas-a...

An example of the local and remote directory structure for brainglobe-atlasapi V2 and V3. V2 stores data in large monolithic archives, V3 stores each component separately.

BrainGlobe@brainglobe· Jul 16

Nice Claude skill to create basic neuroanatomical visualisations with BrainGlobe & blender: github.com/SamedVossber... The single prompt "Use the allen mouse brain atlas to create an animation to show primary visual cortex and primary motor cortex" gives:

BrainGlobe@brainglobe· May 21

As part of this effort, we've just released three new atlases from v2 of the Allen mouse CCF - the brain atlas, fiber tract atlas and developmental brain atlas. Most pipelines have moved to CCFv3, but adding v2 allows atlas comparison and reproducing old analyses. brainglobe.info/blog/ccfv2-a...

BrainGlobe@brainglobe· Mar 17

BrainGlobe has a new roadmap! Somewhat overdue, the March 2026 roadmap summarises our recent progress, and our priorities for the coming year. Read more: brainglobe.info/community/ro...

An illustration of many of the atlases supported by BrainGlobe.

BrainGlobe@brainglobe· Feb 5

The CArea mouse brain atlas has been added to BrainGlobe! This atlas has regions which are automatically clustered based on three dimensional maps of gene expression. Read more in the blog: brainglobe.info/blog/carea-a...

BrainGlobe@brainglobe· Feb 2

New blogpost outlining our work with @athenaakrami.bsky.social at @sainsburywellcome.bsky.social to build light-microscopy based atlases of the rat brain. brainglobe.info/blog/swc-fem...

BrainGlobe@brainglobe· Nov 6

A new MRI mouse brain atlas has been added to BrainGlobe! This atlas from Dorr et al. (2008) is an average of 40 T2-weighted MR images at 32um resolution. Thanks to Saarah Hussain for adding this atlas. More details: brainglobe.info/blog/dorr-mo... Original paper: doi.org/10.1016/j.ne...

Two-dimensional view of the Dorr mouse MRI brain atlas: annotations (left) and reference (right).

BrainGlobe@brainglobe· Oct 10

BrainGlobe branches out! New blog outlining our collaborative work with @giuliapaci.bsky.social from @lmcb-ucl.bsky.social to build anatomical atlases for developmental mechanobiology. brainglobe.info/blog/drosoph...

BrainGlobe@brainglobe· Sep 15

DeMBA (Developmental Mouse Brain Atlas) has now been added to BrainGlobe! This includes every developmental stage from P4 to P56. Each of these 53 atlases includes MRI, LSFM and STPT templates. For more details, see the blog: brainglobe.info/blog/DeMBA Paper: doi.org/10.1038/s414...

Coronal sections of the DeMBA from anterior to posterior at five ages. Each section shows the STPT template on the left side and the transformed Allen Mouse Brain CCFv3 segmentations on the right side.

BrainGlobe@brainglobe· Sep 12

Version 2 of the "Enhanced and Unified Mouse Brain Atlas" has now been added to BrainGlobe. This popular atlas has been updated with corrected annotations and an isotropic 20um reference volume. Thanks to Pavel Vychyk for adding this atlas! brainglobe.info/blog/kim-iso...

Coronal and lateral views of the mouse brain, visualized using the napari viewer

BrainGlobe@brainglobe· Jul 28

The brain atlas of the bumblebee Bombus impatiens created by the @kocherlab.bsky.social is now part of BrainGlobe! This is our first insect brain atlas. Thanks to Scott Wolf for adding it! More details: brainglobe.info/blog/bee-atl... Original paper: doi.org/10.1016/j.cu...

A three-dimensional view of the Kocher lab’s bumblebee brain atlas visualised with brainrender-napari.

BrainGlobe@brainglobe· Jun 10

BrainGlobe has a new atlas, the "CCFv3 augmented mouse atlas"! This atlas is an extended version of the CCFv3, designed to cover the rostral and caudal tips of the mouse brain and includes Nissl templates. More details: brainglobe.info/blog/CCFv3BB... Original paper: doi.org/10.1162/imag...

Different versions of the Common Coordinate Framework: CCFv2 and CCFv3 from the AIBS, as well as the extended and improved CCFv3a-BBP from the Blue Brain Project.

BrainGlobe@brainglobe· Mar 21

New version of brainglobe-heatmap (v0.6.0) released, with automated region annotations. github.com/brainglobe/b...

BrainGlobe@brainglobe· Mar 17

New version of brainglobe-workflows released (v1.4.1)! Includes a fix for a brainmapper bug in which the analysis results for users with 3D tiffs was incorrect. Full documentation: brainglobe.info/documentatio...

Illustration of brainmapper results, showing detected cells, overlaid on a brain image segmented according to the Allen Mouse Brain Atlas.

BrainGlobe@brainglobe· Mar 10

BrainGlobe has a new atlas, for the dwarf cuttlefish (Sepia bandensis). Thanks to UCL student Jung Woo Kim for packaging this atlas! For more details about this (and the rest of BrainGlobe), please see the blog: brainglobe.info/blog/cuttlef... Original paper: doi.org/10.1016/j.cu...

Coronal section of the cuttlefish brain atlas annotations (only right hemisphere shown) and reference image.

BrainGlobe@brainglobe· Feb 21

Nice package to load BrainGlobe atlases into Blender - "BlenderBrain". github.com/ArtemKirsano...

Visualisation of the Allen Mouse Brain Atlas within Blender

BrainGlobe@brainglobe· Feb 20

BrainGlobe has three new mouse brain atlases including: - Multimodal (LSFM & MRI) developmental atlas from Yongsoo Kim's lab - Multimodal (LSFM & MRI) adult atlas from Gubra - High-resolution Australian mouse brain atlas (MRI) See the blog for more details: brainglobe.info/blog/mouse-a...

A visualisation of both the MRI (left) and LSFM (right) templates and their (right-hemisphere) annotations contained in Gubra’s multimodal mouse brain atlas.

BrainGlobe@brainglobe· Feb 4

BrainGlobe has a new atlas, the first non-human primate, the gray mouse lemur (Microcebus murinus). For more details about this (and the rest of BrainGlobe), please see the blog: brainglobe.info/blog/mouse-l...

Three-dimensional view of the Nadkarni mouse lemur MRI atlas using brainrender-napari, with the template image overlaid with just the right hemisphere of the annotations.

BrainGlobe@brainglobe· Oct 31

BrainGlobe has a new atlas, the prairie vole! For more details see the blog: brainglobe.info/blog/prairie... Original paper: doi.org/10.7554/eLif...

BrainGlobe@brainglobe· Aug 13

BrainGlobe has a new atlas, the Axolotl (Ambystoma mexicanum)! For more details see the blog: brainglobe.info/blog/axolotl... Original paper: doi.org/10.1038/s415...

Saggital view of the axotlotl atlas annotations.

BrainGlobe@brainglobe· Aug 2

BrainGlobe now includes an atlas with barrel column annotations from Bolaños-Puchet & Teska et al. Full details on the blog: brainglobe.info/blog/barrel-... Thanks to Axel Bisi for bringing this to BrainGlobe! Original paper: doi.org/10.1162/imag...

Visualisation of some barrel columns using brainrender

BrainGlobe@brainglobe· Aug 1

We've just released the "brainmapper" widget allowing analysis of cellular distributions in whole-brain microscopy images entirely within napari. Full details available on the blog: brainglobe.info/blog/brainma...

A screenshot of the brainmapper widget, showing the distribution of napari points within a BrainGlobe atlas.

BrainGlobe@brainglobe· Jun 21

We've added a new atlas - the blind Mexican cavefish, Astyanax mexicanus. More details on the blog: brainglobe.info/blog/cavefis...

Dorsal view of the cavefish brain atlas annotations.

BrainGlobe@brainglobe· Apr 19

New version of brainrender released, with a new Line Actor (thanks to Paul Brodersen!). To update: pip install brainrender -U github.com/brainglobe/b...

Visualisation of the Allen Mouse Brain Atlas displaying the shortest path within cortex between two points

BrainGlobe@brainglobe· Mar 1

Processing neuroanatomy data in napari? You may find brainrender-napari (github.com/brainglobe/b...) useful. We're slowly porting the original brainrender to napari to provide a consistent neuroanatomy data analysis and visualisation environment.

Screenshot of the brainrender-napari visualisation tool showing a 3D rendering of the larval zebrafish atlas.

BrainGlobe@brainglobe· Dec 14

Interested in making high-quality 2D & 3D neuroanatomical visualisations across multiple species? New versions of brainrender (github.com/brainglobe/b...) and brainglobe-heatmap (github.com/brainglobe/b...) have been released.