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brainglobe.info
BrainGlobe
@brainglobe.info
290 followers 2 following 52 posts
We build open source computational neuroanatomy software that works across species.

https://brainglobe.info

Posts by @adamltyson.com
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brainglobe.info
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).
November 6, 2025 at 4:36 PM
brainglobe.info
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...
October 10, 2025 at 10:40 AM
brainglobe.info
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.
September 15, 2025 at 2:40 PM
brainglobe.info
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
September 12, 2025 at 10:07 AM
brainglobe.info
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.
July 28, 2025 at 3:02 PM
brainglobe.info
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.
June 10, 2025 at 2:50 PM
brainglobe.info
New version of brainglobe-heatmap (v0.6.0) released, with automated region annotations.

github.com/brainglobe/b...
March 21, 2025 at 8:08 AM
brainglobe.info
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.
March 17, 2025 at 9:04 AM
brainglobe.info
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.
March 10, 2025 at 2:53 PM
brainglobe.info
Nice package to load BrainGlobe atlases into Blender - "BlenderBrain".

github.com/ArtemKirsano...
Visualisation of the Allen Mouse Brain Atlas within Blender
February 21, 2025 at 3:44 PM
brainglobe.info
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.
February 20, 2025 at 5:13 PM
brainglobe.info
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.
February 4, 2025 at 2:08 PM
brainglobe.info
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...
October 31, 2024 at 12:16 PM
brainglobe.info
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.
August 13, 2024 at 10:41 AM
brainglobe.info
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
August 2, 2024 at 10:15 AM
brainglobe.info
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.
August 1, 2024 at 11:04 AM
brainglobe.info
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.
June 21, 2024 at 5:18 PM
brainglobe.info
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
April 19, 2024 at 7:55 AM
brainglobe.info
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.
March 1, 2024 at 10:32 AM
brainglobe.info
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.
December 14, 2023 at 7:15 PM