Posted in 2026
Two Virtual Fly Brain atlases of the adult fruit fly nervous system have been added to BrainGlobe
- 09 November 2026
Two atlases based on the JRC2018 unisex templates are now available through BrainGlobe, bringing complementary views of the adult fruit fly (Drosophila melanogaster) nervous system into the same software ecosystem. Both atlases use data from Virtual Fly Brain (VFB) and the unbiased, symmetric templates described by Bogovic et al. (2020). One provides VFB-painted neuropil ROI annotations for the adult brain; the other provides neuropil and domain annotations for the adult ventral nerve cord (VNC).
The first edition of the Allen Mouse Brain Atlas has been added to BrainGlobe
- 09 November 2026
There are few brain atlases as foundational to the field as the first Allen Mouse Brain Atlas, released in 2006. The first edition of the atlas, the Common Coordinate Framework version 1 (CCFv1), was created as part of the inaugural project of the Allen Institute for Brain Sciences which was to create a whole-brain map of gene expression. This framework allowed researchers to align in situ hybridisation (ISH) data to the atlas, which was a valuable tool for neuroscientists.
The LAMBADA developmental mouse brain atlases have been added to BrainGlobe
- 05 November 2026
The structure of cerebral vasculature continues to develop after birth, but its spatiotemporal dynamics have always been unclear. To address this, de Launoit et al. (2026) created the light-sheet-aligned mouse brain annotated developmental atlas (LAMBADA) to align spatial transcriptomics data on key genes governing vascular development. Using seven different timepoints in development (P3, P5, P7, P9, P12, P14 and P21), the authors provide high resolution light-sheet fluorescence microscopy (LSFM) templates which are volume-corrected to in-vivo MRI benchmarks, ensuring that this developmental atlas reflects the natural brain growth trajectories as seen in development. We have packaged this atlas into BrainGlobe to make this resource usable throughout the BrainGlobe ecosystem.
A 2.5 µm adult Danionella cerebrum atlas joins BrainGlobe
- 23 September 2026
Danionella cerebrum is a small teleost fish whose brain remains optically accessible throughout adulthood. Unlike zebrafish, whose skull ossifies as they mature, Danionella lack skull ossification above the brain. This makes non-invasive, cellular-resolution imaging across the adult brain possible. This optical access is a key reason that HHMI’s Janelia Research Campus is developing a Danionella research platform.
The Duke Developmental Rat Brain Atlases have been added to BrainGlobe
- 25 August 2026
The brain continues to develop well after an organism is born. To provide a comprehensive view of the growth of various brain regions in rats, Calabrese et al. (2013) of Duke University created a high resolution averaged T2 MRI atlas of postnatal rat brain development using five specimens each at nine different timepoints (P0, P2, P4, P8, P12, P18, P24, P40, P80). The authors annotated the nine time points with the same 26 developmentally distinct regions, allowing them to plot growth curves for the rat brain by measuring their volumes over time. We have packaged the nine atlases which comprise the Duke Developmental Rat Brain Atlas to be used within BrainGlobe.
Duke Mouse Brain Atlas has been added to BrainGlobe
- 18 August 2026
Mansour et al. (2025) introduced the Duke Mouse Brain Atlas (DMBA), a high-resolution 15 µm isotropic stereotaxic atlas of the adult mouse brain. The atlas combines magnetic resonance histology (MRH), diffusion MRI-derived contrasts, micro-CT, light sheet microscopy, and registered anatomical annotations in a common reference space.
A Brain Atlas for the Tawny Dragon, Ctenophorus decresii, has been added to BrainGlobe
- 12 August 2026
The tawny dragon is an Australian lizard which has shown great promise for neuroevolutionary research, as investigating the variation among reptile species allows for a greater exploration of the processes that govern vertebrate brain development. As this is an emerging model species there was a need for a standardised tawny dragon brain atlas. To this end, Hoops et al. used structural MRI to obtain the average 3D brain from 13 male tawny dragons and segmented 224 structures. This atlas is now available through the BrainGlobe Atlas API, and is the first lizard brain to be added to BrainGlobe.
brainglobe-atlasapi V3 is here!
- 10 August 2026
We’re excited to announce the full release of brainglobe-atlasapi version 3. You can install it (or upgrade) with:
brainglobe-atlasapi V3 pre-release
- 17 July 2026
A pre-release version of brainglobe-atlasapi V3 is now available. You can install it using by running:
Three Atlases for the Allen Common Coordinate Framework v2 Mouse Brain have been added to BrainGlobe
- 19 May 2026
The mouse brain atlases provided by the Allen Institute for Brain Science (AIBS) are widely used in the neuroscience community, and as of the writing of this blog post, the most updated version of their atlas is version 3 of the Common Coordinate Framework (CCF). However, there are many benefits from adding older versions of atlases, namely in terms of keeping a record of the history of atlas versions, as well as reproducing historical results which used older atlases. Therefore, we have packaged the CCFv2 mouse brain atlases provided by the Allen Institute. These include an adult mouse brain atlas with all grey matter regions without fiber tracts, an adult mouse brain atlas with only the fiber tracts, and a developmental adult mouse brain atlas containing information on the developmental taxonomy of various regions. The CCFv2 is a symmetric atlas constructed from the same 528 Nissl stained 25um coronal slices as in CCFv1, but reprocessed for symmetry and to introduce more annotations based on the Allen Reference Atlas.
The Systematic Atlas Packaging Project
- 15 May 2026
The purpose of the BrainGlobe Atlas API is to standardise atlases and provide them to researchers via a common, easy to use, interface. As part of this initiative we have integrated atlases of all kinds, including atlases of mice, rats, bees, cuttlefish, and more. The logical endpoint of all of this would be integrate all existing 3D atlases into BrainGlobe.
New mouse brain atlas based on gene expression
- 05 February 2026
The CArea atlas has been added to BrainGlobe. Regions in this atlas are delineated based on clustering 3D volumes of gene expression, finding voxels with similar “gene expression fingerprints”. Data from over 1000 mice was used to generate both volumes of gene expression, and an average Nissl template. This template is a slightly improved and updated version the CCFv3BBP template (also in BrainGlobe as ccfv3augmented_mouse).
New female rat brain atlases added to BrainGlobe
- 02 February 2026
We’re excited to announce the release of two rat brain atlases generated at the Sainsbury Wellcome Centre (SWC), now available through the BrainGlobe ecosystem.