Posts by Jung Woo Kim
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.
An Atlas for the dwarf cuttlefish, Sepia bandensis has been added to BrainGlobe
- 10 March 2025
Cephalopods are fascinating model organisms for neuroscience research. The dwarf cuttlefish in particular (Sepia bandensis) is known for its camouflage using dynamic skin pattern changes, but it is also known to display social communication behaviour. In 2023, Montague et al. created a magnetic resonance imaging (MRI) atlas by combining data from 8 dwarf cuttlefish brains (4 female, 4 male) using deep learning. The cuttlefish atlas provides researchers with a useful resource for investigating the neural processes governing cephalopod behaviour.