Posts by Alessandro Felder
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.
An Atlas for the domestic cat has been added to BrainGlobe
- 28 February 2025
Stolzberg et al. (2017) created an MRI atlas of the cat brain cortex at 500um resolution, nicknamed the “Catlas”. Former UCL MSc student Henry Crosswell and the BrainGlobe team have now made this atlas available through BrainGlobe. We called it csl_cat_500um, after the Cerebral Systems Lab (CSL) that created this original data. Its main use is to standardise functional studies in cats - note that its annotations only cover the cortex.
An overview of recently added mouse atlases
- 20 February 2025
Eagle-eyed BrainGlobe enthusiasts will have spotted several new atlases appearing in the BrainGlobe Atlas API in recent weeks. In 2025, we’ve made three new mouse brain atlases newly available through BrainGlobe: The Kim developmental mouse brain atlas (version 1), the Gubra multimodal mouse brain atlas and the Australian mouse brain atlas. Mice are widely used in neuroscience, so it’s no surprise there are many mouse brain atlases. In this blogpost, we describe the newly added atlases in more detail, and suggest potential use cases. This blog covers the new murine atlases only - we have also added the first non-human primate brain atlas to BrainGlobe (and brain atlases for a cat and a cuttlefish are underway)!
An Atlas for the non-human primate Microcebus murinus (grey mouse lemur) has been added to BrainGlobe
- 28 January 2025
Thanks to its small size and its close phylogenetic relation to humans (compared to other model organisms), the grey mouse lemur is a practical choice to study brain evolution and disease. Nadkarni et al. made the first publicly available mouse lemur atlas in 2018. They imaged mouse lemur brains with MRI at 91μm resolution. Thanks to Harry Carey (University of Oslo) it is now accessible from BrainGlobe. In reference to its original authors, the atlas is named nadkarni_mri_mouselemur_91um in the BrainGlobe ecosystem.
An Atlas for the regenerative Ambystoma mexicanum (axolotl) has been added to BrainGlobe
- 09 August 2024
Amphibians have long captivated human’s interest. An unusual amphibian amongst these is the Axolotl (Ambystoma mexicanum), which is sometimes used as a model organism for regeneration. In 2021, Lazcano et al. created a magnetic resonance imaging (MRI) atlas of the juvenile axolotl brain. The axolotl atlas enables researchers to gain better insights into the processes underlying central nervous system (CNS) regeneration.
An atlas for the Blind Mexican Cavefish has been added to BrainGlobe
- 21 June 2024
Kozol et al, 2023 recently published a brain atlas of the blind Mexican cavefish Astyanax mexicanus. This species is interesting from an evolutionary point of view, due to divergent phenotypes (surface- and cave-dwelling) that can be hybridised in the lab. Surface-dwelling populations have retained their eyesight, while cave-dwellers have not. The cavefish brain atlas allows us to understand how brains of a single species have changed anatomically and functionally as part of their adaptations to the environment.
Plans for brainrender
- 18 December 2023
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.