A 2.5 µm adult Danionella cerebrum atlas joins BrainGlobe#
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.
Kadobianskyi et al. (2026) built a mixed-sex reference brain from 21 adult fish (11 male and 10 female). The atlas is now available in BrainGlobe as danionella_cerebrum_mixed_2.5um. It provides a 2.5 × 2.5 × 2.5 µm mixed-sex reference brain, a whole-brain annotation, and meshes that can be used in the rest of the BrainGlobe ecosystem.
Figure 1. Dorsal view of animated slices through the mixed-sex Danionella cerebrum atlas. The fluorescence reference image is shown on the left and the corresponding anatomical annotation on the right.
How do I use the new atlas?#
You can use the Danionella Cerebrum atlas for visualisation like other BrainGlobe atlases. You can either open it in Neuroglancer for viewing in the browser here.
or you can view it locally as written below:
Install BrainGlobe (instructions).
Open napari and follow the steps in our download tutorial for the
danionella_cerebrum_mixed_2.5umatlas.Run
napari -w brainrender-napariand visualise the different parts of the atlas as described in our visualisation tutorial.
You can also load the atlas in Python:
from brainglobe_atlasapi import BrainGlobeAtlas
atlas = BrainGlobeAtlas("danionella_cerebrum_mixed_2.5um")
Why are we adding new atlases?#
A key aim of BrainGlobe is to make brain atlases accessible across species, so that researchers can use common analysis and visualisation tools without reimplementing them for every model organism. If you would like to get involved with a similar project, please get in touch.