BrainGlobe

@brainglobe.info

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We build open source computational neuroanatomy software that works across species. https://brainglobe.info Posts by @adamltyson.com

An example of the local and remote directory structure for brainglobe-atlasapi V2 and V3. V2 stores data in large monolithic archives, V3 stores each component separately.
Images of the three new atlases, with "Three Allen CCFv2 mouse brain atlases, now in BrainGlobe" and the BrainGlobe logo below.
An illustration of many of the atlases supported by BrainGlobe.
Two-dimensional view of the CArea Mouse atlas: reference (left) and annotations (right)
Animated GIF showing the SWC rat brain atlas template and annotation images.
Two-dimensional view of the Dorr mouse MRI brain atlas: annotations (left) and reference (right).
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.
Coronal and lateral views of the mouse brain, visualized using the napari viewer
A three-dimensional view of the Kocher lab’s bumblebee brain atlas visualised with brainrender-napari.
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.
Illustration of brainmapper results, showing detected cells, overlaid on a brain image segmented according to the Allen Mouse Brain Atlas.
Coronal section of the cuttlefish brain atlas annotations (only right hemisphere shown) and reference image.
Visualisation of the Allen Mouse Brain Atlas within Blender
A visualisation of both the MRI (left) and LSFM (right) templates and their (right-hemisphere) annotations contained in Gubra’s multimodal mouse brain atlas.
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.
Saggital view of the axotlotl atlas annotations.
Visualisation of some barrel columns using brainrender
A screenshot of the brainmapper widget, showing the distribution of napari points within a BrainGlobe atlas.
Dorsal view of the cavefish brain atlas annotations.
Visualisation of the Allen Mouse Brain Atlas displaying the shortest path within cortex between two points
Screenshot of the brainrender-napari visualisation tool showing a 3D rendering of the larval zebrafish atlas.