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blogpost: true | ||
date: July 22, 2024 | ||
author: Adam Tyson, Axel Bisi | ||
location: London, U.K.; Lausanne, Switzerland | ||
category: brainglobe | ||
language: English | ||
--- | ||
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# A mouse brain atlas with barrel field annotations has been added to BrainGlobe | ||
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[Bolaños-Puchet et al., 2024](https://elifesciences.org/articles/80777) recently published annotations of the mouse | ||
[barrel cortex](https://en.wikipedia.org/wiki/Barrel_cortex) in the | ||
[Allen Mouse Brain Common Coordinate Framework](https://doi.org/10.1016/j.cell.2020.04.007). | ||
The Allen Mouse Brain Atlas (and particularly it's Common Coordinate Framework) has been key to advances in | ||
computational neuroanatomy in the adult mouse. However, this atlas does not contain any barrel cortex annotations. | ||
These annotations allow researchers to much more precisely localise regions of interest within specific barrels, | ||
rather than barrel cortex as a whole. | ||
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<img src="./images/barrel_annotations.png" alt="barrel annotations" width="700"/> | ||
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**Figure 1. Surface view of the barrel annotations.** | ||
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EPFL PhD student Axel Bisi and the BrainGlobe team have now worked together to make the atlas available within the BrainGlobe ecosystem. | ||
Two versions of the atlas are available, at 10μm (`allen_mouse_bluebrain_barrels_10um`) and 25μm resolution (`allen_mouse_bluebrain_barrels_25um`). | ||
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## How do I use the new atlas? | ||
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You can use the atlas like all other BrainGlobe atlases. To visualise the atlas in napari: | ||
* Install BrainGlobe ([instructions](/documentation/index)) | ||
* Download the 25μm version of the atlas by running `brainglobe install -a allen_mouse_bluebrain_barrels_25um` in the terminal (make sure to activate your conda environment first) | ||
* Run `napari -w brainrender-napari` and visualise the different parts of the atlas as described in our [visualisation tutorial](/tutorials/visualise-atlas-napari) | ||
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## Why are we adding new atlases? | ||
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A key goal of BrainGlobe is to ensure that computational neuroanatomy software doesn't need to be rewritten for new | ||
applications requiring novel atlases. We look forward to adding more atlases to BrainGlobe in the near future. | ||
If you'd like to get involved with a similar project, please [get in touch](/contact). |
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