Skip to content

Commit

Permalink
First draft of barrel atlas blog
Browse files Browse the repository at this point in the history
  • Loading branch information
adamltyson committed Jul 22, 2024
1 parent aadf34e commit c338b63
Show file tree
Hide file tree
Showing 2 changed files with 41 additions and 0 deletions.
41 changes: 41 additions & 0 deletions docs/source/blog/barrel-atlas-added.md
Original file line number Diff line number Diff line change
@@ -0,0 +1,41 @@
---
blogpost: true
date: July 22, 2024
author: Adam Tyson, Axel Bisi
location: London, U.K.; Lausanne, Switzerland
category: brainglobe
language: English
---

# A mouse brain atlas with barrel field annotations has been added to BrainGlobe

[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.


<img src="./images/barrel_annotations.png" alt="barrel annotations" width="700"/>

**Figure 1. Surface view of the barrel annotations.**


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`).

## How do I use the new atlas?

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)


## Why are we adding new atlases?

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).
Binary file added docs/source/blog/images/barrel_annotations.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.

0 comments on commit c338b63

Please sign in to comment.