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adamltyson committed Aug 16, 2024
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4 changes: 2 additions & 2 deletions docs/source/blackcap.md
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<!DOCTYPE html>
<html>
<head>
<meta http-equiv="refresh" content="0; url=/projects/blackcap.html">
<meta http-equiv="refresh" content="0; url=/projects/blackcap/index.html">
</head>
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<p>If you are not redirected, <a href="/projects/blackcap.html">click here</a>.</p>
<p>If you are not redirected, <a href="/projects/blackcap/index.html">click here</a>.</p>
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## A digital three-dimensional brain atlas for the blackcap (Sylvia atricapilla)
# A digital three-dimensional brain atlas for the blackcap (Sylvia atricapilla)

## Introduction
BrainGlobe provides a
[consistent interface to existing anatomical atlases from many species](/documentation/brainglobe-atlasapi). However,
[consistent interface to existing anatomical atlases from many species](/documentation/brainglobe-atlasapi/index). However,
digital 3D atlases do not exist for the majority of species.

The Eurasian blackcap (*Sylvia atricapilla*) is a songbird known to navigate by the Earth's magnetic field, making it
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## Process
Full details of the atlas generation process are available in the [preprint](), however it is briefly as follows:
1. Acquire high-resolution whole-brain images using the
[Sainsbury Wellcome Centre Advanced Microscopy Facility serial-section two-photon microscopy platform](https://swc-advanced-microscopy.github.io/facility_webpage/)
2. Crop images to generate individual hemisphere images without damage (we used 18 hemispheres from 10 birds).
[Sainsbury Wellcome Centre serial section two-photon platform](https://swc-advanced-microscopy.github.io/facility_webpage/)
2. Crop images to generate individual hemisphere images without damage (we used 18 hemispheres from 10 birds)
3. Iteratively generate a high signal-to-noise average template image from all the individual images using
[ANTs](http://stnava.github.io/ANTs/) via an [optimised script](https://github.com/CoBrALab/optimized_antsMultivariateTemplateConstruction)
from the [CoBra lab](https://www.cobralab.ca/).
from the [CoBra lab](https://www.cobralab.ca/)
4. Manually annotate brain regions using [ITK-SNAP](http://www.itksnap.org/pmwiki/pmwiki.php)
5. Package the template and annotations image [into the BrainGlobe format](https://brainglobe.info/documentation/brainglobe-atlasapi/adding-a-new-atlas.html).
5. Package the template and annotations image [into the BrainGlobe format](https://brainglobe.info/documentation/brainglobe-atlasapi/adding-a-new-atlas.html)

:::{note}
The template generation process is simplified by
[brainglobe-template-builder](https://github.com/brainglobe/brainglobe-template-builder). This tool will be further
improved to allow others to create their own atlases.
:::

![Atlas generation process](./images/atlas-generation.png)
**Atlas generation process**

## Results
We have initially generated a template reference image at 25 micron isotropic resolution and annotated 19 brain regions.
This atlas is available within BrainGlobe as `oldenburg_blackcap_25um` and is compatible with all BrainGlobe tools.

![Blackcap atlas viewed coronally](./images/animation.gif)
**Blackcap atlas viewed coronally**

## Get involved
The blackcap atlas is version 1, and we anticipate releasing further versions at higher resolutions and with more
regions annotated. If this atlas is useful for your work and would like to contribute, please [get in touch](/contact).

We are creating further novel atlases, and we'd be very happy to chat if you're also interested in making an
atlas for your application.

4 changes: 2 additions & 2 deletions docs/source/projects/index.md
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# Projects

```{toctree}
:maxdepth: 2
blackcap
:maxdepth: 1
blackcap/index
```

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