brainglobe · adamltyson · Aug 16, 2024 · Aug 16, 2024 · Aug 16, 2024 · Aug 20, 2024
diff --git a/docs/source/blackcap.md b/docs/source/blackcap.md
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+<!DOCTYPE html>
+<html>
+<head>
+    <meta http-equiv="refresh" content="0; url=/projects/blackcap/index.html">
+</head>
+<body>
+    <p>If you are not redirected, <a href="/projects/blackcap/index.html">click here</a>.</p>
+</body>
+</html>
diff --git a/docs/source/index.md b/docs/source/index.md
@@ -49,4 +49,5 @@ tutorials/index
 documentation/index
 community/index
 blog/index
+projects/index
 ```
diff --git a/docs/source/projects/blackcap/images/animation.gif b/docs/source/projects/blackcap/images/animation.gif
diff --git a/docs/source/projects/blackcap/images/atlas-generation.png b/docs/source/projects/blackcap/images/atlas-generation.png
diff --git a/docs/source/projects/blackcap/index.md b/docs/source/projects/blackcap/index.md
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+# 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/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 
+a very interesting animal model. However, the lack of a high quality reference atlas hinders computational neuroanatomy 
+research in this species. Anatomical atlases define a standard coordinate system for an organ, and allow data from 
+multiple sources to be aligned and then visualised and analysed together. This makes it easier to integrate results 
+different sources, and facilitates data sharing and collaboration.
+
+For this reason, we collaborated with [Simon Weiler](https://sites.google.com/view/neuroweiler) from the 
+[Sainsbury Wellcome Centre](https://www.sainsburywellcome.org), and the lab of 
+[Henrik Mouritsen](https://uol.de/en/ibu/animal-navigation) at the 
+[Carl von Ossietzky University of Oldenburg](https://uol.de/en) to build a high-quality digital reference atlas 
+of the blackcap brain.
+
+## 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 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/)
+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)
+
+:::{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. 
+
diff --git a/docs/source/projects/index.md b/docs/source/projects/index.md
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+# Projects
+
+```{toctree}
+:maxdepth: 1
+blackcap/index
+```