index.qmd

---
title: BrainGlobe
subtitle: community-driven tools for (atlas-based) computational neuroanatomy
author: "Alessandro Felder"
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## Contents {.smaller}
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* Introduction
* What is an atlas?
* What is BrainGlobe?
* BrainGlobe Atlas API
* Established BrainGlobe tools
* Experimental BrainGlobe tools
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![](img/tracing.png)
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## Introduction

![](img/alessandro.png)

## Introduction {.smaller}

![](img/swc_building_cropped.jpg)

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* [Neuroinformatics Unit](https://neuroinformatics.dev/people){preview-link="true" style="text-align: center"}
  * [Sainsbury Wellcome Centre](https://www.sainsburywellcome.org/web/about-swc){preview-link="false" style="text-align: center"}
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* [UCL Centre for Advanced Research Computing](https://www.ucl.ac.uk/advanced-research-computing/){preview-link="false" style="text-align: center"}
* [UCL Bioimage Interest Group](https://www.ucl.ac.uk/science-technology-platforms/imaging/ucl-bioimage-interest-group){preview-link="false" style="text-align: center"}
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## What is an atlas? {.smaller}

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![](img/allen_mouse_template.png){fig-align=center}
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![](img/allen_mouse_annotation.png){fig-align=center}
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(Neuro-anatomical) atlases consist of a template image, an annotations image and metadata (E.g. [The Allen Mouse Brain Common Coordinate Framework](https://doi.org/10.1016/j.cell.2020.04.007))

## Why is it useful?

* A standardised annotation and a standardised coordinate system 
* Allows registering experimental data can be registered

This facilitates data comparability and (re-)combination, 
and therefore collaboration and data sharing.

Have accelerated neuroscientific discovery, for species where there is an atlas!

{{< include slides/brainglobe.qmd >}}

## Acknowledgements

* Adam Tyson, Niko Sirmpilatze, Igor Tatarnikov
* past and present BrainGlobe contributors

![](img/Chan_Zuckerberg_Initiative.png) ![](img/swc.webp){width=50%}
![](img/funders.webp)

# [BrainGlobe website](https://brainglobe.info/){preview-link="true" style="text-align: center"}