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‎_images/post_slice_detection_screenshot.png‎

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‎_sources/blog/gsoc_2025_brainglobe_registration.md.txt‎

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:blogpost: true
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:date: September 15, 2025
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:author: Saarah Hussain
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:location: London, UK
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:category: Blog
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:language: English
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:image: 0
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# GSoC 2025: brainglobe-registration
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## Introduction
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Hi, I'm [Saarah](https://github.com/saarah815). The intersection of healthcare and software development has
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always been important to me, which is why spending my summer with the
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[Neuroinformatics Unit](https://github.com/neuroinformatics-unit)
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has been the perfect opportunity to bring together the work I love.
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**Project**: [BrainGlobe: Automating Region Selection in brainglobe-registration](https://summerofcode.withgoogle.com/programs/2025/projects/7Xk4Fl7t) <br>
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**Mentors**: [Igor Tatarnikov](https://github.com/IgorTatarnikov), [Alessandro Felder](https://github.com/alessandrofelder), [Adam Tyson](https://github.com/adamltyson)
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---
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## Project Overview
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Over the summer, I worked on extending the
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[`brainglobe-registration`](https://github.com/brainglobe/brainglobe-registration)
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plugin, focusing on making atlas alignment more accessible and less
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error-prone for users without a neuroscience background.
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Thus far, choosing the correct atlas slice and orientation has been a manual
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task – requiring users to scroll through volumes, make rough visual
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judgements, and enter rotation values by hand. My project aimed to automate
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this step, using
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[`BayesianOptimization`](https://github.com/bayesian-optimization/BayesianOptimization)
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to identify the best matching slice and orientation parameters directly
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from the data.
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The result is a new **Automatic Slice Detection widget** in the plugin, which
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not only handles single 2D images but can also align slabs of consecutive
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slices.
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![img_1.png](slice_detection_widget.png)
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The optimiser identifies the atlas slice and rotation parameters that best
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match the moving image, and then updates the Napari widget accordingly:
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![img.png](post_slice_detection_screenshot.png)
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For slabs, the optimiser matches the first and last slices and then
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interpolates alignment parameters across the stack, so that users can align
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larger volumes in one go. I have also written detailed
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[documentation](https://github.com/brainglobe/brainglobe.github.io/pull/362/files?short_path=61a3e19)
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outlining exactly how to use these features.
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In addition to the core project requirements, I also worked on enhancing the
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project following discussions with my mentors. A key part of this work was
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building **clear and informative logging** – every optimisation step logs
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the parameters tested, its similarity score, the corresponding rotated slice
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image, and the rotation parameters. This makes the process more transparent
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and provides a useful record for reproducibility.
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Working on this project has been a valuable experience in bridging methods
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from optimisation and image analysis with practical neuroscience workflows.
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I particularly enjoyed balancing algorithmic design with UX considerations,
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such as keeping the interface intuitive while still exposing enough
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flexibility for advanced use.
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Collaborating with the NIU team also gave me a deeper appreciation of the
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importance of open, well-documented tools in neuroinformatics, and the work
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that goes into making them robust and user-friendly.
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Looking back, the most rewarding part was seeing the tool go from concept to
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a usable feature that I hope will save researchers time and difficulty in
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their workflows. Contributing to the BrainGlobe ecosystem has been a greatly
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rewarding opportunity, and I am incredibly excited to see how these tools
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continue to evolve in the future.
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---
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## Repositories
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- [`brainglobe-registration`](https://github.com/brainglobe/brainglobe-registration)
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- [`fancylog`](https://github.com/neuroinformatics-unit/fancylog)
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- [`brainglobe.github.io`](https://github.com/brainglobe/brainglobe.github.io/)
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---
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*Thank you to my mentors and the incredible team at NIU for all of their support and guidance!*

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<div class="section ablog-post">
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<h2 class="ablog-post-title">
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<a href="blog/gsoc_2025_brainglobe_registration.html">GSoC 2025: brainglobe-registration</a>
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</h2>
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<ul class="ablog-archive">
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<span>15 September 2025</span>
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<a href="blog/author/saarah-hussain.html">Saarah Hussain</a>
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<p class="ablog-post-excerpt"><p>Hi, I’m <a class="reference external" href="https://github.com/saarah815">Saarah</a>. The intersection of healthcare and software development has
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always been important to me, which is why spending my summer with the
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<a href="blog/gsoc_2025_brainglobe_registration.html"><em>Read more ...</em></a>
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<a href="blog/datashuttle_gsoc2025.html">Add Google Drive and AWS to datashuttle - Final GSoC Report</a>

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<p class="ablog-post-excerpt"><p>Hi, I’m <a class="reference external" href="https://github.com/saarah815">Saarah</a>. The intersection of healthcare and software development has
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always been important to me, which is why spending my summer with the
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<a class="reference external" href="https://github.com/neuroinformatics-unit">Neuroinformatics Unit</a>
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has been the perfect opportunity to bring together the work I love.</p>
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<a href="datashuttle_gsoc2025.html">Add Google Drive and AWS to datashuttle - Final GSoC Report</a>

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<span>15 September 2025</span>
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<a href="gsoc_2025_brainglobe_registration.html">GSoC 2025: brainglobe-registration</a>
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<span>15 September 2025</span>
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-
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<a href="gsoc_2025_brainglobe_registration.html">GSoC 2025: brainglobe-registration</a>
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