gsoc_brainglobe_registration_blog

docs/blog/gsoc_2025_brainglobe_registration.md

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+:blogpost: true
+:date: August 25, 2025
+:author: Saarah Hussain
+:location: London, UK
+:category: Blog
+:language: English
+:image: 0
+
+# GSoC 2025: brainglobe-registration
+
+Over the summer, I worked on extending the brainglobe-registration plugin, 
+focusing on making atlas alignment more accessible and less error-prone for 
+users without a neuroscience background. Thus far, choosing the correct atlas 
+slice and orientation has been a manual task – requiring users to scroll 
+through volumes, make rough visual judgements, and enter rotation values by 
+hand. My project aimed to automate this step, using Bayesian optimisation to 
+identify the best matching slice and orientation parameters directly from the 
+data.
+
+The result is a new Automatic Slice Detection widget in the plugin, which not 
+only handles single 2D images but can also align slabs of consecutive slices. 
+For slabs, the optimiser matches the first and last slices and then 
+interpolates alignment parameters across the stack, so that users can align 
+larger volumes in one go. A key part of this work was building clear and 
+informative logging – every optimisation step records the parameters tested, 
+the corresponding rotated slice, and its similarity score. This makes the 
+process more transparent and provides a useful record for reproducibility.
+
+Working on this project has been a valuable experience in bridging methods 
+from optimisation and image analysis with practical neuroscience workflows. 
+I particularly enjoyed balancing algorithmic design with UX considerations, 
+such as keeping the interface intuitive while still exposing enough 
+flexibility for advanced use. Collaborating with the NIU team also gave me a 
+deeper appreciation of the importance of open, well-documented tools in 
+neuroinformatics, and the work that goes into making them robust and 
+user-friendly.
+
+Looking back, the most rewarding part was seeing the tool go from concept to 
+a usable feature that I hope will save researchers time and difficulty in 
+their workflows. Contributing to the BrainGlobe ecosystem has been a greatly 
+rewarding opportunity, and I am incredibly excited to see how these tools 
+continue to evolve in the future.

docs/source/blog/gsoc_2025_brainglobe_registration.md

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