gsoc_brainglobe_registration_blog

docs/blog/gsoc_2025_brainglobe_registration.md

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+# 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.