Launching today

AtlasAlign

Launching today

Align brain microscopy to an atlas, review and export ROIs

11 followers

Align brain microscopy to an atlas, review and export ROIs

11 followers

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AtlasAlign is an open-source Fiji/ImageJ2 plugin for mouse brain atlas alignment and ROI export. Beta.3 adds multichannel and composite viewing, registration pinned to C/Z/T, selected-plane exports, and saved review sessions. Refine alignment, edit anatomical ROIs, and export crops and masks in original image coordinates. Resume individual or batch reviews. Source images stay read-only; researchers review and accept the anatomy. Demo frames show the earlier interface.

Free

Launch tags:GitHub•Science•OpenAI Day

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GPT-6 Astra Challenge

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Maker

Astra helped me build and test AtlasAlign, an open-source Fiji/ImageJ2 plugin for mouse brain microscopy. It made it practical to turn a research workflow into a working tool with safeguards: read-only source images, separate alignment previews, explicit anatomical review, and source-coordinate ROI exports. I used Astra in Codex for implementation, debugging and tests around image integrity and export behavior. The latest version adds multichannel inspection, selected-plane exports and saved review sessions. Astra is part of how I built and tested the software; anatomical decisions remain with the researcher.

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21h ago

Maker

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Hi Product Hunt! I’m Meghamsh, the maker of AtlasAlign. I built it to make mouse brain microscopy alignment and region-of-interest export easier to review in Fiji/ImageJ2. Choose an Allen atlas plane, adjust the alignment, edit anatomical regions, and export crops and masks in the original image coordinates. The source stays read-only, and batch projects let you resume a review later. AtlasAlign is open source and in beta. Anatomical decisions remain with the researcher. The GitHub page includes installation instructions, a demo video, and a mock microscopy example. I’d love feedback from researchers and Fiji users: which part of atlas alignment or ROI export takes the most time in your workflow? Suggestions welcome!

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7d ago