Align brain microscopy to an atlas, review and export ROIs
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.
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!
About AtlasAlign on Product Hunt
“Align brain microscopy to an atlas, review and export ROIs”
AtlasAlign launched on Product Hunt on September 18th, 2026 and earned 55 upvotes and 1 comments, placing #87 on the daily leaderboard. 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.
On the analytics side, AtlasAlign competes within GitHub, Science and OpenAI Day — topics that collectively have 42.8k followers on Product Hunt. The dashboard above tracks how AtlasAlign performed against the three products that launched closest to it on the same day.
Who hunted AtlasAlign?
AtlasAlign was hunted by meghamsh teja konda. A “hunter” on Product Hunt is the community member who submits a product to the platform — uploading the images, the link, and tagging the makers behind it. Hunters typically write the first comment explaining why a product is worth attention, and their followers are notified the moment they post. Around 79% of featured launches on Product Hunt are self-hunted by their makers, but a well-known hunter still acts as a signal of quality to the rest of the community. See the full all-time top hunters leaderboard to discover who is shaping the Product Hunt ecosystem.
For a complete overview of AtlasAlign including community comment highlights and product details, visit the product overview.
meghamsh teja konda