How To... Manually Register Images with BigWarp - John Bogovic

How To... Manually Register Images with BigWarp
By John Bogovic
Presented: April 14th 2022
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John is an expert in image registration and software development and BigWarp is an amazing tool that's crucial for many challenging image registration applications. Please join us if: you're collecting multi-modal data, interested in image registration, and/or interested in Fiji plugins, ImgLib2, or Java bioinformatics.
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- Slides on transformations + inverses: github.com/bog...
- Sample data: figshare.com/s...
- Bigwarp's wiki page: imagej.net/plu...
- Report bugs here github.com/saa... or here forum.image.sc...
- CLI tools that work with bigwarp (and lots of other stuff) are in this repo github.com/saa...
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[@michellejohannsen9823]

I have four fluorescent channels I am trying to register to each other. But I can only find a way to register two images at a time in Big Warp. Is there a way to align all four at once?

[@jbogovic]

Running BigWarp once lets you produce one transformation, so you'll probably need to run it three times - assuming you pick one of your four channels as the fixed image and the three others need different transforms. For a longer discussion consider posting on the forum (link in the description).

[@sissi8020]

Is it possible to register several stacks together? All stacks has a common image.

[@jbogovic]

Yes you can, by giving BigWarp a multichannel image stack as your moving or fixed image. Then you'll be able to see all channels at once, and all moving images will be transformed at the same time. For a longer discussion consider posting on the forum (link in the description).