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BIOP / ijp-imagetoatlas

2D sections to 3D atlas registration with Fiji and QuPath
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Copy registration sequence from one slice and apply it to others #174

Closed penguingiraffe2 closed 6 months ago

penguingiraffe2 commented 10 months ago

Hello! This tool is amazing thank you so much !

In addition to warping the atlas and overlaying the warped atlas onto our images in qupath, i'd like to warp some of the heatmaps that qupath generates so that i can eventually make "average" heatmaps across sections from various brains for various stains.

I can export the heatmaps as TIFF files... is there an easy way to use the registration function that ABBA generates and apply it to other images, such as the heatmap TIFF? I feel as though this would be a better method than backward transforming all the actual images and regenerating the heatmaps from the warped images. Thanks so much.

penguingiraffe2 commented 10 months ago

just realized a nifty workaround is to save the heatmap as an additional channel in FIJI and then simply run through the standard pipeline. I'll close the question but leave this up for other folks to see. Also, in case you have better recommendations for how to go about doing this.

NicoKiaru commented 10 months ago

I think it should be possible to warp the image using the transformation provided by ABBA. I reopen the issue (not a priority though).

NicoKiaru commented 7 months ago

In the upcoming release, there will be a way to copy the registration sequence from one slice to other ones:

image

see commit 01bbe19a909afe

NicoKiaru commented 7 months ago

I re-open this and keep it open until it is documented

NicoKiaru commented 6 months ago

Documentation done in https://github.com/BIOP/ijp-imagetoatlas/commit/bf53bed7b21484f8bd85b079362780db4e999636