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Using ClearMap on previously stitched images #170
Description
Hi,
I have light sheet images of mouse brains that I would like to run ClearMap on. I have however previously already stitched the raw images using terastitcher, and would therefore only like to use ClearMap for atlas registration and later Cellmap. I was wondering if there's a way to input already stitched .tif files and go straight to atlas registration? So far I've tried to make it work by specifying the paths to the stitched images in the "Raw images paths" window in the GUI, skipping stitching altogether, and trying to run the atlas registration but since the images aren't in the expected folders/formats it gets stuck.
Thank you!
Activity
crousseau commentedon Nov 3, 2025
@alexjanis
Thanks for reaching out.
Actually, this is supported but the workflow is not obvious enough in v2. Your intuition was right in specifying your tifs as the source images. The next step (probably not intuitive enough, I'm looking to improve that for v3) is to go to stitching and run it. It will just convert your input to the "stitched file" in the right format for downstream operations.
Let me know if this works.
crousseau commentedon Oct 26, 2026
ClearMap 3.1 supports processing images that have already been stitched.
When using a non-tiled input, the preprocessing workflow can use the existing image as the stitched source, without performing the stitching operation.
Closing this issue as the functionality is already supported.
Feel free to reopen it if you encounter any difficulties with this workflow.