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@ctgriff by any chance do you have the bigstitcher update site enabled ? Since BigStitcher is now shipped by default with Fiji, the update site is no longer needed. Worse: having the update site enabled causes some issues.

Cheers

Yes. I will use SAM but I need to use thresholding. However, when I used to LAB color space it worked well as can see. I think, I've solved the problem for it.

What kind of compute power do you have available? Might be able to get by with OCR. But if u have a GPU available you can go overboard with SAM.

n5 4.0.0 was recently released, so I'm guessing there might be some issue between BigStitcher and n5-hdf5. Tagging @bogovicj @StephanPreibisch and

I'm stitching 3D lightsheet data in BigStitcher. Near the end of the workflow, when I try to export as HDF5, I get this error instead of the export completing:

This is in the most recent version of FIJI, downloaded July 25, 2026. The error occurs at the 'Image Fusion' step.