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abria / TeraStitcher

A tool for fast automatic 3D-stitching of teravoxel-sized microscopy images
http://abria.github.io/TeraStitcher/
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Meaning of the error "cannot compute origin". Trying to stitch --sparse data with three channels #85

Closed ilykos closed 3 years ago

ilykos commented 3 years ago

Usually, in my workflow I am trying to stitch RGB images from the displacement of green channel. My folder structure looks like this:

000000/000000_000000/000000.tif (red) 000000/000000_000000/000010.tif (green) 000000/000000_000000/000020.tif (blue I have attempted to run TeraStitcher with --sparse parameter on data that has some empty tile folders. I am getting following error in TeraStitchers import step:

ERROR: in StackedVolume::applyReferenceSystem(): cannot compute origin. 
Tile (0,0) [00258005/00258005_00149346] has no slice at z=0
ilykos commented 3 years ago

The reason seems to be the lack of images in the corner positions of the grid. Or first and last folder of the folder structure. Putting blank images for each channel into the corners seems to solve the problem.