Rotating individual tiles in bigstitcher?

Hi all,

Happy New Year!

Just before going off on holidays I imaged a large multi-channel tissue section on a new microscope using micro-manager and I am now attempting to use bigstitcher to stitch the tiles together. Bigstitcher accurately uses the OME-TIFF data to place the tiles in the right place, but the images in each tile need to be rotated by 90 degrees for them to line up properly. Any advice on how to do this?

Hello Kwasi!

I’ve never really used BigStitcher, but there seem to be similarities with FIJI “plugins” / “Stitching” / “Grid/Collection stitching”, which I have used. If your tiles are arranged in a grid, instead of rotating the tiles, wouldn’t it be the same if you would rotate the stitching pattern? E.g. instead of row-by-row you would use column-by-column.

Best wishes,

Hi Christian,

That would work, except this isn’t an even grid, but instead follows the contours of the tissue section. I suppose if I could get Bigstitcher to transpose the axes that would also do the job, but I don’t know if I can do that either