What would you align sets of multiple (~20) large (2-4 Gb) #microscopy images?
For smaller subset images ImageJ plugins for transformations based on SIFT landmark correspondence work well. However standard ImageJ (bioformats) file handling doesnโt cope well with such large files. For plugins handling large file manipulation (BigData family) or chunked (e.g. zarr) storage in turn I donโt know how to implement SIFT (or similar) - e.g. for BigWarp I can only find manual landmark annotation, i.e. no option to create landmarks via other plugins.
My images are iterative fluorescence whole slide scans of the same slide with a constant nuclear stain and varying other stains. There is some x/y shift and rotation as well as warping - nothing major, but I need nearly pixel perfect alignment (e.g. QuPath+Warpy worked well on larger images but was too imprecise).
Stitching happens on the fly during imaging and Iโm not sure I can extract the tiles faithfully, so the ASHLAR pipeline didnโt seem applicable. Iโve seen VALIS recommended, but implementation seemed daunting and since the nuclear stain provides reasonable fiducial points the workflow seemed an overkill.
Ideally I would want a scripted solution as this has to scale up to hundreds of such sets eventually and downstream processing is in python+R anyhow.
#imageanalysis #spatial #imaging
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