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spacetx / starfish

starfish: unified pipelines for image-based transcriptomics
https://spacetx-starfish.readthedocs.io/en/latest/
MIT License
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3D image registration #1620

Open pdichiaro opened 4 years ago

pdichiaro commented 4 years ago

For seqFISH it is really difficult to avoid z shifts and to mantain the sample in focus during sequential rounds of hybridization. Aligning images in 2d using maximum intensity Z-projected planes is not so accurate. I think it is necessary to implement the 3d image registration (3d phase correlation) for translation adjustment in x, y and z.

neuromusic commented 4 years ago

Thanks for the suggestion @pdichiaro :D

We are waiting for n-dimensional affine registration to be added to skimage (see #1320), but I'm not sure if the underlying register_translation function that we currently wrap supports n-dimensional translations.

maybe @dganguli or @sofroniewn knows?