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phflot / flow_registration

Flow-Registration toolbox for 2P motion compensation
https://www.snnu.uni-saarland.de/flow-registration/
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ome.tiff saving + swap dimension #24

Open sdaste opened 5 months ago

sdaste commented 5 months ago

Hi,

First thank you for this great package!

Flow_registration outputs multi-channel TIFF stack with dimensions frame x (spatial_1) x (spatial_2) x channel. However, Suite2P (package for cell segmentation) expects frame x channel x (spatial_1) x (spatial_2) dimensions in TIFF stack with 2 channels. Tiff larger than 4Go cannot be read by it either, and ome.tiff files solve this problem.

Would it therefore be possible to swap dimensions as above and save the result in ome.tiff?

Thanks!

phflot commented 5 months ago

Thank you for the feedback! I was not aware about ome.tiff, I'll try to look into this over the weekend and will add an option for suite2p compatible tiff files. For the meantime, there is also the "MULTIFILE_TIFF" option which outputs one file per channel, in case that helps. Best wishes, Philipp