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akhanf authored Feb 20, 2024
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A Snakemake workflow for pre-processing single plane illumination microscopy (SPIM, aka lightsheet microscopy)

Takes datasets produced by the Biotec UltraMicroscope Blaze (as a folder of tif images), and outputs a BIDS-like dataset, with multiscale ome zarr files along with downsampled nifti images.

Also performs simple affine registration to Allen Brain Atlas v3 (mouse atlas), and resamples labels to multiscale ome zarr as well. (WIP)
Takes datasets produced by the Biotec UltraMicroscope Blaze (as a folder of tif images), and outputs a BIDS-like dataset, with a multi-channel multi-scale ome zarr file along with downsampled nifti images.

## Requirements

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