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README.md

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 A Snakemake workflow forp re-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. 
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+Also performs simple affine registration to Allen Brain Atlas v3 (mouse atlas), and resamples labels to multiscale ome zarr as well. (WIP)
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 ## Requirements
 
  - Linux system with Singularity/Apptainer installed.
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 ### WIP:  The usage of this workflow is described in the [Snakemake Workflow Catalog](https://snakemake.github.io/snakemake-workflow-catalog/?usage=khanlab%2Fspimprep).
 
 
-Note: Designed to work with data from the Miltenyi Biotec UltraMicroscope Blaze, but could be adapted to other types of data
 
 ## TODO: