SPIMprep is a Snakemake+SnakeBIDS workflow for pre-processing single plane illumination microscopy (SPIM, aka lightsheet microscopy). It takes TIF images (tiled or prestitched) and outputs a validated BIDS Microscopy dataset, with a multi-channel multi-scale OME-Zarr file for each scan, along with downsampled nifti images.

Supported inputs:

SPIMprep supports a range of inputs, with the type of acquisition specified by including the short-hand name as a substring in the acquisition tag:

• blaze: Raw Ultramicroscope Blaze OME TIFF files, either as 2D or 3D TIFF files
• prestitched: Prestitched images, as a stack of 2D TIF files (e.g. from LifeCanvas)
• imaris: Prestitched into a single Imaris (.ims) file

Installation

SPIMprep requires the Pixi package manager. After installing Pixi, clone the repository and install dependencies:

git clone https://github.com/khanlab/spimprep SPIMprep
cd SPIMprep
pixi install
pixi shell

Usage

Run the workflow using the run.py script:

./run.py --input-path /path/to/data/ --subject M4A1Te3 --stains Abeta PI Lectin --output-bids-dir /path/to/output --work-dir /tmp --cores all --use-conda

The --input-path should be a folder with a sample’s tif files, or a tar file containing the tif files. The acquisition value must contain one of blaze, imaris or prestitched to define which workflow will be used.

Full Documentation: here