MCD to Zarr conversion and stitching
Project description
MCD STITCHER
Stitch rois from MCD files into OME-TIFFS.
Install
pip install mcd_stitcher
Requirements
- click
- numpy
- pandas
- python_dateutil
- xarray
- zarr
- scikit-image
Command line usage
*MCD to Zarr converter
imc2zarr <mcd_folder> <zarr_folder>
*Zarr dataset stitcher
zarr_stitch <zarr_folder>
*Composite MCD to Zarr to Stitch function
mcd_stitch <mcd_folder> <zarr_folder>
Arguments
- mcd_folder:
- The root folder of the IMC scan containing a single and/or multiple mcd files.
- zarr_folder:
- Storage location of converted MCD files in Zarr format and the starting point for stitching zarr files.
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