mcd-stitcher 0.1.3

MCD to Zarr conversion and stitching

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.