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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.

Project details


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mcd_stitcher-0.1.3-py3-none-any.whl (17.5 kB view hashes)

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