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initial_image_processing_VIS

Use this repo to automate creating PNG files from CZI microscopy data to easily visualize them. (works for MIPs, need to validate the successful workflow of non-MIPs)

Visualization includes:

  1. Scale-bar configuration
  2. Color configuration of each channel including naming
  3. Panel creation of specified channels

Example output:

Example Panel

Step-by-step instructions:

  • Add raw_data folder and subsequent .czi files
  • Add python_results folder
  • Delete the example_figures folder (not necessity for script to work)
  • Configure the variables to work for your use-case
  • Add description of experiment below

Description of Experiment

n/a

Current Bugs to Fix

no bugs