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)

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Visualization includes:

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

Example output:

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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

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Description of Experiment

n/a

Current Bugs to Fix

no bugs