🔧 Configuration

You can explore parameters related to different parts of the pipeline:

• Core cutting
• Understand channel selection logic for core cutting

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Full configuration file example:

# core cutting

image_dir: "C:/path_to_image_directory"
temp_dir: "C:/path_to_temporary_directory"
output_dir: "C:/path_to_output_directory"
core_info: "C:/path_to/core_metadata.csv"

include_channels: ['002_DAPI']
exclude_channels: ['005_pRB']
use_channels: ['DAPI','CD3']

margin: 10
mask_value: 0
max_pyramid_levels: 3

transfer_cleanup_enabled: True
core_cleanup_enabled: True