# Template for a user configuration settings file

plates_dir:
sources_dir:
layers_dir:
plate_format: 384
workflow:
  stages:
    - name: conversion
      steps:
        - name: metaextract
          args:
        - name: metaconfig
          args:
            format: cellvoyager
        - name: imextract
          args:
    - name: preprocessing
      steps:
        - name: align
          args:
            ref_channel: 1
            ref_cycle: 2
        - name: corilla
          args:
    - name: pyramid_creation
      steps:
        - name: illuminati
          args:
            align: Yes
            illumcorr: Yes
            clip: Yes
    - name: image_analysis
      steps:
        - name: jterator_segment
          args:
        - name: jterator_measure
          args:


# Template for a user configuration settings file

plates_dir:
sources_dir:
layers_dir:
plate_format: 384
workflow:
  stages:
    - name: image_conversion
      steps:
        - name: metaextract
          args:
        - name: metaconfig
          args:
            format: cellvoyager
        - name: imextract
          args:
    - name: image_preprocessing
      steps:
        - name: align
          args:
            ref_channel: 1
            ref_cycle: 2
        - name: corilla
          args:
    - name: pyramid_creation
      steps:
        - name: illuminati
          args:
            align: Yes
            illumcorr: Yes
            clip: Yes
    - name: image_analysis
      steps:
        - name: jterator_segment
          args:
        - name: jterator_measure
          args:


Update user config file template
Update user config file template
