Workflow parameters

Parameters under the namespace workflow regulate the function of the pipeline as a whole.

By default, the pipeline starts from the registration step (ASHLAR), proceeds through UnMICST, S3segmenter, and stops after executing the quantification MCQuant step.

start-at

Name of the first step to be executed by the pipeline

• Valid values: illumination, registration, background (background only), dearray (TMA only), segmentation, watershed, quantification, downstream
• Default: registration
• Example:

workflow:
  start-at: segmentation

stop-at

Name of the final step to be executed by the pipeline

• Valid values: illumination, registration, background (background only), dearray (TMA only), segmentation, quantification, downstream
• Default: quantification
• Example:

workflow:
  stop-at: downstream

Additional examples: Specifying start and stop modules

Use start-at and stop-at workflow parameters to execute any contiguous section of the pipeline. Remember, by default the pipeline will run from ASHLAR through MCQuant.

Example 1: Running illumination correction and registration only

workflow:
  start-at: illumination
  stop-at: registration

Example 2: Start by dearraying an already-registered TMA image

workflow:
  tma: true
  start-at: dearray

Note: Starting at any step beyond registration requires pre-computed output of the previous steps placed at the correct location in the project directory.

tma

If true, MCMICRO treats input data as a TMA. If false, the input is assumed to be a whole-slide image

• Valid values: true, false
• Default: false
• Example:

workflow:
  tma: true

segmentation-channel

One or more channels to use for segmentation, specified using 1-based indexing; values will be forwarded to all segmentation modules

• Valid values: one or more positive integers, each separated with a space
• Default: 1
• Example:

workflow:
  segmentation-channel: 1 5

segmentation-recyze

Whether the image should be reduced to the channels specified in segmentation-channel prior to being provided to the segmentation modules.

• Valid values: true, false
• Default: false
• Example:

workflow:
  segmentation-channel: 5
  segmentation-recyze: true

ilastik-model

A custom .ilp file to be used as the classifier model for ilastik

• Valid values: A full path to any file
• Default: None
• Example:

workflow:
  ilastik-model: /full/path/to/mymodel.ilp

segmentation

A list of segmentation modules to run

• Valid values: One or more of unmicst, ilastik, mesmer, cypository, cellpose specified as a YAML list
• Default: unmicst
• Example:

workflow:
  segmentation: [unmicst, ilastik]

downstream

A list of downstream modules to run

• Valid values: One or more of naivestates, scimap, fastpg, scanpy, flowsom
• Default: scimap
• Example:

workflow:
  downstream: [scanpy, flowsom]

viz

Whether to generate a vizualization with Auto-Minerva

• Valid values: true, false
• Default: false
• Example:

workflow:
  viz: true

qc-files

Whether QC files should be copied, moved or symbolically linked from work directories to the project directory

• Valid values: copy, move, symlink
• Default: copy
• Example:

workflow:
  qc-files: move

background

Whether background subtraction should be performed, and the computed intermediates used in further processing

• Valid values: true, false
• Default: false
• Example:

workflow:
  background: true

background-method

Which background subtraction module to use when background: true.

• Valid values: backsub, imagej-rolling-ball
• Default: backsub
• Example:

workflow:
  background-method: backsub