Table of contents
Workflow parameters
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
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
, 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
Wheter 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
Wheter background subtraction should be performed, and the computed intermediates used in further processing
- Valid values:
true
,false
- Default:
false
- Example:
workflow:
background: true