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config_template.yml
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config_template.yml
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---
pipeline: <PIPELINE NAME>
output_dir: profiles
platemap_well_column: Metadata_well_position
compartments:
- cells
- cytoplasm
- nuclei
aggregate:
perform: true
plate_column: Metadata_Plate
well_column: Metadata_Well
method: median
fields: all
image_feature_categories:
- Count
- Intensity
annotate:
perform: true
well_column: Metadata_Well
external :
perform: true
file: <metadata file name>
merge_column: <Column to merge on>
normalize:
perform: true
method: mad_robustize
features: infer
mad_robustize_fudge_factor: 0
image_features: true
min_cells: 1
normalize_negcon:
perform: true
method: mad_robustize
features: infer
mad_robustize_fudge_factor: 0
image_features: true
min_cells: 1
feature_select:
perform: true
features: infer
level: batch
gct: false
image_features: true
operations:
- variance_threshold
- correlation_threshold
- drop_na_columns
- blocklist
min_cells: 1
feature_select_negcon:
perform: true
features: infer
level: batch
gct: false
image_features: true
operations:
- variance_threshold
- correlation_threshold
- drop_na_columns
- blocklist
min_cells: 1
quality_control:
perform: true
summary:
perform: true
row: Metadata_Row
column: Metadata_Col
heatmap:
perform : true
options:
compression: gzip
float_format: "%.5g"
samples: all
---
batch: <FIRST BATCH NAME>
plates:
- name: <FIRST PLATE NAME>
process: true
- name: <SECOND PLATE NAME>
process: true
process: true
---
batch: <SECOND BATCH NAME>
plates:
- name: <FIRST PLATE NAME>
process: true
- name: <SECOND PLATE NAME>
process: true
process: true