extract_channel_images

Small Nextflow pipeline for extracting individual channel images from multiplex TIFF images from COMET, MIBI, and OPAL.

What it does

• Reads all TIFF images from an input folder.
• Auto-detects channel names from:
  • OME metadata (COMET / OPAL / generic OME-TIFF)
  • MIBI JSON page descriptions (channel.target)
  • MIBI PageName tags
• Optionally renames channels using a JSON marker mapping file.
• Writes one output TIFF per channel per input image.

Inputs

• --input_dir (required): Folder containing TIFF files.
• --marker_mapping (optional): JSON file with raw_channel_name -> output_channel_name.
• --outdir (optional): Output folder (default: results).
• --pattern (optional): File glob applied within input_dir (default: *).

Usage

Run with conda profile:

nextflow run main.nf \
	-profile conda \
	--input_dir /path/to/images \
	--marker_mapping /path/to/marker_mapping.json \
	--outdir /path/to/output

Run with container profile:

nextflow run main.nf \
	-profile docker \
	--input_dir /path/to/images \
	--marker_mapping /path/to/marker_mapping.json \
	--outdir /path/to/output

Run on HPC with Singularity:

nextflow run main.nf \
	-profile singularity,medium \
	--input_dir /path/to/images \
	--marker_mapping /path/to/marker_mapping.json \
	--outdir /path/to/output

Run for very large images on SLURM (combine runtime + resource profiles):

nextflow run main.nf \
	-profile conda,large \
	--input_dir /path/to/images \
	--marker_mapping /path/to/marker_mapping.json \
	--outdir /path/to/output

Run without mapping file:

nextflow run main.nf \
	-profile conda \
	--input_dir /path/to/images \
	--outdir /path/to/output

Output layout

For each input image, the pipeline creates one folder in outdir:

• <image_name>/
  • <channel_1>.tiff
  • <channel_2>.tiff
  • ...

Channel names are sanitized for filenames. If multiple channels map to the same output name, numeric suffixes are added (for example _2, _3).

Quick test

Generate tiny synthetic OPAL and MIBI test inputs and run the built-in test profile:

python tests/create_test_data.py
nextflow run main.nf -profile test

Test outputs are written to tests/results.