nfcore/imcyto is a bioinformatics analysis pipeline used for Image Mass Cytometry analysis.
The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It comes with docker containers making installation trivial and results highly reproducible.
- Split mcd file by ROI, and save full and ilastik stacks separately based on specification in
- Apply preprocessing filters to full stack tiff files (
- Merge images from ilastik stack to obtain RGB image of cell nuclei and membranes to generate a composite tiff (
- Use composite tiff to classify pixels as membrane, nuclei or background, and save probabilities map as tiff (
- Use probability tiffs and preprocessed full stack tiffs for single cell segmentation to generate a cell mask as tiff and then overlay cell mask onto full stack tiff images to extract single cell information generating a csv file (
iii. Download the pipeline and test it on a minimal dataset with a single command
nextflow run nf-core/imcyto -profile test,<docker/singularity>
iv. Start running your own analysis!
nextflow run nf-core/imcyto \ --input "./mcd/*.mcd" \ --metadata 'metadata.csv' \ --full_stack_cppipe './plugins/full_stack_preprocessing.cppipe' \ --ilastik_stack_cppipe './plugins/ilastik_stack_preprocessing.cppipe' \ --segmentation_cppipe './plugins/segmentation.cppipe' \ --ilastik_training_ilp './plugins/ilastik_training_params.ilp' \ -profile <docker/singularity>
See usage docs for all of the available options when running the pipeline.
The nf-core/imcyto pipeline comes with documentation about the pipeline, found in the
- Pipeline configuration
- Running the pipeline
- Output and how to interpret the results
It would not have been possible to develop this pipeline without the guidelines, scripts and plugins provided by the Bodenmiller Lab. Thank you too!
If you would like to contribute to this pipeline, please see the contributing guidelines.
You can cite the
nf-core pre-print as follows:
Ewels PA, Peltzer A, Fillinger S, Alneberg JA, Patel H, Wilm A, Garcia MU, Di Tommaso P, Nahnsen S. nf-core: Community curated bioinformatics pipelines. bioRxiv. 2019. p. 610741. doi: 10.1101/610741.