SIMPLI: Single-cell Identification from MultiPLexed Images

SIMPLI is a platform agnostic pipeline for the analysis of highly multiplexed histological imaging data.

<img src="assets/Fig1.png" width="829" height="500">

Documentation

More Information about SIMPLI and its use can be found in the wiki.

• Installation

  • SIMPLI installation

• Running SIMPLI

  • SIMPLI command line parameters and configuration

• SIMPLI analysis workflow

  • Documentation for every step of the workflow

Quick start

To try SIMPLI:

1. Install Singularity
2. Install Nextflow
3. Run: nextflow run ciccalab/SIMPLI -profile test

This will run SIMPLI on minimal example dataset distributed in this repository. For more details on the example dataset and the associated analysis workflow see the example-workflow page.

The expected installation time on a desktop computer (Ubuntu 21.04) is of about 20 minutes. The expected run time with the example run on a desktop computer (Ubuntu 21.04) is of about 45 minutes.

Citation

If you used SIMPLI for your analysis please cite our preprint:

A SIMPLI (Single-cell Identification from MultiPLexed Images) approach for spatially-resolved tissue phenotyping at single-cell resolution
Michele Bortolomeazzi, Lucia Montorsi, Damjan Temelkovski, Mohamed Reda Keddar, Amelia Acha-Sagredo, Michael J. Pitcher, Gianluca Basso, Luigi Laghi, Manuel Rodriguez-Justo, Jo Spencer & Francesca D. Ciccarelli
Nature Communications volume 13, Article number: 781 (2022)
DOI: https://doi.org/10.1038/s41467-022-28470-x

SIMPLI is a software developed in the Ciccarelli group.
We are part of The School of Cancer Studies of King's College London and of The Francis Crick Institute.

SIMPLI was originally maintained and developed by Michele Bortolomeazzi.

License

SIMPLI is released under the CRICK Non-commercial Licence Agreement v 2.0.. No permission is required from the rights-holder for non-commercial research uses. Commercial use will require a license from the rights-holder. For further information see the license or contact translation@crick.ac.uk.