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 and Francesca D. Ciccarelli ()
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Michele Bortolomeazzi: The Francis Crick Institute
Lucia Montorsi: The Francis Crick Institute
Damjan Temelkovski: The Francis Crick Institute
Mohamed Reda Keddar: The Francis Crick Institute
Amelia Acha-Sagredo: The Francis Crick Institute
Michael J. Pitcher: King’s College London
Gianluca Basso: IRCCS Humanitas Research Hospital
Luigi Laghi: IRCCS Humanitas Research Hospital
Manuel Rodriguez-Justo: University College London Cancer Institute
Jo Spencer: King’s College London
Francesca D. Ciccarelli: The Francis Crick Institute

Nature Communications, 2022, vol. 13, issue 1, 1-14

Abstract: Abstract Multiplexed imaging technologies enable the study of biological tissues at single-cell resolution while preserving spatial information. Currently, high-dimension imaging data analysis is technology-specific and requires multiple tools, restricting analytical scalability and result reproducibility. Here we present SIMPLI (Single-cell Identification from MultiPLexed Images), a flexible and technology-agnostic software that unifies all steps of multiplexed imaging data analysis. After raw image processing, SIMPLI performs a spatially resolved, single-cell analysis of the tissue slide as well as cell-independent quantifications of marker expression to investigate features undetectable at the cell level. SIMPLI is highly customisable and can run on desktop computers as well as high-performance computing environments, enabling workflow parallelisation for large datasets. SIMPLI produces multiple tabular and graphical outputs at each step of the analysis. Its containerised implementation and minimum configuration requirements make SIMPLI a portable and reproducible solution for multiplexed imaging data analysis. Software is available at “SIMPLI [ https://github.com/ciccalab/SIMPLI ]”.

Date: 2022
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DOI: 10.1038/s41467-022-28470-x

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