A SIMPLI (Single-cell Identification from MultiPLexed Images) approach for spatially-resolved tissue phenotyping at single-cell resolution.
Journal
Nature communications
ISSN: 2041-1723
Titre abrégé: Nat Commun
Pays: England
ID NLM: 101528555
Informations de publication
Date de publication:
09 02 2022
09 02 2022
Historique:
received:
07
04
2021
accepted:
25
01
2022
entrez:
10
2
2022
pubmed:
11
2
2022
medline:
8
3
2022
Statut:
epublish
Résumé
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 ]".
Identifiants
pubmed: 35140207
doi: 10.1038/s41467-022-28470-x
pii: 10.1038/s41467-022-28470-x
pmc: PMC8828885
doi:
Substances chimiques
Antibodies
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
781Subventions
Organisme : Cancer Research UK
ID : C43634/A25487
Pays : United Kingdom
Organisme : Wellcome Trust
ID : FC001002
Pays : United Kingdom
Organisme : Medical Research Council
Pays : United Kingdom
Organisme : Cancer Research UK
ID : C604/A25135
Pays : United Kingdom
Organisme : Wellcome Trust
Pays : United Kingdom
Organisme : Cancer Research UK
ID : C7893/A26233
Pays : United Kingdom
Organisme : Arthritis Research UK
ID : FC001002
Pays : United Kingdom
Informations de copyright
© 2022. The Author(s).
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