ArticleNature communications2022
A SIMPLI (Single-cell Identification from MultiPLexed Images) approach for spatially-resolved tissue phenotyping at single-cell resolution.
Article in Nature communications, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed.
- Spatialproteomics: an interoperable toolbox for analyzing highly multiplexed fluorescence image data.Nature methods · 2026Article
- Spotlight on challenges and novel methods in highly multiplexed tissue imaging-based spatial proteomics.Journal of translational medicine · 2026Review
- CROCHET: a versatile pipeline for automated analysis and visual atlas creation from single-cell spatialomic data.bioRxiv : the preprint server for biology · 2026Article
- Antibody-Based Multiplex Image Analysis: Standard Analytical Workflows and Artificial Intelligence Tools for Pathologists.Laboratory investigation; a journal of technical methods and pathology · 2025Review
- CytoSpatio: Learning cell type spatial relationships using multirange, multitype point process models.PLoS computational biology · 2025Article
- Intracellular accumulation of amyloid-ß is a marker of selective neuronal vulnerability in Alzheimer's disease.Nature communications · 2025Article
- Quantitative benchmarking of nuclear segmentation algorithms in multiplexed immunofluorescence imaging for translational studies.Communications biology · 2025Article
- Integrated workflow for analysis of immune enriched spatial proteomic data with IMmuneCite.Scientific reports · 2025Article
- Spatial Patterning Analysis of Cellular Ensembles (SPACE) finds complex spatial organization at the cell and tissue levels.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- From surfing to diving into the tumor microenvironment through multiparametric imaging mass cytometry.Frontiers in immunology · 2025Review
- Context-dependent effects of CDKN2A and other 9p21 gene losses during the evolution of esophageal cancer.Nature cancer · 2025Article
- AI-based hardware and software tools in microscopy to boost research in immunology and virology.Frontiers in immunology · 2025Review
- MeXpose-A Modular Imaging Pipeline for the Quantitative Assessment of Cellular Metal Bioaccumulation.JACS Au · 2024Article
- Deep cell phenotyping and spatial analysis of multiplexed imaging with TRACERx-PHLEX.Nature communications · 2024Article
- Spatial Patterning Analysis of Cellular Ensembles (SPACE) discovers complex spatial organization at the cell and tissue levels.bioRxiv : the preprint server for biology · 2024Article
- Characterisation of premature cell senescence in Alzheimer's disease using single nuclear transcriptomics.Acta neuropathologica · 2024Article
- Software Tools for 2D Cell Segmentation.Cells · 2024Review
- Spatial Multiplexing and Omics.Nature reviews. Methods primers · 2024Article
- mxfda: a comprehensive toolkit for functional data analysis of single-cell spatial data.Bioinformatics advances · 2024Article
- Rarity: discovering rare cell populations from single-cell imaging data.Bioinformatics (Oxford, England) · 2023Article
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11 authors.
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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 ]".
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