A full list of publications is available on Google Scholar


Nature Methods (11/2021)

Highly multiplexed tissue imaging makes detailed molecular analysis of single cells possible in a preserved spatial context. However, reproducible analysis of large multichannel images poses a substantial computational challenge. Here, we describe a modular and open-source computational pipeline, MCMICRO, for performing the sequential steps needed to transform whole-slide images into single-cell data. We demonstrate the use of MCMICRO on tissue and tumor images acquired using multiple imaging platforms, thereby providing a solid foundation for the continued development of tissue imaging software.


Denis Schapiro*, Artem Sokolov*, Clarence Yapp*, Yu-An Chen, Jeremy L. Muhlich, Joshua Hess, Allison L. Creason, Ajit J. Nirmal, Gregory J. Baker, Maulik K. Nariya, Jia-Ren Lin, Zoltan Maliga, Connor A. Jacobson, Matthew W. Hodgman, Juha Ruokonen, Samouil L. Farhi, Domenic Abbondanza, Eliot T. McKinley, Daniel Persson, Courtney Betts, Shamilene Sivagnanam, Aviv Regev, Jeremy Goecks, Robert J. Coffey, Lisa M. Coussens, Sandro Santagata and Peter K. Sorger

Nature Methods 09/2017

Single-cell, spatially resolved omics analysis of tissues is poised to transform biomedical research and clinical practice. We have developed an open-source, computational histology topography cytometry analysis toolbox (histoCAT) to enable interactive, quantitative, and comprehensive exploration of individual cell phenotypes, cell–cell interactions, microenvironments, and morphological structures within intact tissues. We highlight the unique abilities of histoCAT through analysis of highly multiplexed mass cytometry images of human breast cancer tissues.

Denis Schapiro*, Hartland W Jackson*, Swetha Raghuraman, Jana R Fischer, Vito RT Zanotelli, Daniel Schulz, Charlotte Giesen, Raúl Catena, Zsuzsanna Varga, Bernd Bodenmiller

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Nature Methods 04/2014

Mass cytometry enables high-dimensional, single-cell analysis of cell type and state. In mass cytometry, rare earth metals are used as reporters on antibodies. Analysis of metal abundances using the mass cytometer allows determination of marker expression in individual cells. Mass cytometry has previously been applied only to cell suspensions. To gain spatial information, we have coupled immunohistochemical and immunocytochemical methods with high-resolution laser ablation to CyTOF mass cytometry. This approach enables the simultaneous imaging of 32 proteins and protein modifications at subcellular resolution; with the availability of additional isotopes, measurement of over 100 markers will be possible. We applied imaging mass cytometry to human breast cancer samples, allowing delineation of cell subpopulations and cell-cell interactions and highlighting tumor heterogeneity. Imaging mass cytometry complements existing imaging approaches. It will enable basic studies of tissue heterogeneity and function and support the transition of medicine toward individualized molecularly targeted diagnosis and therapies.


Charlotte Giesen*, Hao AO Wang*, Denis Schapiro, Nevena Zivanovic, Andrea Jacobs, Bodo Hattendorf, Peter J Schüffler, Daniel Grolimund, Joachim M Buhmann, Simone Brandt, Zsuzsanna Varga, Peter J Wild, Detlef Günther, Bernd Bodenmiller

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bioRxiv 05/2020

The advancement of technologies to measure highly multiplexed spatial data requires the development of scalable methods that can leverage the spatial information. We present MISTy, a flexible, scalable and explainable machine learning framework for extracting interactions from spatial omics data. MISTy builds multiple views focusing on different spatial or functional contexts to dissect different effects, such as those from direct neighbours versus those from distant cells. MISTy can be applied to different spatially resolved omics data with dozens to thousands of markers. We evaluate the performance of MISTy on an in silico dataset and demonstrate its applicability on two breast cancer datasets measured with imaging mass cytometry and spatial transcriptomics, respectively. We show the relevance of the information extracted when separating the effect of close and distant cells. Finally, we demonstrate the integration of activities of pathways estimated in a spatial context for the analysis of intercellular signaling.


Jovan Tanevski, Attila Gabor, Ricardo Omar Ramirez Flores, Denis Schapiro, Julio Saez-Rodriguez

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Cell Reports 10/2019

Technological advances enable assaying multiplexed spatially resolved RNA and protein expression profiling of individual cells, thereby capturing molecular variations in physiological contexts. While these methods are increasingly accessible, computational approaches for studying the interplay of the spatial structure of tissues and cell-cell heterogeneity are only beginning to emerge. Here, we present spatial variance component analysis (SVCA), a computational framework for the analysis of spatial molecular data. SVCA enables quantifying different dimensions of spatial variation and in particular quantifies the effect of cell-cell interactions on gene expression. In a breast cancer Imaging Mass Cytometry dataset, our model yields interpretable spatial variance signatures, which reveal cell-cell interactions as a major driver of protein expression heterogeneity. Applied to high-dimensional imaging-derived RNA data, SVCA identifies plausible gene families that are linked to cell-cell interactions. SVCA is available as a free software tool that can be widely applied to spatial data from different technologies.

Damien Arnol, Denis Schapiro, Bernd Bodenmiller, Julio Saez-Rodriguez, Oliver Stegle

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