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The TissueMaps project

In the TissueMaps project we combine quantitative digital pathology with in situ RNA sequencing. In situ RNA sequencing maintains the spatial information of gene expression and thereby merges profiling data with digital pathology. This provides a better understanding of tumor heterogeneity and the tumor micro-environment. In the long term perspective, we believe it will lead to better diagnostics, prognostics, and treatment. Image analysis and visualization is done at multiple scales, combining molecular detail with cm-scaled tumor heterogeneity.


The project is funded by the European Research Council 2016-2021, through a consolidator grant to Carolina Wählby.

People involved:

Carolina Wählby
PI, PhD, Professor in Quantitative Microscopy
Maxime Bombrun
Petter Ranefall
PhD, Associate Professor
Xiaoyan Qian
PhD student at the Dept of Biochemistry and Biophysics at Stockholm University, co-supervised with Mats Nilsson (main supervisor)
Marco Mignardi
International PostDoc, sharing his time between us and the Quake lab, Dept. of Bioengineering, at Stanford, CA, USA
Joakim Lindblad
PhD, Senior Researcher
Gabriele Partel
PhD student
Leslie Solorzano
PhD student


Key background publication:

R. Ke, M. Mignardi, A. Pacureanu, J. Svedlund, J. Botling, C. Wählby, and M. Nilsson.

In situ sequencing for RNA analysis in preserved tissue and cells.

Nature Methods, 2013 (10), 857-860. doi: 10.1038/nmeth.2563. PMID: 23852452

Other publications related to the project are listed here.