Resources

Vizgen is developing the next generation of genomics tools to expand on the capabilities of spatially resolved transcriptomics. Our technology will aide the acceleration of biological research and discovery to advance human health. Access supporting resources by selecting the category below.

Publications

Advances in spatial transcriptomic data analysis

Ruben Dries, Jiaji Chen, Natalie del Rossi, Mohammed Muzamil Khan, Adriana Sistig, and Guo-Cheng Yuan
Genome Research

Spatial transcriptomics is a rapidly growing field that promises to comprehensively characterize tissue organization and architecture at the single-cell or subcellular resolution. Such information provides a solid foundation for mechanistic understanding of many biological processes […]

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Publications

Cell segmentation in imaging-based spatial transcriptomics

Viktor Petukhov, Rosalind J. Xu, Ruslan A. Soldatov, Paolo Cadinu, Konstantin Khodosevich, Jeffrey R. Moffitt & Peter V. Kharchenko
Nature Biotechnology (2021)

Single-molecule spatial transcriptomics protocols based on in situ sequencing or multiplexed RNA fluorescent hybridization can reveal detailed tissue organization. However, distinguishing the boundaries of individual cells in such data is challenging and can hamper downstream […]

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Publications

Spatially resolved cell atlas of the mouse primary motor cortex by MERFISH

Meng Zhang, Stephen W. Eichhorn, Brian Zingg, Zizhen Yao, Kaelan Cotter, Hongkui Zeng, Hongwei Dong & Xiaowei Zhuang
Nature volume 598, pages137–143 (2021)

A mammalian brain is composed of numerous cell types organized in an intricate manner to form functional neural circuits. Single-cell RNA sequencing allows systematic identification of cell types based on their gene expression profiles and […]

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Publications

GABA-receptive microglia selectively sculpt developing inhibitory circuits

Emilia Favuzzi, Shuhan Huang, Giuseppe A. Saldi, Loïc Binan, Leena A.Ibrahim, Marian Fernández-Otero, Yuqing Cao, Ayman Zeine, Adwoa Sefah, Karen Zheng, Qing Xu, Elizaveta Khlestova, Samouil L. Farhi, Richard Bonneau, Sandeep Robert Datta, Beth Stevens, Gord Fishell
Cell (2021)

Microglia, the resident immune cells of the brain, have emerged as crucial regulators of synaptic refinement and brain wiring. However, whether the remodeling of distinct synapse types during development is mediated by specialized microglia is […]

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Publications

Spatial transcriptome profiling by MERFISH reveals fetal liver hematopoietic stem cell niche architecture

Yanfang Lu, Miao Liu, Jennifer Yang, Sherman M. Weissman, Xinghua Pan, Samuel G. Katz, Siyuan Wang
Cell Discovery 7, 47 (2021)

Abstract: The hematopoietic stem cell (HSC) niche has been extensively studied in bone marrow, yet a more systematic investigation into the microenvironment regulation of hematopoiesis in fetal liver is necessary. Here we investigate the spatial […]

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Publications

Cell segmentation-free inference of cell types from in situ transcriptomics data

Jeongbin Park, Wonyl Choi, Sebastian Tiesmeyer, Brian Long, Lars E. Borm, Emma Garren, Thuc Nghi Nguyen, Bosiljka Tasic, Simone Codeluppi, Tobias Graf, Matthias Schlesner, Oliver Stegle, Roland Eils & Naveed Ishaque
Nature Communications 12, 3545 (2021)

Multiplexed fluorescence in situ hybridization techniques have enabled cell-type identification, linking transcriptional heterogeneity with spatial heterogeneity of cells. However, inaccurate cell segmentation reduces the efficacy of cell-type identification and tissue characterization. Here, we present a […]

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Publications

Interactions between cancer cells and immune cells drive transitions to mesenchymal-like states in glioblastoma

Toshiro Hara, Rony Chanoch-Myers, Nathan D. Mathewson, Chad Myskiw, Lyla Atta, Lillian Bussema, Stephen W. Eichhorn, Alissa C. Greenwald, Gabriela S. Kinker, Christopher Rodman, L. Nicolas Gonzalez Castro, Hiroaki Wakimoto, Orit Rozenblatt-Rosen, Xiaowei Zhuang, Jean Fan, Tony Hunter, Inder M. Verma, Kai W. Wucherpfennig, Aviv Regev, Mario L. Suva` & Itay Tirosh
Cancer Cell (2021)

The mesenchymal subtype of glioblastoma is thought to be determined by both cancer cell-intrinsic alterations and extrinsic cellular interactions, but remains poorly understood. Here, we dissect glioblastoma-to-microenvironment interactions by single-cell RNA sequencing analysis of human tumors and model systems, combined […]

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