MERFISH Spatial profiling technology

Merfish

Multiplexed Error-Robust Fluorescence in situ Hybridization

MERFISH is a massively multiplexed single-molecule imaging technology capable of simultaneously measuring the copy number and spatial distribution of hundreds to tens of thousands of RNA species in individual cells.

  • Combinatorial Labeling
  • Sequential Imaging
  • Error Robust Barcoding

MERFISH Advantages

Learn More

High Spatial Resolution

Localize RNA transcripts with subcellular resolution.

High Throughput

Profile a square centimeter of tissue in a single run.

High Sensitivity

Detect difficult-to-characterize lowly expressed genes with single-molecule sensitivity.

High Multiplexing Power

Custom multiplexing from 100s of RNAs to transcriptome-scale.

Peer-Reviewed Publications

Deep profiling of the expression of RNAs in single cells in their native context with MERFISH has revealed cell type, state, organization, interactions, and function within cell culture and tissue.

The expanding vistas of spatial transcriptomics

Luyi Tian, Fei Chen, and Evan Z. Macosko

Nature 2022

READ MORE
Pyramidal neuron subtype diversity governs microglia states in the neocortex

Jeffrey A. Stogsdill, Kwanho Kim, Loïc Binan, Samouil L. Farhi, Joshua Z. Levin & Paola Arlotta

Nature 2022

READ MORE
SPEX: A modular end-to-end analytics tool for spatially resolved omics of tissues

Ximo Pechuan Jorge, Xiao Li, Tyler Risom, Artem Zubkov, Evgeniy Tabatsky, Aleksandr Prilipko, Xin Ye, Zhen Shi, malgorzata Nowicka, Frank Peale, Derrek Hibar, James Ziai, Raj Jesudason, Darya Orlova

bioRxiv (2022)

READ MORE
Spatially resolved transcriptomics and the kidney: Many opportunities

Eryn E. Dixon, Haojia Wu, Elizabeth Sulvarán-Guel, Juanru Guo, Benjamin D. Humphreys

Kidney International (2022)

READ MORE
Conservation and divergence of cortical cell organization in human and mouse revealed by MERFISH

Rongxin Fang, Chenglong Xia, Jennie L. Close, Meng Zhang, Jiang He, Zhengkai Huang, Aaron R. Halpern, Brian Long, Jeremy A. Miller, Ed S. Lein, Xiaowei Zhuang

Science (2022)

READ MORE
Orexin neurons inhibit sleep to promote arousal

Roberto De Luca, Stefano Nardone, Kevin P. Grace, Anne Venner, Michela Cristofolini, Sathyajit S. Bandaru, Lauren T. Sohn, Dong Kong, Takatoshi Mochizuki, Bianca Viberti, Lin Zhu, Antonino Zito, Thomas E. Scammell, Clifford B. Saper, Bradford B. Lowell, Patrick M. Fuller, Elda Arrigoni

Nature Communications (2022)

READ MORE
Intratumoral mregDC and CXCL13 T helper niches enable local differentiation of CD8 T cells following PD-1 blockade

Assaf Magen, Pauline Hamon, Nathalie Fiaschi, Leanna Troncoso, Etienne Humblin, Darwin D'souza, Travis Dawson, Matthew D. Park, Joel Kim, Steven Hamel, Mark Buckup, Christie Chang, Alexandra Tabachnikova, Hara Schwartz, Nausicaa Malissen, Yonit Lavin, Alessandra Soares-Schanoski, Bruno Giotti, Samarth Hegde, Raphael Mattiuz, Clotilde Hennequin, Jessica Le Berichel, Zhen Zhao, Stephen Ward, Isabel Fiel, Colles Price, Nicolas Fernandez, Jiang He, Baijun Kou, Michael Dobosz, Lianjie Li, Christina Adler, Min Ni, Yi Wei, Wei Wang, Namita T. Gupta, Kunal Kundu, Kamil Cygan, Raquel P. Deering, Alex Tsankov, Seunghee Kim-Schulze, Sacha Gnjatic, Ephraim Kenigsberg, Myron Schwartz, Thomas U. Marron, Gavin Thurston, Alice O. Kamphorst, Miriam Merad

bioRxiv doi:10.1101/2022.06.22.497216 (2022)

READ MORE
Spatial Transcriptomics-correlated Electron Microscopy

Peter Androvic, Martina Schifferer, Katrin Perez Anderson, Ludovico Cantuti-Castelvetri, Hao Ji, Lu Liu, Simon Besson-Girard, Johanna Knoferle, Mikael Simons, Ozgun Gokce

bioRxiv doi:10.1101/2022.05.18.492475

READ MORE
AGBT 2022 Poster: In Situ Single-cell Transcriptomic Imaging in Formalin-fixed Paraffin-embedded Tissues with MERSCOPETM

Jiang He, Lizhi He, Timothy Wiggin, Alex S Genshaft, Rob Foreman, Natalia Petrenko, Nicholas Fernandez, Renchao Chen, Colles Price, George Emanuel

READ MORE
Concordance of MERFISH Spatial Transcriptomics with Bulk and Single-cell RNA Sequencing

Jonathan Liu, Vanessa Tran, Venkata Naga Pranathi Vemuri, Ashley Byrne, Michael Borja, Snigdha Agarwal, Ruofan Wang, Kyle Awayan, Abhishek Murti, Aris Taychameekiatchai, Bruce Wang, George Emanuel, Jiang He, John Haliburton, Angela Oliveira Pisco, Norma Neff

bioRxiv doi: 10.1101/2022.03.04.483068 (2022)

READ MORE
Vizbi Poster: Web based Visual Exploration of the Mouse Liver at Single-Cell Resolution with Vizgen MERFISH Open Data Set

READ MORE
Spatial transcriptomic reconstruction of the mouse olfactory glomerular map suggests principles of odor processing

I-Hao Wang, Evan Murray, Greg Andrews, Hao-Ching Jiang, Sung Jin Park, Elisa Donnard, Violeta Durán-Laforet, Daniel M. Bear, Travis E. Faust, Manuel Garber, Christina E. Baer, Dorothy P. Schafer, Zhiping Weng, Fei Chen, Evan Z. Macosko & Paul L. Greer

Nature Neuroscience (2022)

READ MORE
Comparative analysis of MERFISH spatial transcriptomics with bulk and single-cell RNA sequencing

Jonathan Liu, Vanessa Tran, Venkata Naga Pranathi Vemuri, Ashley Byrne, Michael Borja, Snigdha Agarwal, Ruofan Wang, Kyle Awayan, Abhishek Murti, Aris Taychameekiatchai, Bruce Wang, George Emanuel, Jiang He, John Haliburton, Angela Oliveira Pisco, Norma Neff

bioRxiv doi:10.1101/2022.03.04.483068

READ MORE
Using MERSCOPE to Generate a Cell Atlas of the Mouse Brain that Includes Lowly Expressed Genes

George Emanuel & Jiang He

Microscopy Today (2021)

READ MORE
Advances in spatial transcriptomic data analysis

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

Genome Research

READ MORE
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)

READ MORE
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)

READ MORE
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)

READ MORE
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)

READ MORE
Multi scale diffeomorphic metric mapping of spatial transcriptomics datasets

Michael I. Miller, Jean Dan, Daniel Tward

CVPR (2021)

READ MORE
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)

READ MORE
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)

READ MORE
Spatial organization of the transcriptome in individual neurons

Guiping Wang, Cheen-Euong Ang, Jean Fan, Andrew Wang, Jeffrey R. Moffitt, Xiaowei Zhuang

bioRxiv doi:10.1101/2020.12.07.414060 (2020)

READ MORE
Genome-Scale Imaging of the 3D Organization and Transcriptional Activity of Chromatin

Jun-Han Su, Pu Zheng, Seon S. Kinrot, Bogdan Bintu, Xiaowei Zhuang

Cell 182(6):1641-1659.e26 (2020)

READ MORE
Molecular, spatial and projection diversity of neurons in primary motor cortex revealed by in situ single-cell transcriptomics

Meng Zhang, Stephen W. Eichhorn, Brian Zingg, Zizhen Yao, Hongkui Zeng, Hongwei Dong, Xiaowei Zhuang

bioRxiv doi:10.1101/2020.06.04.105700 (2020)

READ MORE
Multiplexed imaging of nucleome architectures in single cells of mammalian tissue

Miao Liu, Yanfang Lu, Bing Yang, Yanbo Chen, Jonathan S. D. Radda, Mengwei Hu, Samuel G. Katz & Siyuan Wang

Nature Communications 11, 2907 (2020)

READ MORE
Imaging-based pooled CRISPR screening reveals regulators of lncRNA localization

Chong Wanga,Tian Lua, George Emanuel, Hazen P. Babcock and Xiaowei Zhuang

PNAS 116 (22) 10842-10851 (2019)

READ MORE
Mammalian gene expression variability is explained by underlying cell state

Robert Foreman, Roy Wollman

Mol Syst Biol (2020)16:e9146

READ MORE
Spatial transcriptome profiling by MERFISH reveals subcellular RNA compartmentalization and cell cycle-dependent gene expression

Chenglong Xia, Jean Fan, George Emanuel, Junjie Hao, and Xiaowei Zhuang

PNAS 116, 19490-19499 (2019)

READ MORE
Multiplexed detection of RNA using MERFISH and branched DNA amplification

Chenglong Xia, Hazen P. Babcock, Jeffrey R. Moffitt & Xiaowei Zhuang

Scientific Reports 9, 7721 (2019)

READ MORE
Molecular, spatial, and functional single-cell profiling of the hypothalamic preoptic region

Jeffrey R. Moffitt, Dhananjay Bambah-Mukku, Stephen W. Eichhorn, Eric Vaughn, Karthik Shekhar, Julio D. Perez, Nimrod D. Rubinstein, Junjie Hao, Aviv Regev, Catherine Dulac, Xiaowei Zhuang

Science 362, 6416-eaau5324 (2018)

READ MORE
Multiplexed imaging of high-density libraries of RNAs with MERFISH and expansion microscopy

Guiping Wang, Jeffrey R. Moffitt & Xiaowei Zhuang

Scientific Reports 8, 4847 (2018)

READ MORE
High-Throughput, Image-Based Screening of Genetic Variant Libraries

George Emanuel, Jeffrey R. Moffitt & Xiaowei Zhuang

Nature Methods 14, 1159-1162 (2017)

READ MORE

If you are interested in applying MERFISH to your research, click here to learn more about Vizgen’s early engagement programs

Top