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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.

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eBook: What Does High-Quality Spatial Genomics Data Look Like?

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Application & Technical Notes

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Illuminate Biology with Spatially Resolved, Single-Cell Transcriptomics

Spatial Omics Zoom Seminar Three: http://spatialomics.net/ Speaker: Dr. Jiang He, Founding Member and Director of Scientific Affairs Dr. Jiang He presents the importance of spatial transcriptomics profiling and introduces the Vizgen MERFISH platform technology, describing…

Cell segmentation in imaging-based spatial transcriptomics

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…

HCA Poster 2021: MERSCOPE Reveals the Transcriptional Organization of the Mouse Brain

We mapped 483 genes with MERSCOPETM across full mouse brain coronal slices. Enabled by MERFISH technology, MERSCOPE measures the position of individual molecules with single molecule resolution and high detection efficiency. For this demonstration, we…

MERFISH Enables Mapping of Cellular Diversity with Spatial Context at Subcellular Resolution

The brain, a lung, a tumor: each contains a complex array of cell types arranged in an intricate spatial pattern that is critical to their role within the tissue. The recently developed multiplexed error-robust fluorescence…

Tissue Clearing Sample Verification

Read this technical note to learn key points about tissue clearing for different types of human and mouse tissues. It also provides examples of different clearing conditions for human lung tissue sections.

Cell Boundary Staining On Different Tissue Types

Read technical note for information on how to select the optimal cell boundary stain to use on different tissue types. It provides examples of cell boundary staining for various mouse and human tissue sections.

Fixation and Permeabilization of Tissues Sample Verification

Read this technical note to learn key points about the fixation and permeabilization process during sample verification. It provides examples of different fixation and permeabilization conditions on mouse retina tissue sections.

Autofluorescence Quenching

Read this technical note to learn key points about autofluorescence background and autofluorescence quenching during the sample verification process. It provides examples of using the MERSCOPE Photobleacher to remove Lipofuscin Autofluorescence from human heart and…

MERSCOPE Product Bulletin

This product bulletin contains an overview of the MERSCOPE platform.

MERSCOPE Cultured Cells Sample Preparation

Rev F, April 2024. This user guide explains how to properly prepare cultured cell samples to run on the MERSCOPE instrument and includes the protocol, materials, and technical tips.

Sample Verification Kit

This user guide explains how to verify that the RNA quality after sample preparation will result in adequate MERFISH imaging quality with the MERSCOPE Instrument. It includes the protocol, materials, and examples.

Fresh and Fixed Frozen Tissue Sample Preparation

Rev F, April 2024 This user guide explains how to properly prepare fresh and fixed frozen tissue sections to run on the MERSCOPE instrument and includes the protocol, materials, and technical tips.

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

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…

MERSCOPE Instrument User Guide

Rev J, April 2025 This user guide contains the information needed for setting up, running, maintaining, and troubleshooting Vizgen’s MERSCOPE instrument.

GABA-receptive microglia selectively sculpt developing inhibitory circuits

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…

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

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…

Multi scale diffeomorphic metric mapping of spatial transcriptomics datasets

Abstract: Spatially resolved transcriptomic imaging is a family of promising new technologies that can produce a series of images that quantify gene expression at every pixel. These technologies, such as multiplex error-robust fluorescence in situ…

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

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…

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

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…

Spatial organization of the transcriptome in individual neurons

Neurons are highly polarized cells with complex neurite morphology. Spatial organization and local translation of RNAs in dendrites and axons play an important role in many neuronal functions. Here we performed super-resolution spatial profiling of…

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Featured Resource

eBook: What Does High-Quality Spatial Genomics Data Look Like?

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