In-house Spatial Transcriptomics

In-house Spatial Transcriptomics

In-house Laboratory Services

Vizgen’s MERSCOPE® Platform offers an unprecedented view of the spatial organization of biological systems and will help enable researchers looking to gain deeper insights into a wide range of biological domains, from fundamental biology through translational medicine. Leverage our in-house sample processing and MERFISH  spatial profiling expertise to accelerate your scientific research and yield fundamental insights faster. Vizgen offers flexible custom projects and proof of principle projects. Demand is high, start planning your project today.

  • Receive expert guidance and support from initial project consultation to data delivery.
  • Gain access to MERFISH data without constraints on your own lab resources.
  •  Leverage the high-quality MERFISH data in your research and manuscripts.

Experience MERFISH with Ease and Expertise


Comprehensive Spatial Genomic Profiling

MERSCOPE uses MERFISH technology to directly map and quantify the spatial distribution of RNA and proteins in your tissue samples.


High-quality Spatial Genomics Data Generation

MERSCOPE’s combination of optimized optics and MERFISH technology generates high resolution and high-quality spatial genomics data that will provide unique biological insights to help your lab decode biological complexity with confidence.


Access to Vizgen’s Scientific Expertise

Vizgen’s Lab Services team is comprised of scientists with a wide range of demonstrated knowledge in cell and molecular biology, single-cell genomics, and imaging technologies, along with computational biologists and project managers to oversee data analysis and project execution. Vizgen offers the greatest depth of MERFISH expertise and instrument operation experience available.

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Our Offerings

Custom Lab Services

Excited to get your hands on MERFISH data generated on the MERSCOPE® Platform, but have limited resources in your lab or time constraints for data generation? Custom projects allow you to work with our lab services team to design a project that fits your research needs.

Our MERFISH experts will:
  • Optimize a custom designed gene panel specific to your species and research application.
  • Develop and validate a protocol for your species and sample type.
  • Deliver high-quality MERFISH data for your team to analyze.

Spatial Profiling Lab Service Project Details

Our expert lab services scientists will plan, lead, and execute your spatial genomic profiling project, communicating with you each step of the way. Custom projects include 6 key steps: project consultation, custom panel design or panel selection, sample shipment, custom MERFISH protocol development or standard protocols, MERSCOPE spatial imaging, and MERFISH data delivery.
See Example Data

Project Workflow


Meet with our team to discuss your project in detail and receive a statement of work.

Custom Panel Design or Panel Selection

We assist with selecting the gene panel and protein co-detection strategy most relevant for each biological question and optimize for your species and tissue type or help you choose a predefined panel.

Sample Shipment

Ship your samples to our laboratory headquartered in Cambridge, MA

MERFISH Protocol Development or Standard Protocol

We develop a sample processing and MERFISH protocol specific to custom project samples or use a standard protocol for POP studies.

MERSCOPE Spatial Imaging

Our team spatially profiles the gene and protein expression of your tissue samples with MERSCOPE.  Vizgen scientists have access to the largest centralized collection of MERSCOPE instruments enabling a rapid turn-a-round of high-quality data.

MERFISH Data Delivery

You receive decoded MERFISH datasets packaged into easy-to-read tables and high-resolution images to analyze along with a final report.


Using MERFISH technology, researchers at the Allen Institute were able to gather cellular-resolution spatial transcriptomic data that advanced us significantly closer toward our goal of creating a taxonomy of cell types and a description of their connectivity within brain circuits – laying the groundwork to one day understanding how brain circuits function.

In the hands of the research community, I believe that MERSCOPE will be a powerful tool for standardizing the way we characterize different cell types, not just in the brain, but also in the rest of the body, ultimately bringing a deeper level of understanding to all life science research .”

Hongkui Zeng, Ph.D.

Executive VP & Director of the Allen Institute for Brain Science


Examples of research applications evaluated within lab services.  Vizgen has successfully tested more than 60 tissue types from multiple species.


Spatially profile the gene expression of whole tissue sections down to the sub-cellular level to accurately characterize cells within the brain. Detect low and high abundance genes to create complete molecular cell atlases.



Investigate the tumor microenvironment by identifying novel cell-cell communication and interactions between cancer cells and immune cells. Unlock high-quality spatial genomics data from FFPE tissue sections.


Kidney Disease

Preserve and explore the spatial architecture of complex tissues to understand the structure-function relationships of cells and disease pathophysiology. Visualize spatial gene expression to discover and map new cell types and states.

Start Your Project

Interested in starting a MERFISH spatial profiling project at Vizgen? Fill out the form below and a member of the Lab Services team will get in touch within 2-3 business days to set up a project consultation call.

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    Frequently Asked Questions

    Learn more about MERSCOPE
    Learn more about MERFISH
    Read about our Neuroscience Showcase
    Demand is high, get in touch with us to start planning your project.