What is cell atlasing?

Cell atlasing is the systematic mapping of every cell type in a tissue, organ, or organism, typically at single-cell resolution and in spatial context. A cell atlas serves as the reference framework against which disease states, drug responses, and developmental changes are compared. Modern spatial cell atlases preserve tissue architecture so cells are mapped by their anatomical position, not just their transcriptional identity.

How is a spatial cell atlas different from scRNA-seq?

Single-cell RNA sequencing (scRNA-seq) dissociates tissue into individual cells before sequencing, which destroys all spatial information; you learn which cells exist, but not where they are or who their neighbors were. A spatial cell atlas profiles cells inside intact tissue, so positional state, microenvironment, niche composition, and cell-cell relationships are preserved. For atlas-grade reference work, this distinction is decisive.

What tissues can be used for cell atlasing?

MERSCOPE Ultra supports both fresh-frozen and FFPE tissue across brain, lung, liver, gut, vasculature, tumor biopsies, and reproductive tissues. Published atlases using MERFISH cover whole mouse brain (Allen Institute), aged human cortex (SEA-AD), and healthy human liver (Weizmann). Tissue compatibility is the primary determinant of which pre-designed panel to start with. See the interactive tissue selector above

How long does it take to build a cell atlas?

A consortium-scale spatial cell atlas typically takes 12–24 months end-to-end, panel design and validation (2–3 months), tissue acquisition and processing (3–6 months), imaging and data acquisition (3–6 months), and analysis, annotation, and publication (4–9 months). Using a pre-designed panel can compress the first phase substantially. Vizgen’s genomics specialists scope timeline in the strategy session.

What is a healthy-donor reference atlas, and why does it matter?

A healthy-donor reference atlas is built from tissue donated by living, healthy individuals, not from adjacent-normal tissue taken from patients with disease. The distinction matters because adjacent-normal tissue is systematically altered by proximity to disease, so atlases built on it are calibrated against biased biology. The 2026 Weizmann liver atlas demonstrated this directly: only healthy-donor reference maps reveal correct human liver zonation

How does atlas data inform drug target nomination and biomarker discovery?

A spatial cell atlas provides the coordinate framework against which disease-state tissue can be compared. This enables: (1) identifying which cell populations change in disease and where, (2) qualifying biomarkers in their anatomical context rather than as bulk averages, (3) characterizing multicellular neighborhoods that predict therapy response

Cell Atlasing with MERFISH 2.0™: Build Spatial Reference Atlases

Every downstream discovery, biomarker, and therapeutic insight depends on the accuracy of the cell atlas. MERSCOPE Ultra™, powered by MERFISH 2.0™, maps cell types and tissue architecture in intact samples at sub-cellular resolution, creating high-confidence spatial reference atlases that make disease biology interpretable.

Book a 30-Minute Atlas Strategy Session Explore Publicly Released Datasets

FEATURED INSIGHT

Why Healthy-Donor Reference Atlases Change Everything

Most biomarker and target-discovery programs benchmark against adjacent-normal tissue from patients with disease. The first healthy-donor human liver atlas (Yakubovsky, Bahar Halpern et al., Nature 2026) showed that healthy-donor spatial reference maps reveal correct human liver zonation, biology that adjacent-normal samples systematically miss.

“Adjacent-normal tissue is not truly normal.”

Translation: if your atlas is built on adjacent-normal tissue, your downstream targets and biomarkers may be calibrated against biased biology. A healthy-donor spatial reference changes the answer.

Side-by-side static image comparison: adjacent-normal liver zonation vs. healthy-donor liver zonation, sourced from the Weizmann paper figures (with permission).

Read the Weizmann Liver Atlas Case Study

FOR ACADEMIC ATLAS PROGRAMS

I’m building a spatial atlas.

Panel design, tissue clearing workflows, and data release pathways for consortium-scale programs.

See Atlas Panels and Workflows

FOR BIOPHARMA R&D TEAMS

I’m using spatial atlas data to advance a program.

Target validation, biomarker qualification, and translational evidence built on spatially anchored reference data.

See Translational Use Cases

OUR SOLUTION

The Vizgen Cell Atlasing Workflow

The platform configuration that produces reference-grade spatial data, with four integrated pillars

MERSCOPE Ultra

Map millions of cells per experiment across whole tissue sections up to 3 cm². Single-cell resolution from tissue layers to vascular margins, across small and large tissue sections.

MERFISH 2.0™ Chemistry

Error-robust barcoding maintains high detection for up to 1,000 genes. Subcellular transcript localization. Reproducible data that meets the Cell Atlasing Consortium data quality standards.

Tissue Clearing

Optimized clearing protocols maintain RNA integrity across different tissue types. Validated on FFPE and fresh-frozen samples from brain, liver, lung, and tumor biopsies, enabling consortium-scale imaging without sacrificing molecular detection.

Data Analysis

End-to-end analysis pipeline from raw decoded transcripts to annotated cell types and spatial neighborhoods. Multi-omics readouts and advanced segmentation that researchers can build on, not artifacts they have to defend.

THE WORKFLOW

The Atlas-to-Action Workflow

Three stages that move a spatial program from reference data to program-level decisions, each one anchored to a published atlas that proves the stage works.

Establish the ground truth your entire program will inherit from.

Use MERSCOPE Ultra with a pre-designed or custom panel to map every cell type and vascular population in healthy tissue. Every cell is assigned spatial coordinates. The resulting atlas becomes the coordinate framework against which all downstream disease data is compared.

YOU LEAVE THIS STAGE WITH:

A single-cell, spatially resolved reference map, publication-ready, consortium-compatible, and suitable as the baseline for longitudinal or multi-cohort disease studies.

WHO THIS SERVES:

Academic atlas PIs, consortium scientists, Core facility directors

PROOF

Allen Brain Cell Atlas- 4.3M cells, whole mouse brain, 500-gene MERSCOPE Pan Neuro panel (Yao et al., Nature 2023

Explore Pre-Designed Panels

WHAT MERSCOPE CAPTURES

Five Dimensions of Tissue Biology

Spatial context is not a feature; it is the biology. Cell identity, circuit function, and disease mechanisms are encoded in where cells are and who their neighbors are.

What MERSCOPE Ultra Unlocks	What You See	Why It Changes Your Biology
Cell Identity in Context	Every cell profiled in its native microenvironment, niche, state, and signaling intact	Resolve populations that dissociated atlases collapse into one cluster
Circuit Architecture	Synaptic, paracrine, and contact-based cell relationships mapped in intact tissue	Understand the wiring, not just which cells exist, but how they connect
Tissue Layer Organization	Laminar structure, cortical depth, and zonation gradients preserved at single-cell resolution	Capture layer-specific programs that dissociated data merges or loses
Vascular Context	Endothelial subtypes, pericytes, smooth muscle, and astrocyte endfeet in anatomical context	Annotate vascular and neurovascular units that dissociation destroys
Disease Overlay	Pathology mapped against a healthy spatial reference, cell by cell, region by region	Anchor disease transcriptomics to tissue structure, what changes, where, and in what relationship

Ready to see what an atlas-grade platform looks like for your tissue?

30-minute working session with a Vizgen genomics specialist. Panel review, workflow scoping, sample strategy.

Tell us about your program (optional, but speeds up the call):

I am a…

Timeline…

Book Atlas Strategy Session Explore our Pre-Designed Panels

OFF-THE-SHELF PANELS

Pre-designed Panels for Cell Atlasing

Verified, off-the-shelf panels for the tissues and disease areas that define today’s atlas programs. MERSCOPE Pre-designed Panels powered by MERFISH 2.0 eliminate the time-intensive process of custom gene panel design for labs entering spatial atlasing. Each panel is built using recognized biological databases and published literature, for sensitivity, reproducibility, and broad tissue compatibility.

TISSUE TYPE

SPATIAL ATLAS PRIORITIES

Gene Panels

Brain & Nervous System

Map cortical layers, glial heterogeneity, and the blood-brain barrier
Enable CNS target validation
Identify neurodegeneration biomarkers

Immune / Gut

Map intestinal immune niches and vascular endothelium
Enable IBD target validation
Characterize gut oncology TME

Lung

Map epithelial lineages and the alveolar-capillary interface
Analyze fibrosis disease overlays
Map checkpoint biomarkers

Liver

Map hepatocyte zonation and Kupffer cell distribution
Enable liver cancer atlases and DILI reference mapping
Support hepatic target validation

Vasculature

Localize endothelial subtypes, pericytes, and smooth muscle cells
Enable cardiovascular target validation
Support anti-angiogenic research

Reproduction & Development

Build uterine and ovarian atlases
Map fetal limb and spine development
Enable reproductive oncology and endometriosis research

Human Tumor EMT

PEER-REVIEWED RESEARCH

MERFISH-Enabled Cell Atlasing in Peer-Reviewed Research

Allen Brain Cell Atlas — Whole Mouse Brain Transcriptomic & Spatial Atlas

Yao et al. & Zhang et al., Nature, December 2023

Institution:: Allen Institute for Brain Science (Hongkui Zeng lab)
Panel Used:: MERSCOPE PanNeuro 500-gene (Allen Institute dataset)
Scale:: 4.3M spatially resolved cells, 59 serial coronal sections, entire adult mouse brain

KEY SPATIAL FINDINGS:

Each cell type showed a defined spatial address with high concordance between spatial and transcriptomic identity across 11 brain regions
Rare cell types, including specialized interneurons and perivascular populations, are resolved beyond dissociated datasets
The MERSCOPE 500-gene panel recapitulates whole-transcriptome scRNA-seq cell-type taxonomy

View Publication

PUBLIC SPATIAL REFERENCES

Atlas-Scale Datasets

Data Release Program Multiple tissue types / updated regularly Browse all publicly available MERSCOPE datasets. Browse All Datasets

Allen Brain Cell Atlas 4.3M cells / whole mouse brain Consortium-grade neuroscience reference (Nature 2023) Explore Dataset

Human Liver Atlas Consortium-grade liver atlas (Nature, 2026) Explore Dataset

Frequently Asked Questions

Cell atlasing is the systematic mapping of every cell type in a tissue, organ, or organism, typically at single-cell resolution and in spatial context. A cell atlas serves as the reference framework against which disease states, drug responses, and developmental changes are compared. Modern spatial cell atlases preserve tissue architecture so cells are mapped by their anatomical position, not just their transcriptional identity.
Single-cell RNA sequencing (scRNA-seq) dissociates tissue into individual cells before sequencing, which destroys all spatial information; you learn which cells exist, but not where they are or who their neighbors were. A spatial cell atlas profiles cells inside intact tissue, so positional state, microenvironment, niche composition, and cell-cell relationships are preserved. For atlas-grade reference work, this distinction is decisive.
MERSCOPE Ultra supports both fresh-frozen and FFPE tissue across brain, lung, liver, gut, vasculature, tumor biopsies, and reproductive tissues. Published atlases using MERFISH cover whole mouse brain (Allen Institute), aged human cortex (SEA-AD), and healthy human liver (Weizmann). Tissue compatibility is the primary determinant of which pre-designed panel to start with. See the interactive tissue selector above
A consortium-scale spatial cell atlas typically takes 12–24 months end-to-end, panel design and validation (2–3 months), tissue acquisition and processing (3–6 months), imaging and data acquisition (3–6 months), and analysis, annotation, and publication (4–9 months). Using a pre-designed panel can compress the first phase substantially. Vizgen’s genomics specialists scope timeline in the strategy session.
A healthy-donor reference atlas is built from tissue donated by living, healthy individuals, not from adjacent-normal tissue taken from patients with disease. The distinction matters because adjacent-normal tissue is systematically altered by proximity to disease, so atlases built on it are calibrated against biased biology. The 2026 Weizmann liver atlas demonstrated this directly: only healthy-donor reference maps reveal correct human liver zonation

Ready to build your spatial reference atlas?

Talk to a Vizgen genomics specialist about the right panel, workflow, and data strategy for your cell atlasing program.

CONSULT

Request a Panel and Workflow Consultation

30-minute call with a Vizgen genomics specialist. Panel review, tissue-specific recommendations.

Request Consultation