Spatial genomics is giving researchers a Google Maps–like view of tissues, revealing how cells and genes behave in their native neighborhoods.

From bulk averages to cellular neighborhoods

Traditional genomics has been extraordinarily powerful but fundamentally dislocating: tissues are dissociated, cells are mixed, and spatial context is lost. Single-cell RNA-seq restored some resolution by profiling individual cells, yet it still left a key question unanswered: where exactly in the tissue did each cell sit, and who were its neighbors?

Spatial genomics answers that question by measuring gene expression directly in intact tissue slices, often alongside protein markers, so that scientists can see how cells organize into functional communities. Technologies such as MERFISH, which uses multiplexed error-robust in situ hybridization, now allow the detection of thousands of genes at single-cell resolution across large tissue areas. AACR Journals

Platforms and chemistry innovation

In 2026, platform innovation is accelerating. Vizgen’s MERSCOPE Ultra platform and MERFISH 2.0 chemistry, for example, increase the imaging area and speed while boosting sensitivity, enabling mapping of entire tumor sections or organ samples at high resolution. Vizgen+1 The merger of spatial genomics and multiplexed proteomic companies, such as the combination of Vizgen and Ultivue, is creating integrated spatial multi-omics ecosystems capable of profiling RNA and proteins simultaneously in situ. Vizgen

To expand access, vendors are launching certified service provider programs that allow hospitals and biopharma firms to outsource spatial projects to specialized labs while keeping data securely integrated into their own analysis pipelines. Vizgen As costs decrease and workflows standardize, spatial genomics is moving from a small number of elite centers to a broader network of translational and clinical research sites.

Rethinking the tumor microenvironment and immune response

Cancer research has been an early beneficiary. Spatial maps reveal how cancer cells interact with immune cells, stromal components and vasculature across different regions of a tumor. In immuno-oncology, for example, spatial genomics can distinguish between “hot” tumor regions teeming with cytotoxic T cells and “cold” zones where immune exclusion or suppression dominates.

These insights are shaping both biomarker discovery and therapeutic strategy. Drug developers use spatial data to identify niches where resistance emerges or where combination therapies might be most effective. Clinicians, in turn, are exploring how spatial patterns correlate with response to checkpoint inhibitors, CAR-T therapies or bispecific antibodies, which could lead to more precise patient selection and adaptive treatment planning. Vizgen

Beyond cancer: Neurology, cardiology and infectious disease

Spatial multi-omics is expanding rapidly into other fields. In neurology, it is being used to map neuronal subtypes, glial cells, and microglia across brain regions affected by disorders such as Alzheimer’s disease or epilepsy, revealing region-specific vulnerabilities that bulk approaches obscure. In cardiology, spatial profiling of failing hearts can uncover fibrotic lesions, inflammatory infiltrates, and metabolic gradients that guide novel therapeutic targets.

In infectious disease and immunology, researchers are mapping how pathogens and host immune cells interact within tissues such as the lung or gut, providing a more nuanced view of host–pathogen dynamics and vaccine responses. These spatial datasets are increasingly integrated with single-cell sequencing, proteomics, and digital pathology, yielding multi-dimensional atlases of disease. Vizgen

Computational pipelines and AI for spatial data

The explosion of spatial data is driving a parallel boom in computational methods. New algorithms can segment cells in complex tissue images, deconvolve overlapping signals, and infer cell–cell interactions based on proximity and ligand–receptor co-expression. AI models trained on large spatial atlases can classify tissue regions, identify novel cellular niches, and predict how microenvironment changes might affect disease progression or treatment response.

Cloud-based platforms now allow researchers and clinicians to overlay spatial gene-expression maps with radiologic and histopathologic images, effectively creating a multi-scale digital twin of a patient’s tumor or organ. These integrated views help tumor boards and research teams align genomic insights with the visual cues pathologists have relied on for decades. Vizgen

Barriers to clinical adoption

Despite the excitement, spatial genomics is still early on the road to routine clinical use. Current barriers include complex workflows, high data volumes, and the need for rigorous assay validation in accordance with regulatory standards. Many clinical laboratories lack the imaging infrastructure and computational expertise required for end-to-end spatial pipelines.

To address this, vendors and consortia are focusing on standardized panels for specific indications, such as lung cancer or inflammatory bowel disease, with predefined gene sets and interpretation frameworks. Service models and automated analysis pipelines are designed to lower entry barriers. Still, long-term sustainability will depend on clear clinical use cases where spatial readouts change management and improve outcomes. Vizgen+1

Closing thoughts and looking forward

By 2026, spatial genomics and multi-omics have firmly established themselves as the next layer of resolution in understanding disease, moving the field beyond lists of differentially expressed genes to maps of cellular neighborhoods and microenvironments. The key question now is how quickly these insights can be translated into actionable diagnostics, prognostics, and therapeutic strategies.

Over the next decade, expect spatial readouts to become a standard component of translational studies and selected clinical workflows, especially in oncology and immune-mediated diseases. As assays, analytics and reimbursement mature, health systems will be able to move from treating tumors and organs as homogeneous structures to managing the diverse neighborhoods within them—a shift that could fundamentally change how we think about precision medicine.

Reference sites

Vizgen expands single-cell spatial transcriptomics with MERSCOPE Ultra and MERFISH 2.0 – Vizgen – https://vizgen.com/vizgen-announces-merscope-ultra-chemistry-2-0/

Top 10 spatial biology companies of 2024 – Vizgen – https://vizgen.com/top-10-spatial-biology-companies-of-2024/

Vizgen launches Certified Service Provider (CSP) program, expanding access to single-cell spatial genomics technology – Vizgen – https://vizgen.com/vizgen-launches-certified-service-provider-csp-program-expanding-access-to-single-cell-spatial-genomics-technology/

Improved spatially resolved single-cell transcriptomics with the Vizgen MERSCOPE platform – Cancer Research (AACR Abstract LB333) – https://aacrjournals.org/cancerres/article/84/7_Supplement/LB333/742740/Abstract-LB333-Improved-spatially-resolved-single

Vizgen newsroom and resources on spatial genomics – Vizgen – https://vizgen.com/category/news/

Mark Samuel, Contributor, Health Management, Montreal, Quebec.
Peter Jonathan Wilcheck, Co-Editor, Miami, Florida.

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