Why Spatial Multi-Omics? Preserving the Molecular Architecture of Tissues

Traditional bulk RNA sequencing measures the average gene expression across millions of cells, masking the diversity and spatial organization within complex tissues. Although single-cell RNA sequencing (scRNA-seq) can identify individual cell populations, it requires tissue dissociation, resulting in the loss of critical spatial relationships between cells and their surrounding microenvironment.

Spatial transcriptomics overcomes these limitations by combining gene expression profiling with spatial localization, enabling researchers to visualize where genes are expressed while preserving the native architecture of the tissue. This provides a more complete understanding of cellular interactions, tissue organization, and biological function.

Recognized as Nature Methods' "Method of the Year" in 2020, spatial transcriptomics has rapidly evolved into a powerful suite of technologies that integrates sequencing, imaging, and multi-omics approaches. These platforms enable researchers to investigate complex biological systems with unprecedented spatial and molecular resolution.

Comprehensive Spatial Transcriptomics Technologies

At N2Jenomics Lab Pvt. Ltd., we offer a complete portfolio of industry-leading spatial transcriptomics platforms, allowing researchers to choose the most appropriate technology for their specific scientific objectives.

Our platform offerings include:

• • Visium™ Spatial Gene Expression for unbiased whole-transcriptome profiling with spatial coordinates.

• • Visium HD™ for enhanced spatial resolution and detailed tissue architecture analysis.
• • Stereo-seq for ultra-high-resolution, genome-wide spatial transcriptomics across large tissue sections.
• • Xenium™ In Situ for imaging-based, single-molecule RNA detection with true subcellular resolution and precise cell boundary mapping.

Tailored Solutions for Every Research Question

Each spatial technology provides unique strengths. Sequencing-based platforms generate comprehensive, genome-wide expression profiles while maintaining spatial context, making them ideal for tissue-wide discovery studies. Imaging-based approaches deliver highly sensitive visualization of selected transcripts at single-molecule resolution, enabling precise characterization of individual cells and their microenvironments.

By offering multiple complementary technologies under one roof, we help researchers select the most suitable platform based on sample type, resolution requirements, target coverage, and experimental goals. As projects progress, workflows can be seamlessly adapted or expanded without the need to transition to another service provider.

End-to-End Scientific Partnership

Beyond sequencing, our experienced scientists provide complete project support, including:

• • Platform selection and feasibility assessment
• • Experimental design and study planning
• • Tissue processing and quality evaluation
• • Library preparation or in situ assay workflows
• • High-throughput sequencing or imaging
• • Advanced spatial bioinformatics analysis
• • Cell type annotation and spatial mapping
• • Multi-omics data integration
• • Biological interpretation and publication-ready reporting

With cutting-edge instrumentation, dedicated molecular biology expertise, and advanced bioinformatics capabilities, N2Jenomics Lab Pvt. Ltd. enables researchers to uncover the molecular geography of tissues, revealing how cells interact, organize, and function within their native biological environment across applications in cancer research, neuroscience, immunology, developmental biology, regenerative medicine, and precision healthcare.

Platform Comparison: Choosing the Right Spatial Technology

Each platform has distinct strengths. Use this table to match your experimental priorities to the right service — or consult our scientific team for a personalized recommendation.

Our Spatial Transcriptomics Services at a Glance

At N2Jenomics Lab Pvt. Ltd., we offer a complete portfolio of industry-leading spatial transcriptomics technologies designed to address a broad range of biological and clinical research applications. Every project follows our comprehensive end-to-end workflow—from sample quality assessment and tissue processing to sequencing, advanced bioinformatics, and publication-ready data delivery.

Whether your goal is whole-transcriptome discovery, single-cell spatial profiling, subcellular transcript localization, or large-scale tissue mapping, our experts help you select the platform best suited to your research objectives.

10x Visium™ Spatial Gene Expression (Fresh Frozen)

Whole-Transcriptome Spatial Gene Expression

• Spatial Resolution 

-  55 µm capture spots, typically representing approximately 1–10 cells per spot.

• Transcript Coverage

• - Unbiased whole-transcriptome profiling using poly(A)-based RNA capture.
• - No prior probe design is required, enabling comprehensive gene discovery.

• Supported Species

• - Compatible with any organism that has a reference genome or transcriptome.

• Sample Compatibility

• - Fresh frozen, OCT-embedded tissue with high RNA integrity (recommended RIN ≥7).

• Bioinformatics Analysis
Our analysis pipeline includes:

• - Space Ranger processing
• - Spatial quality assessment
• - Tissue clustering and visualization
• - Spatially variable gene identification
• - Cell deconvolution (RCTD, Cell2location)
• - Ligand–receptor interaction analysis
• - Seurat and Squidpy-based downstream analysis

• Ideal Applications

• - Whole-transcriptome discovery studies
• - Tumor microenvironment characterization
• - Developmental biology
• - Non-model organism research
• - Comparative tissue profiling
• - Large cohort spatial transcriptomics projects

10x Visium HD™

High-Definition Spatial Transcriptomics at Near Single-Cell Resolution

• Spatial Resolution

• - High-density 2 µm capture features with flexible analysis bins (8 µm or 16 µm), providing nearly continuous tissue coverage.

• Transcript Coverage

• - Probe-based whole-transcriptome profiling covering approximately 18,000 human genes and 20,000 mouse genes.

• Supported Species

• - Validated for human and mouse samples.

• Sample Compatibility

• - Fresh frozen and FFPE tissues processed using the CytAssist™ workflow.

• Bioinformatics Analysis

• - Space Ranger HD processing
• - Cell segmentation
• - Multi-resolution spatial analysis
• - Cell2location deconvolution
• - Cell-type annotation
• - Differential spatial expression analysis

Ideal Applications

• - Single-cell-scale spatial atlases
• - Clinical FFPE tissue studies
• - High-resolution tumor microenvironment profiling
• - Rare cell population mapping
• - Precision medicine research

10x Xenium™ In Situ

Subcellular Single-Molecule Spatial Gene Expression

• Spatial Resolution

• - Approximately 200 nm, enabling visualization of individual RNA molecules at subcellular resolution.

• Transcript Coverage

• - Highly sensitive targeted gene expression panels with support for up to 5,000 predefined or custom-designed genes.

• Supported Species

• - Human and mouse, with custom probe panel development available for specialized applications.

• Sample Compatibility

• - Fresh frozen and FFPE tissue sections (typically 10 µm thick).

• Bioinformatics Analysis

• - Xenium Ranger processing
• - Cell segmentation
• - Cell-type classification
• - Spatial neighborhood analysis
• - Biomarker visualization
• - Integration with Visium™ datasets and single-cell RNA sequencing (scRNA-seq)

• Ideal Applications

• - Biomarker validation
• - Single-molecule RNA localization
• - Cell morphology and transcript correlation
• - Spatial immunology
• - Clinical translational research
• - Multiplex imaging workflows

Stereo-seq

Ultra-High-Resolution Spatial Transcriptomics for Large Tissue Sections

• Spatial Resolution

• - Approximately 220 nm DNA Nanoball (DNB) capture spots, enabling subcellular spatial analysis across exceptionally large tissue areas.

• Transcript Coverage

• - Whole-transcriptome profiling using:
• - Poly(A)-based chemistry for fresh frozen tissues.
• - Probe-based chemistry for emerging FFPE workflows.

• Supported Species

• - Suitable for virtually any species with an available reference genome, including model and non-model organisms.

• Sample Compatibility

• - Fresh frozen tissues (primary workflow).
• - FFPE tissues through Stereo-seq V2 workflows.

• Bioinformatics Analysis

• - SAW pipeline processing
• - Large-scale tissue reconstruction
• - Bin-to-cell aggregation
• - Seurat and Scanpy analysis
• - Cell clustering
• - Spatial domain identification
• - Cross-section tissue stitching

• Ideal Applications

• - Whole-organ spatial mapping
• - Whole-embryo transcriptomic atlases
• - Brain and liver spatial studies
• - Comparative genomics
• - Cross-species spatial biology
• - Large-area, high-resolution tissue profiling

End-to-End Spatial Transcriptomics Solutions

Regardless of the platform selected, every project at N2Jenomics Lab Pvt. Ltd. benefits from our integrated workflow, including:

• - Scientific consultation and platform selection
• - Experimental design and feasibility assessment
• - Tissue processing and quality control
• - Spatial library preparation or in situ assay setup
• - High-throughput sequencing or imaging
• - Comprehensive bioinformatics analysis
• - Cell-type annotation and spatial mapping
• - Multi-omics integration
• - Biological interpretation
• - Publication-ready reports, figures, and data deliverables

Our multidisciplinary team ensures that each project is optimized for your research objectives, delivering reliable, high-resolution spatial data that accelerates discoveries in cancer biology, neuroscience, immunology, developmental biology, regenerative medicine, pathology, and precision healthcare.

How to Choose: Decision Guide by Research Question

Match your primary research question to the platform best suited to answer it. Most complex projects benefit from a combination of platforms — our scientific team can help design a multi-platform strategy.

Key Applications of Spatial Multi-Omics

Spatial multi-omics is transforming biological and biomedical research by revealing where genes are expressed, how cells interact, and how tissue architecture influences biological function. By preserving spatial context, researchers can investigate complex cellular ecosystems that cannot be resolved using conventional bulk or single-cell sequencing alone.

At N2Jenomics Lab Pvt. Ltd., our comprehensive portfolio of Visium™, Visium HD™, Xenium™ In Situ, and Stereo-seq platforms enables researchers to select the most appropriate technology for virtually any spatial biology application.

1. Tumor Microenvironment (TME) Profiling

Cancer tissues consist of diverse cell populations that continuously communicate with one another. Spatial transcriptomics enables researchers to visualize the organization of tumor cells, immune infiltrates, stromal components, and surrounding healthy tissue within their native microenvironment.

Our spatial analysis workflows support:

• • Tumor core and invasive margin characterization

• • Immune cell infiltration mapping
• • Cancer-associated fibroblast (CAF) analysis
• • Spatial biomarker discovery
• • Cell-cell communication and ligand-receptor interaction analysis
• • Identification of therapeutic targets
• • Precision oncology research

• Platform selection is optimized according to the desired spatial resolution, sample type, and research objectives.

2. Neuroscience & Brain Atlas Construction

The nervous system contains highly specialized cell populations arranged in complex anatomical structures. Spatial transcriptomics provides unprecedented insight into neuronal organization while preserving tissue architecture.

Applications include:

• • Cortical layer characterization
• • Hippocampal and cerebellar mapping
• • Brain development studies
• • Neurodegenerative disease research
• • Neural circuit organization
• • Cell-type-specific spatial expression profiling
• • Construction of comprehensive brain atlases

By combining whole-transcriptome sequencing with single-cell and subcellular imaging technologies, researchers can generate highly detailed spatial maps of the nervous system.

3. Developmental Biology & Embryonic Research

Understanding embryonic development requires monitoring gene expression across both time and space. Spatial transcriptomics allows researchers to visualize developmental processes while maintaining the structural organization of tissues.

Common applications include:

• • Whole-embryo spatial transcriptomics
• • Organogenesis studies
• • Cell lineage mapping
• • Morphogen gradient analysis
• • Tissue differentiation
• • Developmental signaling pathways
• • Comparative developmental genomics

• Large-area imaging platforms such as Stereo-seq enable high-resolution mapping across entire embryos and developing organs.

4. Disease Pathology & Clinical Research

Spatial technologies have significantly expanded the molecular analysis of archived clinical specimens, particularly FFPE (Formalin-Fixed Paraffin-Embedded) tissues.

Researchers can investigate:

• • Disease-associated molecular signatures
• • Biomarker discovery and validation
• • Treatment response evaluation
• • Tumor heterogeneity
• • Tissue pathology
• • Precision medicine research
• • Retrospective clinical cohort studies

These capabilities allow valuable hospital and biobank specimens to be revisited using modern spatial genomics approaches.

5. Integrated Spatial Multi-Omics

Combining complementary technologies provides a more comprehensive understanding of complex biological systems.

Our integrated workflows can incorporate:

• • Spatial transcriptomics
• • Single-cell RNA sequencing (scRNA-seq)
• • Bulk RNA sequencing
• • Spatial proteomics
• • Epigenomics
• • Imaging data
• • Histopathology
• • Immunofluorescence

• Advanced bioinformatics pipelines integrate these datasets to identify cellular interactions, signaling pathways, and molecular mechanisms with greater biological accuracy.

What to Expect: Our End-to-End Spatial Transcriptomics Workflow

At N2Jenomics Lab Pvt. Ltd., every spatial transcriptomics project follows a carefully designed workflow that ensures high-quality data generation, rigorous quality control, and comprehensive scientific support from project initiation through publication.

Step 1. Scientific Consultation & Experimental Design

Every project begins with a detailed consultation to understand your research objectives and experimental requirements.

Our experts assist with:

• • Platform selection
• • Study design
• • Sample planning
• • Species compatibility assessment
• • Tissue preservation recommendations
• • Experimental replication strategy
• • Budget optimization
• • Multi-platform workflow planning

Step 2. Sample Quality Assessment & Tissue Processing

All submitted specimens undergo comprehensive quality evaluation before processing.

Quality assessment includes:

• • RNA integrity evaluation (RIN)
• • FFPE quality assessment (DV200)
• • Histological review
• • Tissue morphology inspection
• • Sample documentation
• • Cryosectioning or FFPE section preparation
• • H&E staining
• • Immunofluorescence staining (when applicable)

If a sample does not meet quality requirements, our team provides a detailed evaluation and recommendations before proceeding.

Step 3. Library Preparation & Spatial Data Generation

Following successful quality control, platform-specific workflows are performed using validated laboratory protocols.

Depending on the selected technology, this stage includes:

• • Spatial library preparation
• • Probe hybridization
• • Tissue imaging
• • Barcode capture
• • High-throughput sequencing
• • In situ molecular imaging
• • Library quality control
• • Instrument performance validation

• Sequencing-based platforms utilize advanced Illumina or DNBSEQ systems, while imaging-based workflows employ dedicated high-resolution spatial imaging instruments.

Step 4. Primary Data Processing & Quality Control

Raw data are processed using platform-specific computational pipelines to generate accurate spatial gene expression datasets.

Primary analyses include:

• • Image registration
• • Sequence alignment
• • Spatial barcode assignment
• • Gene counting
• • Cell segmentation
• • Quality metric evaluation
• • Technical performance assessment

• Every dataset undergoes stringent quality review before downstream biological analysis begins.

Step 5. Advanced Bioinformatics & Data Interpretation

Our experienced bioinformatics scientists perform comprehensive downstream analyses tailored to each project.

Available analyses include:

• • Spatial clustering
• • Differential gene expression
• • Spatially variable gene identification
• • Cell-type annotation
• • Cell deconvolution
• • Cell-cell communication analysis
• • Ligand-receptor interaction analysis
• • Pathway enrichment
• • Spatial neighborhood analysis
• • Multi-omics integration
• • Interactive data visualization

• Final deliverables include publication-ready figures, comprehensive reports, processed datasets, and interactive visualization files compatible with leading spatial genomics software.

Step 6. Ongoing Scientific Collaboration

Our commitment extends beyond data delivery.

We provide continued scientific support through:

• • Data interpretation consultations
• • Follow-up analyses
• • Manuscript preparation assistance
• • Figure generation
• • Reviewer response support
• • Additional bioinformatics analyses
• • Long-term collaboration for multi-phase projects

By combining advanced spatial transcriptomics technologies with experienced molecular biologists, bioinformaticians, and dedicated project managers, N2Jenomics Lab Pvt. Ltd. delivers complete spatial multi-omics solutions that help researchers uncover the spatial organization of biology and accelerate discoveries in oncology, neuroscience, immunology, developmental biology, pathology, regenerative medicine, and precision healthcare.

1. How do I choose the right spatial transcriptomics platform for my project?

Selecting the most suitable platform depends on your research objectives, sample type, desired spatial resolution, and the level of transcriptome coverage required.

Key considerations include:

• Spatial Resolution:

  • • Visium™ Spatial Gene Expression provides multicellular resolution (55 µm spots), making it ideal for tissue-wide discovery studies.

  • • Visium HD™ offers near single-cell resolution with high-density capture features.
  • • Stereo-seq delivers ultra-high spatial resolution (approximately 220 nm) across exceptionally large tissue sections.
  • • Xenium™ In Situ enables single-molecule RNA detection with true subcellular precision.
• Transcriptome Coverage:
  • • Visium™ and Stereo-seq perform unbiased whole-transcriptome profiling.
  • • Visium HD™ uses validated probe panels covering approximately 18,000 human and 20,000 mouse genes.
  • • Xenium™ targets predefined or custom gene panels for highly sensitive in situ analysis.
• Sample Compatibility:
  • • Fresh frozen tissues are compatible with all major platforms.
  • • FFPE tissues are supported by Visium HD™ and Xenium™ workflows.
• Species Support:
  • • Visium™ and Stereo-seq are suitable for many organisms with an available reference genome or transcriptome.
  • • Visium HD™ and Xenium™ are primarily optimized for human and mouse studies, with custom solutions available for selected applications.

Our scientific team will evaluate your samples and research goals to recommend the most appropriate platform—or a combination of platforms—for your study.

2. Can multiple spatial technologies be used within the same project?

Yes. Many advanced spatial biology studies combine complementary platforms to obtain a more comprehensive view of tissue organization and gene expression.

For example:

• • Visium™ or Visium HD™ can be used for unbiased tissue-wide transcriptome profiling.
• • Xenium™ In Situ can then validate and localize selected biomarkers at single-molecule resolution using adjacent tissue sections.
• • Stereo-seq can provide ultra-high-resolution mapping across larger tissue areas.

Our team manages tissue sectioning, experimental coordination, and cross-platform bioinformatics integration to ensure consistent, biologically meaningful results.

3. What sample quality is recommended for spatial transcriptomics?

High-quality tissue preservation is essential for obtaining reliable spatial gene expression data.

• Fresh Frozen Samples

• - Recommended RNA Integrity Number (RIN): ≥7
• - Minimum acceptable RIN: ≥6
• - Rapid tissue freezing and appropriate storage are strongly recommended.

• FFPE Samples

• - Recommended DV200 value: ≥30%
• - Proper fixation and processing improve RNA quality and downstream performance.
• Before library preparation, we perform comprehensive tissue quality assessment and provide a detailed quality control report with recommendations regarding sample suitability.

4. Can spatial transcriptomics be performed on non-model organisms?

Yes. Several of our spatial transcriptomics platforms are well suited for non-model species.

Platforms such as Visium™ Spatial Gene Expression and Stereo-seq can be applied to a wide variety of organisms provided that suitable reference genome or transcriptome resources are available for downstream analysis.

These technologies have broad applications in:

• • Agricultural research
• • Plant genomics
• • Aquatic biology
• • Veterinary research
• • Evolutionary biology
• • Ecological genomics
• • Comparative genomics

• For imaging-based platforms such as Visium HD™ and Xenium™ In Situ, species availability depends on validated or custom-designed probe panels. Our experts can advise on feasibility for your organism of interest.

5. What data and bioinformatics deliverables are included?

Each spatial multi-omics project includes comprehensive laboratory and bioinformatics deliverables designed to support downstream research and publication.

Typical deliverables include:

• • Raw sequencing or imaging data
• • Primary analysis outputs generated using platform-specific pipelines
• • Sample quality control reports
• • Spatial gene expression matrices
• • Cell segmentation and annotation (where applicable)
• • Spatial clustering analysis
• • Differential gene expression analysis
• • Spatially variable gene identification
• • Cell-type deconvolution
• • Cell–cell communication and ligand–receptor interaction analysis
• • High-resolution visualization overlays on histological images
• • Publication-ready figures and summary reports

• Interactive data formats compatible with leading spatial analysis software are also available to facilitate collaborative exploration and downstream interpretation.

6. Can you provide customized downstream bioinformatics analysis?

Absolutely. In addition to our standard analysis pipelines, we offer a wide range of advanced bioinformatics services tailored to your research objectives.

Customized analyses may include:

• • Multi-platform spatial data integration
• • Single-cell RNA-seq integration
• • Spatial multi-omics integration
• • Pathway and functional enrichment analysis
• • Cell neighborhood analysis
• • Spatial trajectory and lineage inference
• • Biomarker discovery
• • Comparative cohort analysis
• • Customized statistical analysis
• • Manuscript-ready visualizations and publication support

Our experienced bioinformatics team works closely with researchers to ensure that every dataset is analyzed using the most appropriate computational approaches for meaningful biological interpretation.