Spatial Cell Type Mapping Service

Biological tissues are not random assortments of cells; they are highly organized ecosystems. Spatial Cell Type Mapping allows researchers to transcend the limitations of "bulk" or "dissociated" single-cell analysis. By preserving the physical coordinates of every transcript, we help you build a 3D atlas of gene expression. Whether you are identifying rare cell niches in a tumor or charting neuronal circuits in the brain, our platform provides the spatial context necessary to turn raw data into biological insight.

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Metabolic differences between normal and diseased tissues

What is
Workflow
Deliverables
Platform
Applications
Why choose
FAQs

What is Spatial Cell Type Mapping?

Spatial Cell Type Mapping is an advanced analytical framework that integrates Spatial Transcriptomics (ST) with Single-Cell RNA Sequencing (scRNA-seq).

While scRNA-seq provides a high-resolution "parts list" of cell types, it requires tissue dissociation, which destroys the spatial context. Spatial mapping uses computational deconvolution and probabilistic modeling to project those high-resolution cell types back onto a physical tissue slice. This allows us to identify exactly which cells are neighbors, how they communicate, and how their proximity influences disease progression or tissue development.

Our Precision Workflow

We provide an end-to-end solution, moving from your raw tissue block to a fully annotated spatial map.

cell type mapping workflow

Deliverables

Deliverable Module	What You Get	Solves For You
Publication-Ready Spatial Maps	High-res vector graphics (PDF/SVG): Cell type distribution heatmaps Multi-panel composite figures overlaid on H&E background with key regions annotated	Insert directly into manuscripts
Complete Data Package	Cell composition table (Excel/CSV): Spot ID, cell type, proportion, confidence score Spatial coordinate files: Ready for ImageJ, QuPath, or custom pipelines	Seamless integration into downstream analysis Zero technical barriers to exploration
Expert Interpretation Report	Key findings summary + QC metrics + biological insights Marker gene validation plots confirming spatia accuracy	Quickly grasp scientific value Robust evidence for peer review responses

The Technology Platform

We utilize industry-leading platforms to ensure your data is robust and publication-ready:

Visium (10x Genomics): Ideal for whole-transcriptome discovery across large tissue areas.
Xenium / MERFISH: High-plex, sub-cellular resolution for targeted gene panels, allowing you to see individual RNA molecules within a cell.
Proprietary AI Pipeline: Our custom computational suite handles noise reduction and improves the accuracy of cell-type deconvolution in "dense" tissue environments.

Key Applications

Immune Profiling: Map the "Immune Cold" vs. "Immune Hot" zones in tumors to understand immunotherapy resistance.
Neurobiology: Define the molecular boundaries of brain regions and identify cell-type specific changes in Alzheimer's or Parkinson's.
Developmental Biology: Track lineage commitment and organogenesis in embryonic tissues.
Pathology Refinement: Supplement traditional H&E staining with molecular data to identify "hidden" disease states.

Why Choose Our Services?

Expertise in Difficult Tissues: We have optimized protocols for "tough" samples, including fatty tissues, highly necrotic tumors, and fibrotic samples.
Data Integration: We don't just give you a spreadsheet. We integrate your spatial data with existing scRNA-seq datasets for a "best of both worlds" analysis.
Client-Centric Delivery: Every project includes a dedicated project manager and a post-delivery session with a bioinformatician to help you interpret your results.

FAQs

How many cells are in a single "spot"?

Depending on the platform (e.g., Visium), a spot is usually 55 μm in diameter, containing 1 to 10 cells. We use computational deconvolution to estimate the exact cell-type proportions within each spot.

Can I use my own scRNA-seq data as a reference?

Absolutely. In fact, using a matched scRNA-seq reference from the same study significantly increases the accuracy of the spatial mapping.

Learn about other Q&A.

* For Research Use Only. Not for use in diagnostic procedures.

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From Our Clients

"I recently used their proteomics service for a project analyzing protein interactions in yeast models. The team was very responsive and helped clarify the methodology they employed, which made me feel confident in the results. The data quality was solid, with clear identification of several key proteins involved in our study. Their thorough analysis enabled me to pinpoint specific interactions that I hadn't considered before, which significantly improved the direction of my research. I appreciate their professionalism and support throughout the process."

Sarah Thompson, University of California, Berkeley

"Our lab collaborated with them on a project studying cancer biomarkers. The proteomics analysis provided was detailed and focused, specifically highlighting the differential expression of proteins between healthy and tumor samples. Their clear explanations of the data helped my team understand the biological implications. I also appreciated their willingness to revise the reports based on our feedback, ensuring that we had everything we needed for our publication. This collaborative spirit was invaluable."

Emily Rodriguez, Stanford University

"Our lab worked with them on a project studying the effects of diet on gut microbiota using proteomics. They used a label-free quantification method to analyze proteins in fecal samples before and after dietary intervention. The results showed significant changes in protein expression linked to microbial activity. This was pivotal for our hypothesis about diet-microbiota interactions. The clarity of their data presentation made it easy for our team to integrate these findings into our ongoing research."

Dr. Lisa Wong, University of Toronto

"My experience with Creative Proteomics during the mass spectrometry analysis was excellent. We sent in human saliva and mouse brain tissue samples, which they expertly analyzed using both LC-MS and GC-MS techniques. The results were invaluable, revealing key metabolites in the saliva and identifying biomarkers linked to brain function in the brain tissue."

Dr. Emily Carter, Senior Research Scientist

"The overall service from Creative Proteomics was outstanding. They made the entire process seamless and efficient, allowing us to focus on our research. We worked with leaf and root samples from various Arabidopsis genotypes for targeted metabolomics analysis. Their thorough profiling of primary and secondary metabolites gave us important insights into how the plants respond metabolically to environmental stress."

Dr. Laura Henderson, Plant Physiologist

"We had a pleasant collaboration with Creative Proteomics on mass spectrometry analysis of lipids. They conducted a detailed analysis of lipid species, providing us with important insights into lipid metabolism and its relationship with metabolic syndrome disease states."

Dr. Sarah Mitchell, Research Scientist

Online Inquiry

Please submit a detailed description of your project. We will provide you with a customized project plan to meet your research requests. You can also send emails directly to for inquiries.

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