ArticleCommunications biology2023
3D reconstruction of skin and spatial mapping of immune cell density, vascular distance and effects of sun exposure and aging.
Article in Communications biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed, 21 citations in OpenAlex.
- HuBMAP Data Portal: a resource for multimodal spatial and single-cell data of healthy human tissues.ArXiv · 2026Article
- Volumetric Cyclic Immunofluorescence for 3D Spatial Profiling of Immune Structures in Human FFPE Tissue.bioRxiv : the preprint server for biology · 2026Article
- Uncovering Immune Niches in Health and Disease Using Spatial Transcriptomics.European journal of immunology · 2026Review
- Cell Type Populations for 3D Anatomical Structures of the Human Reference Atlas.Scientific data · 2026Article
- Annotation-Free Prediction of Cancer Cells and Glands and Spatial Analysis of Immune Cells.bioRxiv : the preprint server for biology · 2025Article
- Highly multiplexed 3D profiling of cell states and immune niches in human tumors.Nature methods · 2025Article
- Exploring endothelial cell environments across organs in spatially resolved omics data.bioRxiv : the preprint server for biology · 2025Article
- Review
- Generalized cell phenotyping for spatial proteomics with language-informed vision models.bioRxiv : the preprint server for biology · 2025Article
- Constructing and Using Cell Type Populations of the Human Reference Atlas.bioRxiv : the preprint server for biology · 2025Article
- A real-time virtual liver simulator using position based dynamics with compliant constraints for medical applications.Scientific reports · 2025Article
- Human BioMolecular Atlas Program (HuBMAP): 3D Human Reference Atlas construction and usage.Nature methods · 2025Article
- Three-Dimensional Curved Workflow-Based Optical Coherence Tomography Angiography for Enhancing Atopic Dermatitis Theranostics.Research (Washington, D.C.) · 2025Article
- Human BioMolecular Atlas Program (HuBMAP): 3D Human Reference Atlas Construction and Usage.bioRxiv : the preprint server for biology · 2024Article
- The influence of viscosity of hydrogels on the spreading and migration of cells in 3D bioprinted skin cancer models.Frontiers in cell and developmental biology · 2024Review
- 3D reconstruction of skin and spatial mapping of immune cell density, vascular distance and effects of sun exposure and aging.Communications biology · 2023Article
Corrections and comments
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Authors and funding
17 authors at 3 institutions in 1 country.
Funding
Abstract
Mapping the human body at single cell resolution in three dimensions (3D) is important for understanding cellular interactions in context of tissue and organ organization. 2D spatial cell analysis in a single tissue section may be limited by cell numbers and histology. Here we show a workflow for 3D reconstruction of multiplexed sequential tissue sections: MATRICS-A (Multiplexed Image Three-D Reconstruction and Integrated Cell Spatial - Analysis). We demonstrate MATRICS-A in 26 serial sections of fixed skin (stained with 18 biomarkers) from 12 donors aged between 32-72 years. Comparing the 3D reconstructed cellular data with the 2D data, we show significantly shorter distances between immune cells and vascular endothelial cells (56 µm in 3D vs 108 µm in 2D). We also show 10-70% more T cells (total) within 30 µm of a neighboring T helper cell in 3D vs 2D. Distances of p53, DDB2 and Ki67 positive cells to the skin surface were consistent across all ages/sun exposure and largely localized to the lower stratum basale layer of the epidermis. MATRICS-A provides a framework for analysis of 3D spatial cell relationships in healthy and aging organs and could be further extended to diseased organs.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.