Spatial Biology
Spatial Biology - Related Videos
11:57
Measuring Spatially- and Directionally-varying Light Scattering from Biological Material
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Cited by 5 •
2013
We present a non-destructive method for sampling spatial variation in the direction of light scattered from structurally complex materials. By keeping the material intact, we preserve gross-scale scattering behavior, while concurrently capturing fine-scale directional contributions with high-resolution imaging. Results are visualized in software at biologically-relevant positions and scales.
08:52
Spatial Molecular Imaging of the Glycome Using Mass Spectrometry
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Cited by 1 •
2025
This protocol details the key steps to enable rigorous and reproducible measurement of both glycogen and N-linked glycans using mass spectrometry imaging.
07:51
Spatial Cueing
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2023
Source: Laboratory of Jonathan Flombaum—Johns Hopkins University Attention refers to the limited human ability to select some information for processing at the expense of other stimuli in the environment. Attention operates in all sensory modalities: vision, hearing, touch, even taste and smell. It is most often studied in the visual domain though. A common way to study visual attention is with a spatial cueing paradigm. This paradigm allows researchers to measure the consequences of focusing...
10:16
Mining Spatial Transcriptomics Datasets using DeepSpaceDB
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2025
This article introduces a protocol for using DeepSpaceDB, a dynamic, interactive database for spatial transcriptomics, offering analysis workflows and examples to explore tissue organization and disease-related gene expression.
06:05
Multiplex Immunofluorescence Combined with Spatial Image Analysis for the Clinical and Biological Assessment of the Tumor Microenvironment
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Cited by 11 •
2023
In this article, a protocol for manual tyramide signal amplification (TSA) multiplex immunofluorescence (mIF) combined with image analysis and spatial analysis is described. This protocol can be used with formalin-fixed paraffin-embedded (FFPE) sections for the staining of two to six antigens per slide depending on the slide scanner available in the laboratory.
FAQs
Spatial Biology interprets molecular features together with their physical positions, allowing researchers to examine how tissue organization relates to biological activity. Rather than treating gene expression or protein patterns as isolated measurements, investigators can associate them with particular cells, tissue regions, and neighboring structures. This spatial context helps explain why similar molecular features may have different significance in different parts of a tumor.
Intratumoral heterogeneity refers to differences among regions or cell populations within the same tumor. Spatially resolved measurements show where these differences occur, helping distinguish localized molecular states from patterns shared throughout the tumor. In cancer research, this regional view can support tumor classification and reveal why treatment response may vary between areas rather than appearing uniform across the entire tumor.
The locations of tumor, immune, and other cellular features can reveal how cells are organized relative to one another within the tumor microenvironment. Spatial patterns may identify regions where particular cell populations coexist or are separated, providing context for interpreting immune organization and local biological behavior. This information strengthens analysis of how tissue structure contributes to disease characteristics.
Imaging preserves and records tissue architecture, while spatially resolved molecular profiling measures features such as gene expression or proteins at defined locations. Used together, these approaches connect visible tissue structures with molecular states and cellular identities. The combined information can distinguish biologically different regions that might otherwise appear similar when examined without their positional context.
A cancer-focused workflow begins with intact tissue so that cellular and structural positions remain available for analysis. Researchers then combine imaging with spatially resolved measurements of gene expression, proteins, or other molecular features. The resulting data are interpreted by relating molecular signals to cells, tissue regions, and the surrounding tumor microenvironment, producing a location-aware view of tumor organization.
Spatial Biology is especially useful when treatment response differs across regions of a tumor. By preserving location while measuring molecular features, researchers can compare areas associated with different response patterns and examine their cellular organization. These regional insights may support biomarker discovery and help guide more precise therapeutic strategies by showing that response can depend on local tumor context.
Spatial biology can identify molecular features that are concentrated in specific tumor regions or associated with particular cellular organizations. Such location-linked patterns may help distinguish tumor classes and reveal markers connected to disease behavior or treatment response. Because the measurements retain tissue context, candidate biomarkers can be interpreted alongside the cells and structures in which they occur.