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Related Concept Videos

X-ray Diffraction of Biological Samples01:10

X-ray Diffraction of Biological Samples

X-ray diffraction or XRD is an analytical tool that utilizes X-rays to study ordered structures such as crystalline organic and inorganic samples, polycrystalline materials, proteins, carbohydrates, and drugs.
According to Bragg's law, when X-rays strike the sample positioned on a stage, the rays areĀ  scattered by the electron clouds around the sample atoms. TheĀ  X-ray diffraction or scattering is caused by constructive interference of the X-ray waves that reflect off the internal crystal...
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Imaging Biological Samples with Optical Microscopy

Optical microscopy uses optic principles to provide detailed images of samples. Antonie van Leeuwenhoek designed the first compound optical microscope in the 17th century to visualize blood cells, bacteria, and yeast cells. In 1830, Joseph Jackson Lister created an essentially modern light microscope. The 20th century saw the development of microscopes with enhanced magnification and resolution.
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Super-resolution Fluorescence Microscopy

Super-resolution fluorescence microscopy (SRFM) provides a better resolution than conventional fluorescence microscopy by reducing the point spread function (PSF). PSF is the light intensity distribution from a point that causes it to appear blurred. Due to PSF, each fluorescing point appears bigger than its actual size, and it is the PSF interference of nearby fluorophores that causes the blurred image. Various approaches to achieving higher resolution through SRFM have recently been developed.

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Updated: Jun 15, 2026

Spatial Profiling of Protein and RNA Expression in Tissue: An Approach to Fine-Tune Virtual Microdissection
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SPEX: A modular end-to-end platform for high-plex tissue spatial omics analysis.

Xiao Li1,2, Ximo Pechuan-Jorge1,3, Tyler Risom1

  • 1Genentech, Inc., South San Francisco 94080, CA, USA.

Gigascience
|August 29, 2025
PubMed
Summary
This summary is machine-generated.

SPEX (Spatial Expression Explorer) is a user-friendly web platform simplifying spatial omics data analysis. It overcomes coding barriers, enabling biologists to explore tissue architecture and gain insights from complex molecular data.

Keywords:
clusteringgraphical user interfaceopen sourcesegmentationspatial analysisspatial proteomicsspatial transcriptomicsuser friendly web platform

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Area of Science:

  • Molecular Biology
  • Bioinformatics
  • Computational Biology

Background:

  • Advancements in transcriptomics and proteomics enable spatially resolved molecular characterization of tissue.
  • High-throughput spatial omics technologies generate vast datasets requiring sophisticated computational analysis.
  • A significant hurdle for widespread adoption is the need for advanced coding fluency in spatial omics data analysis.

Purpose of the Study:

  • To introduce SPEX (Spatial Expression Explorer), a web-based platform designed to democratize spatial omics data analysis.
  • To provide a user-friendly interface that simplifies the integration and application of computational methods for spatial omics.
  • To facilitate deeper understanding of tissue biology in homeostasis and disease through accessible spatial omics exploration.

Main Methods:

  • Development of SPEX, a web-based platform with a modular analysis pipeline.
  • Integration of open-source image data management, analysis modules (image processing, single-cell, spatial analysis), and data visualization.
  • User-friendly interface design to lower the barrier for biologists without advanced coding skills.

Main Results:

  • SPEX offers streamlined access to essential spatial omics analysis steps.
  • The platform integrates image processing, single-cell analysis, and spatial analysis modules.
  • Demonstrated ability to facilitate biological discovery in diverse spatial omics datasets, from healthy to tumor tissues.

Conclusions:

  • SPEX effectively addresses the need for accessible spatial omics data analysis tools.
  • The platform empowers the broader biology research community to leverage spatial omics data.
  • SPEX facilitates the discovery of biological insights in complex tissue architecture, advancing understanding of homeostasis and disease.