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Related Concept Videos

Subcellular Fractionation01:32

Subcellular Fractionation

The homogenate obtained after cell lysis contains various membrane-bound organelles that can be further separated into pure fractions by subcellular fractionation. These isolates are used to study specific cellular components, analyze localized protein activity, and are even employed in diagnostics. Fractionation is typically achieved using centrifugation methods, the most common being density-gradient and differential centrifugation.
Differential Centrifugation
Differential centrifugation is...
Phase Contrast and Differential Interference Contrast Microscopy01:26

Phase Contrast and Differential Interference Contrast Microscopy

Phase-Contrast Microscopes
In-phase-contrast microscopes, interference between light directly passing through a cell and light refracted by cellular components is used to create high-contrast, high-resolution images without staining. It is the oldest and simplest type of microscope that creates an image by altering the wavelengths of light rays passing through the specimen. Altered wavelength paths are created using an annular stop in the condenser. The annular stop produces a hollow cone of...

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Related Experiment Video

Updated: Jun 30, 2026

Automated Quantification of Hematopoietic Cell – Stromal Cell Interactions in Histological Images of Undecalcified Bone
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A quantitative spatial cell-cell colocalizations framework enabling comparisons between in vitro assembloids and

Gina Bouchard1, Weiruo Zhang1, Ilayda Ilerten1

  • 1Department of Biomedical Data Science, Stanford University, Stanford, CA, USA.

Nature Communications
|February 6, 2025
PubMed
Summary
This summary is machine-generated.

This study introduces a new framework to compare spatial features in biological samples, enabling better understanding of disease and drug response through quantitative cell colocalization analysis.

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Area of Science:

  • Spatial biology
  • Quantitative biology
  • Cancer research

Background:

  • Spatial omics advances tissue characterization but lacks cross-sample comparison methods.
  • Comparing spatial features across diverse biological samples under varying conditions remains a challenge.
  • Developing quantitative frameworks is crucial for advancing spatial omics research.

Purpose of the Study:

  • To propose a quantitative framework for cataloging and comparing cell subpopulation colocalizations across biological samples.
  • To enable standardized analysis of spatial features in multiplexed imaging data.
  • To facilitate the investigation of spatial biology in disease and drug response.

Main Methods:

  • Developed a quantitative framework for normalized cell-pair colocalization analysis.
  • Applied the framework to multiplexed immunofluorescence images of lung adenocarcinoma (LUAD) organoid assembloids.
  • Utilized cancer-associated fibroblasts from human tumors in assembloid construction.

Main Results:

  • Assembloids successfully recapitulate human LUAD tumor-stroma spatial organization.
  • Drug-perturbation studies revealed drug-induced spatial rearrangements mirroring those in treatment-naïve tumors.
  • The framework enables quantification of spatial data for building disease- and drug-associated feature catalogs.

Conclusions:

  • The proposed framework provides a robust method for comparing spatial features across diverse biological samples.
  • Assembloids serve as a valid model for studying the spatial biology of human diseases like LUAD.
  • The findings offer insights into drug resistance mechanisms and spatial reorganization in cancer treatment.