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Related Concept Videos

Fixation and Sectioning01:03

Fixation and Sectioning

Two basic types of preparation are used to visualize specimens with a light microscope: wet mounts and fixed specimens.
The simplest type of preparation is the wet mount, in which the specimen is placed in a drop of liquid on the slide. A liquid specimen can be directly deposited on the slide using a dropper. Solid specimens, such as skin scraping, can be placed on the slide before adding a drop of liquid to prepare the wet mount. Sometimes the liquid is simply water, but stains are often added...

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SAPHIR: a Shiny application to analyze tissue section images.

Elodie Germani1, Hugues Lelouard2, Mathieu Fallet2

  • 1Université de Rennes 1, Rennes, 35000, France.

F1000Research
|May 12, 2021
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Summary

Researchers developed SAPHIR, an R shiny application for analyzing complex immunofluorescence images. This tool aids in accurate cell characterization and spatial analysis within tissues, reducing bias in histological data interpretation.

Keywords:
Tissue cellular quantificationcell-cell interactionshisto-cytometryimage cytometryscatterplotspatial cellular profiling

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Area of Science:

  • Computational Biology
  • Biotechnology
  • Medical Imaging Analysis

Background:

  • Immunofluorescence and confocal microscopy generate complex, high-dimensional data for cell population studies.
  • Analyzing these intricate histological images is challenging, risking bias and misinterpretation.

Purpose of the Study:

  • To develop an R shiny application, SAPHIR, for robust histo-cytometry analysis.
  • To provide a user-friendly tool for accurate characterization of cell phenotypes, numbers, locations, and interactions within tissues.

Main Methods:

  • Developed SAPHIR, an R shiny application utilizing scatterplot representations of segmented image data.
  • Implemented features for data filtering, cell subset selection, and visualization of selections within the original images.

Main Results:

  • SAPHIR enables detailed characterization of labeled cells, including phenotype, quantity, and spatial distribution.
  • The application facilitates the analysis of cell-cell interactions and provides statistical insights.
  • Visualization tools link scatterplot data back to the histological images for context.

Conclusions:

  • SAPHIR offers a powerful solution for unbiased analysis of complex immunofluorescence data.
  • The application enhances the ability to study cell populations and their tissue microenvironments.
  • SAPHIR supports basic and medical research by improving histological image interpretation.