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Related Experiment Video

Updated: Oct 8, 2025

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A Systematic, Open-Science Framework for Quantification of Cell-Types in Mouse Brain Sections Using Fluorescence

Juan C Sanchez-Arias1, Micaël Carrier1,2, Simona D Frederiksen1

  • 1Division of Medical Sciences, University of Victoria, Victoria, BC, Canada.

Frontiers in Neuroanatomy
|December 24, 2021
PubMed
Summary

This study introduces an open-science workflow for quantifying cell density in mouse brains using microscopy. The FIJI-ImageJ-based method simplifies experimental design, staining, and analysis for neurobiology research.

Keywords:
experimental designfluorescence microscopyimage analysismouse brainneuroscienceopen sciencereproducibility

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Area of Science:

  • Neurobiology
  • Microscopy
  • Image Analysis

Background:

  • Microscopy advancements drive neurobiology discoveries, but workflow limitations hinder tool adoption.
  • Implementing image processing tools requires comprehensive approaches from design to data presentation.
  • Open science principles (open-source, user-friendliness) are crucial for accessibility.

Purpose of the Study:

  • To provide a compendium of resources and a FIJI-ImageJ workflow for cell density quantification.
  • To establish a semi-automated, open-science-based method for analyzing mouse brain samples.
  • To support researchers by offering a flexible framework for diverse neuroscience projects.

Main Methods:

  • Developed a FIJI-ImageJ-based workflow for semi-automated cell density quantification.
  • Integrated principles of experimental design, histological and immunofluorescence staining, and microscopy imaging.
  • Included recommendations for statistical analysis and data presentation.
  • Validated the workflow by quantifying neuronal density in the mouse barrel cortex.

Main Results:

  • Successfully quantified neuronal density in the mouse barrel cortex using pan-neuronal and interneuron markers.
  • Demonstrated the utility of the proposed framework for cell density analysis.
  • Validated the semi-automated, open-science approach for improved accuracy and reproducibility.

Conclusions:

  • The proposed framework simplifies and enhances cell density quantification in neuroscience research.
  • The FIJI-ImageJ-based workflow promotes open science principles, increasing accessibility and flexibility.
  • This methodology supports researchers of all experience levels in neuroscience studies.