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Updated: Sep 13, 2025

Workflow for High-content, Individual Cell Quantification of Fluorescent Markers from Universal Microscope Data, Supported by Open Source Software

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Efficient cytoplasmic cell quantification using a semi-automated FIJI-based tool.

Lucas Unger¹, Ulrik Larsen², Shayla Sharmine²

¹Mohn Research Center for Diabetes Precision Medicine, Department of Clinical Science, Faculty of Medicine, University of Bergen, Glasblokkene 1, Haukelandsbakken 15, 5009, Bergen, Norway. lucas.unger@uib.no.

Scientific Reports

|July 28, 2025

Summary

This summary is machine-generated.

We developed a semi-automated counting macro (SAM) for efficient quantification of subcellular structures in research. SAM enhances the reliability and standardization of immunostaining analysis, particularly in diabetes research.

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Last Updated: Sep 13, 2025

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Area of Science:

Cell biology
Immunohistochemistry
Biomedical research

Background:

Quantification of subcellular structures like nuclei and proteins is crucial in biological research.
Current high-throughput quantification methods for staining assays are often time-consuming and present challenges in accuracy and standardization.

Purpose of the Study:

To present a novel FIJI-based semi-automated counting macro (SAM) for efficient and accurate quantification of immunostaining.
To validate the accuracy of SAM against manual and other automated counting methods.
To improve the reliability, efficiency, and standardization of immunostaining analysis in scientific research, with a focus on diabetes research.

Main Methods:

Development of a FIJI-based semi-automated counting macro named SAM.
Validation of SAM's accuracy through comparison with manual counting techniques.
Comparison of SAM's performance against other existing automated counting methods.

Main Results:

SAM provides accurate quantification of subcellular structures.
The macro demonstrates comparable or superior accuracy to manual and other automated methods.
SAM significantly reduces the time and effort required for high-throughput analysis of immunostaining.

Conclusions:

SAM offers a reliable, efficient, and standardized tool for immunostaining analysis.
This automated quantification method can accelerate research in fields such as diabetes.
The developed macro contributes to advancing high-throughput biological assay quantification.