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Updated: Jul 12, 2025

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

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Published on: December 16, 2014

BBQ methods: Streamlined workflows for Bacterial Burden Quantification in infected cells by confocal microscopy.

Jacques Augenstreich¹, Michael Shuster¹, Yongqiang Fan^1,2

¹Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742 USA.

Biorxiv : the Preprint Server for Biology

|October 24, 2023

Summary

New automated methods improve bacterial burden quantification (BBQ) in macrophages. These techniques offer reliable, unbiased, and rapid bacterial load assessment for host-pathogen research.

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Kinetic Visualization of Single-Cell Interspecies Bacterial Interactions

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Published on: August 5, 2020

Area of Science:

Microbiology
Immunology
Cell Biology

Background:

Accurate quantification of bacterial burden within macrophages (BBQ) is vital for understanding host-pathogen dynamics.
Existing BBQ methods have limitations, necessitating improved techniques for reliable analysis.
Confocal microscopy data analysis is key for studying intracellular bacterial infections.

Approach:

Introduced two novel automated workflows for Bacterial Burden Quantification (BBQ) using confocal microscopy data.
Developed a refined fluorescence quantification method excluding uninfected cells.
Implemented a bacterial volume calculation method to reduce fluorescence-based biases.

Key Points:

Utilized PyImageJ and Cellpose software for automated data analysis.
Validated workflows with Salmonella Typhimurium and Mycobacterium tuberculosis models.
Achieved reliable, unbiased, and rapid quantification of bacterial load.

Conclusions:

The novel automated workflows provide effective tools for accurate bacterial burden assessment.
These methods enhance the study of bacterial interactions within host cells.
The developed techniques offer valuable insights for diverse research applications in microbiology and immunology.