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Imaging Biological Samples with Optical Microscopy

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Optical microscopy uses optic principles to provide detailed images of samples. Antonie van Leeuwenhoek designed the first compound optical microscope in the 17th century to visualize blood cells, bacteria, and yeast cells. In 1830, Joseph Jackson Lister created an essentially modern light microscope. The 20th century saw the development of microscopes with enhanced magnification and resolution.
In optical microscopy, the specimen to be viewed is placed on a glass slide and clipped on the stage...

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Open Source High Content Analysis Utilizing Automated Fluorescence Lifetime Imaging Microscopy

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Qudi-HiM: an open-source acquisition software package for highly multiplexed sequential and combinatorial optical

Franziska Barho¹, Jean-Bernard Fiche¹, Marion Bardou¹

¹Centre de Biologie Structurale, Centre National de la Recherche Scientifique, UMR5048, Montpellier, 34090, France.

Open Research Europe

|August 30, 2023

Summary

This summary is machine-generated.

We developed Qudi-HiM, a Python software package, to automate multiplexed imaging for spatial multi-omics. This tool enhances the study of single-cell biology and chromatin organization on custom microscopes.

Keywords:

chromosome organization multiplexed imaging optical microscopy transcription

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Area of Science:

Cellular and Molecular Imaging
Biotechnology
Bioinformatics

Background:

Multiplexed imaging allows simultaneous detection of multiple biological molecules (proteins, DNA, RNA) for spatial multi-omics at single-cell resolution.
The Hi-M (High-content Imaging - Multiplexing) approach was recently developed to investigate chromatin spatial organization within single cells.

Purpose of the Study:

To develop a modular software package, Qudi-HiM, enabling Hi-M sequential imaging on custom microscope setups.
To automate the acquisition and analysis of complex imaging data for spatial multi-omics studies.

Main Methods:

Development of Qudi-HiM, a Python 3 software package with modules for automated image acquisition, microfluidics handling, and real-time monitoring.
Implementation of robust acquisition of thousands of 3D multicolor microscopy images.
Integration of remote monitoring and real-time analysis capabilities.

Main Results:

Qudi-HiM successfully automates multiplexed sequential imaging for Hi-M on custom microscopes.
The software facilitates the handling of microfluidics devices and provides real-time data analysis.
Qudi-HiM is versatile and can be utilized as a standalone tool for various imaging modalities.

Conclusions:

Qudi-HiM provides a robust and flexible software solution for advanced spatial multi-omics research.
The developed tool enhances the accessibility and efficiency of high-resolution cellular imaging.
Qudi-HiM supports the broader scientific community in advancing single-cell spatial biology studies.