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The development of flow cytometry techniques began in 1934 with initial attempts by Andrew Moldavan, a bacteriologist who counted the cells in a flowing capillary system. Moldavan pumped cells through a capillary tube focused under a microscope for visualization. The invention of photometry allowed the measurement of differentially-stained cells, and Louis Kamentsky developed the first multiparameter flow cytometer in 1965 to identify and count the cancer cells in cervical tissue specimens.
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Multicolor Flow Cytometry-based Quantification of Mitochondria and Lysosomes in T Cells
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TockyPrep: data preprocessing methods for flow cytometric fluorescent timer analysis.

Masahiro Ono1

  • 1Department of Life Sciences, Imperial College London, Imperial College Road, London, SW7 2AZ, United Kingdom. m.ono@imperial.ac.uk.

BMC Bioinformatics
|February 8, 2025
PubMed
Summary
This summary is machine-generated.

This study introduces TockyPrep, an R package that standardizes preprocessing for Fluorescent Timer protein data in flow cytometry. This enhances the accuracy and reproducibility of single-cell temporal analysis using Timer-of-cell-kinetics-and-activity (Tocky) tools.

Keywords:
Data preprocessingFlow CytometryFluorescent Timer ProteinNr4a3-TockyTocky

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Area of Science:

  • Biotechnology
  • Cell Biology
  • Bioinformatics

Background:

  • Fluorescent Timer proteins offer insights into cellular dynamics at the single-cell level.
  • Existing Timer protein analysis in flow cytometry faces challenges due to instrument variability and lack of standardized preprocessing.
  • The Timer-of-cell-kinetics-and-activity (Tocky) tools utilize Fast-FT Timer proteins for monitoring cellular activities.

Purpose of the Study:

  • To develop and implement automated data preprocessing methods for Timer fluorescence data.
  • To standardize Timer data analysis for improved reproducibility and accuracy in flow cytometry.
  • To enhance the quantitative analysis of cellular activities using Timer proteins.

Main Methods:

  • Introduction of the TockyPrep R package for automated preprocessing.
  • Implementation of a trigonometric transformation method for Timer protein dynamics.
  • Identification and application of normalization methods for immature and mature Timer fluorescence data.

Main Results:

  • The TockyPrep package automates the preprocessing of Timer fluorescence data for single-cell analysis.
  • Trigonometric transformation and normalization methods are included to elucidate Timer protein dynamics and maturation.
  • The package standardizes data analysis, addressing variability in flow cytometry experiments.

Conclusions:

  • TockyPrep provides essential tools for preprocessing and visualizing Timer fluorescence data.
  • The package is available on GitHub, facilitating its adoption and use.
  • TockyPrep is expected to improve the application of Fluorescent Timer proteins, including Tocky tools, in biological research.