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Related Experiment Video

Updated: Jul 12, 2025

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PACMan: A software package for automated single-cell chlorophyll fluorometry.

Olle Pontén1,2, Linhong Xiao1, Jeanne Kutter1

  • 1Department of Organismal Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.

Cytometry. Part a : the Journal of the International Society for Analytical Cytology
|October 21, 2023
PubMed
Summary

We developed PACMan, open-source software to automate microscopy for studying microalgae photosynthesis. This automation significantly increases experimental throughput for photophysiology research.

Keywords:
Chlamydomonas reinhardtiiMICROSCOPY-PAMSymbiodiniaceaemicroalgaemicrofluidicsmicroscopy automationpulse-amplitude-modulated chlorophyll fluorometry

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Area of Science:

  • Microalgal photophysiology
  • Ecotoxicology
  • Biotechnology

Background:

  • Microalgae are vital unicells for ecological and biotechnological studies.
  • Investigating microalgal photosynthesis under varying conditions is crucial.
  • Current methods using pulse-amplitude-modulated (PAM) chlorophyll fluorimeters have limited throughput.

Purpose of the Study:

  • To enhance the throughput of MICROSCOPY-PAM systems for microalgae research.
  • To introduce PACMan (PAM Automation Control Manager), an open-source Python software.
  • To provide a user-friendly solution for automated image acquisition and hardware control.

Main Methods:

  • Developed PACMan software for automated image acquisition and microscopy stage control.
  • Integrated PACMan with a MICROSCOPY-PAM system and external hardware.
  • Utilized microfluidic devices for high-throughput single-cell analysis.
  • Developed PAMalysis tool for automated calculation of maximum quantum efficiencies (Fv/Fm).

Main Results:

  • Achieved a 10-fold increase in experimental throughput compared to manual operation.
  • Successfully tracked photophysiology of over 1000 individual cells from green algae and dinoflagellates.
  • Demonstrated high accuracy of automated analysis with a <0.5% median difference in Fv/Fm calculations compared to manual methods.

Conclusions:

  • PACMan and PAMalysis significantly increase experimental throughput for microalgae photophysiology studies.
  • The software facilitates high-throughput analysis of individual microalgal cells.
  • These tools are expected to advance research in microalgae ecology, ecotoxicology, and biotechnology.