{"entity": "publication", "iuid": "f2fe68a2bd124841ae2931b1c3413fda", "timestamp": "2026-10-18T01:04:43.055Z", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/f2fe68a2bd124841ae2931b1c3413fda.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/f2fe68a2bd124841ae2931b1c3413fda"}}, "title": "PACMan: A software package for automated single-cell chlorophyll fluorometry.", "authors": [{"family": "Pont\u00e9n", "given": "Olle", "initials": "O", "orcid": "0000-0002-8061-2060", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/137743ee1acd4c90a6ce1f620a5f5949.json"}}, {"family": "Xiao", "given": "Linhong", "initials": "L"}, {"family": "Kutter", "given": "Jeanne", "initials": "J"}, {"family": "Cui", "given": "Yuan", "initials": "Y"}, {"family": "W\u00e4hlby", "given": "Carolina", "initials": "C", "orcid": "0000-0002-4139-7003", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/833afe3444d84c24be12ea1468563bea.json"}}, {"family": "Behrendt", "given": "Lars", "initials": "L", "orcid": "0000-0002-8988-2032", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/037bb8f29ff24e95b3358ab1f0ff2ee6.json"}}], "type": "journal article", "published": "2024-03-00", "journal": {"title": "Cytometry A", "issn": "1552-4930", "volume": "105", "issue": "3", "pages": "203-213", "issn-l": "1552-4922"}, "abstract": "Microalgae, small photosynthetic unicells, are of great interest to ecology, ecotoxicology and biotechnology and there is a growing need to investigate the ability of cells to photosynthesize under variable conditions. Current strategies involve hand-operated pulse-amplitude-modulated (PAM) chlorophyll fluorimeters, which can provide detailed insights into the photophysiology of entire populations- or individual cells of microalgae but are typically limited in their throughput. To increase the throughput of a commercially available MICROSCOPY-PAM system, we present the PAM Automation Control Manager ('PACMan'), an open-source Python software package that automates image acquisition, microscopy stage control and the triggering of external hardware components. PACMan comes with a user-friendly graphical user interface and is released together with a stand-alone tool (PAMalysis) for the automated calculation of per-cell maximum quantum efficiencies (= Fv /Fm ). Using these two software packages, we successfully tracked the photophysiology of >1000 individual cells of green algae (Chlamydomonas reinhardtii) and dinoflagellates (genus Symbiodiniaceae) within custom-made microfluidic devices. Compared to the manual operation of MICROSCOPY-PAM systems, this represents a 10-fold increase in throughput. During experiments, PACMan coordinated the movement of the microscope stage and triggered the MICROSCOPY-PAM system to repeatedly capture high-quality image data across multiple positions. Finally, we analyzed single-cell Fv /Fm with the manufacturer-supplied software and PAMalysis, demonstrating a median difference <0.5% between both methods. We foresee that PACMan, and its auxiliary software package will help increase the experimental throughput in a range of microalgae studies currently relying on hand-operated MICROSCOPY-PAM technologies.", "doi": "10.1002/cyto.a.24808", "pmid": "37864330", "labels": {"Lars Behrendt": "", "SciLifeLab Fellow": ""}, "xrefs": [], "notes": [], "created": "2023-11-29T19:53:59.960Z", "modified": "2026-09-23T13:14:41.043Z"}