University of Oulu

Dunker, S., Boyd, M., Durka, W., Erler, S., Harpole, W. S., Henning, S., Herzschuh, U., Hornick, T., Knight, T., Lips, S., Mäder, P., Švara, E. M., Mozarowski, S., Rakosy, D., Römermann, C., Schmitt‐Jansen, M., Stoof‐Leichsenring, K., Stratmann, F., Treudler, R., … Wilhelm, C. (2022). The potential of multispectral imaging flow cytometry for environmental monitoring. Cytometry Part A, 101(9), 782–799.

The potential of multispectral imaging flow cytometry for environmental monitoring

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Author: Dunker, Susanne1,2; Boyd, Matthew3; Durka, Walter4,2;
Organizations: 1Department of Physiological Diversity, Helmholtz-Centre for Environmental Research (UFZ), Leipzig, Germany
2German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
3Department of Anthropology, Lakehead University, Thunder Bay, Canada
4Department of Community Ecology, Helmholtz-Centre for Environmental Research (UFZ), Halle, Germany
5Institute for Bee Protection, Julius Kühn Institute (JKI)-Federal Research Centre for Cultivated Plants, Braunschweig, Germany
6Institute of Biology, Martin Luther University Halle-Wittenberg, Halle, Germany
7Department of Experimental Aerosol and Cloud Microphysics, Leibniz Institute for Tropospheric Research (TROPOS), Leipzig, Germany
8Alfred-Wegner-Institute Helmholtz Centre of Polar and Marine Research, Polar Terrestrial Environmental Systems, Potsdam, Germany
9Institute of Environmental Sciences and Geography, University of Potsdam, Potsdam, Germany
10Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
11Department of Bioanalytical Ecotoxicology, Helmholtz-Centre for Environmental Research – UFZ, Leipzig, Germany
12Department of Computer Science and Automation, Technische Universität Ilmenau, Ilmenau, Germany
13Faculty of Biological Sciences, Friedrich-Schiller-University Jena, Jena, Germany
14Institute of Ecology and Evolution, Friedrich-Schiller-University Jena, Jena, Germany
15Department of Dermatology, Venerology and Allergology, University of Leipzig Medical Center, Leipzig, Germany
16Ecology and Genetics, University of Oulu, Oulu, Finland
17Department of Lake Research, Helmholtz-Centre for Environmental Research – UFZ, Magdeburg, Germany
18Faculty of Life Sciences, Institute of Biology, University of Leipzig, Leipzig, Germany
Format: article
Version: published version
Access: open
Online Access: PDF Full Text (PDF, 6.7 MB)
Persistent link:
Language: English
Published: John Wiley & Sons, 2022
Publish Date: 2022-12-01


Environmental monitoring involves the quantification of microscopic cells and particles such as algae, plant cells, pollen, or fungal spores. Traditional methods using conventional microscopy require expert knowledge, are time-intensive and not well-suited for automated high throughput. Multispectral imaging flow cytometry (MIFC) allows measurement of up to 5000 particles per second from a fluid suspension and can simultaneously capture up to 12 images of every single particle for brightfield and different spectral ranges, with up to 60x magnification. The high throughput of MIFC has high potential for increasing the amount and accuracy of environmental monitoring, such as for plant-pollinator interactions, fossil samples, air, water or food quality that currently rely on manual microscopic methods. Automated recognition of particles and cells is also possible, when MIFC is combined with deep-learning computational techniques. Furthermore, various fluorescence dyes can be used to stain specific parts of the cell to highlight physiological and chemical features including: vitality of pollen or algae, allergen content of individual pollen, surface chemical composition (carbohydrate coating) of cells, DNA- or enzyme-activity staining. Here, we outline the great potential for MIFC in environmental research for a variety of research fields and focal organisms. In addition, we provide best practice recommendations.

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Series: Cytometry. Part A
ISSN: 1552-4922
ISSN-E: 1552-4930
ISSN-L: 1552-4922
Volume: 101
Issue: 9
Pages: 782 - 799
DOI: 10.1002/cyto.a.24658
Type of Publication: A2 Review article in a scientific journal
Field of Science: 1181 Ecology, evolutionary biology
1182 Biochemistry, cell and molecular biology
1172 Environmental sciences
Funding: The authors thank the German Research Foundation for support via the iDiv Flexpool Funding projects Grant Number: 34600865-16 (“Kick-off-Meeting PolDiv”), Grant Number: 34600830-13, (“PolDiv”-Project) and Grant Number: RA-373/20 (iCyt - Support Unit). Susanne Dunker, Patrick Mäder and Silvio Erler were further supported by the Federal Ministry of Food and Agriculture (BMEL) via the project “NutriBee” (Grant Number: 2819NA066, 2819NA102, 2819NA106), based on a decision of the parliament of the Federal Republic of Germany via the Federal Office for Agriculture and Food (BLE) under the Federal Programme for Ecological Farming and Other Forms of Sustainable Agriculture (BÖLN). Katrin Wendt-Potthoff was supported by the BMBF project MikroPlaTaS (grant number 02WPL1448A). The authors thank Wolfgang Osswald for providing honey samples for a proof-of-concept study. Open Access funding enabled and organized by Projekt DEAL.
Dataset Reference: The raw data (.rif-files) of the figures presented in this study are available via
Copyright information: © 2022 The Authors. This is an open access article under the terms of the Creative Commons Attribution-NonCommercial License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited and is not used for commercial purposes.