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An automated workflow for fungal cell counting, cell size and data analysis: enhancing throughput and accuracy with the cell analysis and counting tool using ilastik software (caactus).

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Title: An automated workflow for fungal cell counting, cell size and data analysis: enhancing throughput and accuracy with the cell analysis and counting tool using ilastik software (caactus).
Authors: Scheler J; Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, Schöpfstraße 41, Innsbruck, 6020, Tyrol, Austria. jakob.scheler@i-med.ac.at.; Department of Medicine I, Gastroenterology, Hepatology, Endocrinology & Metabolism, Medical University of Innsbruck, Anichstraße 35, Innsbruck, 6020, Tyrol, Austria. jakob.scheler@i-med.ac.at., Kutra D; Cell biology and biophysics, European Molecular Biology Laboratory (EMBL), Meyerhofstraße 1, Heidelberg, 69117, Baden-Württemberg, Germany., Beliveau V; Institute for Human Genetics, Medical University of Innsbruck, Schöpfstraße 24, Innsbruck, 6020, Tyrol, Austria., Seiler J; Department of Statistics, University of Innsbruck, Universitätsstraße 15, Innsbruck, 6020, Tyrol, Austria., Pröll S; Digital Cadiology Lab, University Clinic of Internal Medicine III, Medical University of Innsbruck, Anichstraße 35, Innsbruck, 6020, Tyrol, Austria., Sittel H; Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, Schöpfstraße 41, Innsbruck, 6020, Tyrol, Austria., Nowak-Rainer A; Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, Schöpfstraße 41, Innsbruck, 6020, Tyrol, Austria., Holzer H; Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, Schöpfstraße 41, Innsbruck, 6020, Tyrol, Austria., Lass-Flörl C; Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, Schöpfstraße 41, Innsbruck, 6020, Tyrol, Austria., Binder U; Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, Schöpfstraße 41, Innsbruck, 6020, Tyrol, Austria. ulrike.binder@i-med.ac.at.
Source: BMC microbiology [BMC Microbiol] 2026 May 13; Vol. 26 (1). Date of Electronic Publication: 2026 May 13.
Publication Type: Journal Article
Journal Info: Publisher: BioMed Central Country of Publication: England NLM ID: 100966981 Publication Model: Electronic Cited Medium: Internet ISSN: 1471-2180 (Electronic) Linking ISSN: 14712180 NLM ISO Abbreviation: BMC Microbiol Subsets: MEDLINE
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  Data: <searchLink fieldCode="AU" term="%22Scheler+J%22">Scheler J</searchLink>; Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, Schöpfstraße 41, Innsbruck, 6020, Tyrol, Austria. jakob.scheler@i-med.ac.at.; Department of Medicine I, Gastroenterology, Hepatology, Endocrinology & Metabolism, Medical University of Innsbruck, Anichstraße 35, Innsbruck, 6020, Tyrol, Austria. jakob.scheler@i-med.ac.at.<br /><searchLink fieldCode="AU" term="%22Kutra+D%22">Kutra D</searchLink>; Cell biology and biophysics, European Molecular Biology Laboratory (EMBL), Meyerhofstraße 1, Heidelberg, 69117, Baden-Württemberg, Germany.<br /><searchLink fieldCode="AU" term="%22Beliveau+V%22">Beliveau V</searchLink>; Institute for Human Genetics, Medical University of Innsbruck, Schöpfstraße 24, Innsbruck, 6020, Tyrol, Austria.<br /><searchLink fieldCode="AU" term="%22Seiler+J%22">Seiler J</searchLink>; Department of Statistics, University of Innsbruck, Universitätsstraße 15, Innsbruck, 6020, Tyrol, Austria.<br /><searchLink fieldCode="AU" term="%22Pröll+S%22">Pröll S</searchLink>; Digital Cadiology Lab, University Clinic of Internal Medicine III, Medical University of Innsbruck, Anichstraße 35, Innsbruck, 6020, Tyrol, Austria.<br /><searchLink fieldCode="AU" term="%22Sittel+H%22">Sittel H</searchLink>; Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, Schöpfstraße 41, Innsbruck, 6020, Tyrol, Austria.<br /><searchLink fieldCode="AU" term="%22Nowak-Rainer+A%22">Nowak-Rainer A</searchLink>; Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, Schöpfstraße 41, Innsbruck, 6020, Tyrol, Austria.<br /><searchLink fieldCode="AU" term="%22Holzer+H%22">Holzer H</searchLink>; Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, Schöpfstraße 41, Innsbruck, 6020, Tyrol, Austria.<br /><searchLink fieldCode="AU" term="%22Lass-Flörl+C%22">Lass-Flörl C</searchLink>; Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, Schöpfstraße 41, Innsbruck, 6020, Tyrol, Austria.<br /><searchLink fieldCode="AU" term="%22Binder+U%22">Binder U</searchLink>; Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, Schöpfstraße 41, Innsbruck, 6020, Tyrol, Austria. ulrike.binder@i-med.ac.at.
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