Bi9393 Analytical cytometry

Faculty of Science
Autumn 2025
Extent and Intensity
2/0/0. 2 credit(s) (fasci plus compl plus > 4). Type of Completion: zk (examination).
In-person direct teaching
Teacher(s)
doc. Mgr. Karel Souček, Ph.D. (lecturer)
prof. Mgr. Lukáš Kubala, Ph.D. (lecturer)
doc. RNDr. Alena Hyršlová Vaculová, Ph.D. (lecturer)
Mgr. Hana Polášek-Sedláčková, Ph.D. (lecturer)
Guaranteed by
doc. Mgr. Karel Souček, Ph.D.
Department of Experimental Biology – Biology Section – Faculty of Science
Contact Person: doc. Mgr. Karel Souček, Ph.D.
Supplier department: Department of Experimental Biology – Biology Section – Faculty of Science
Timetable
Thu 8:00–9:50 BFU
Prerequisites
No limitation for enrollment.
Course Enrolment Limitations
The course is also offered to the students of the fields other than those the course is directly associated with.
fields of study / plans the course is directly associated with
there are 8 fields of study the course is directly associated with, display
Course objectives
At the end of the course, students will be able to: - understand the basic principles and applications of modern methods of analytical cytometry such as flow cytometry, cell separation, light digital microscopy; understand the basic principles of data analysis, interpretation and presentation.
Learning outcomes
The student will learn detailed principles of flow cytometry and fluorescent microscopy, including practical applications of these methodologies.
Syllabus
General introduction to flow cytometry - basic principles and development of technology (principles of flow cytometry and sorting, fluorescence - sources of excitation, optical systems and methods of fluorescence detection - signal processing and compensation - visualization, analysis and software processing of data). Biological applications of flow cytometry - cell biology (nucleic acid analysis, analysis of cell functions, principle and practical possibilities of multiparameter analyses) - cytogenetics - hydrobiology (Karel Souček, 5 lectures). Flow cytometry methods in the study of cell death: examples of selected methods, principles, practical applications, interpretation, comparison, one- and multi-color analyses (Alena Hyršlová Vaculová, 1 lecture) • Application of flow cytometry in clinical immunology and hematology – immunophenotyping, functional tests of immune cells, lymphocyte activation, phagocyte activation, microbicidal activity of phagocytes, determination of platelet functional properties (Lukáš Kubala, 2 lectures) • Principles of light and digital microscopy (Hana Polášek-Sedláčková, 3 lectures) - principles of optical microscopy (magnification vs. resolution, objectives and their parameters, optical aberrations and correction of objectives), microscopic techniques (light field, dark field, phase contrast, Normansky contrast), visualization of cellular processes (staining methods, fluorescence probes), principles of fluorescence microscopy. - Wide-field fluorescence microscopy, confocal fluorescence microscopy (laser scanning, rotating disk), introduction to high-content imaging, principles of super-resolution microscopy (SIM, STED, PALM, MINFLUX), study of protein dynamics (time-lapse, FRAP, FCS, FLIM, FRET, microirradiation). - Principles of digital microscopy, digital camera (sensitivity vs. resolution, quantum efficiency, dynamic range and bit depth), digital image, principles of image analysis (background correction, deconvolution, segmentation, particle analysis), artificial intelligence in image analysis, principles of image integrity and principles.
Literature
    recommended literature
  • Practical Flow Cytometry
  • Flow Cytometry: Instrumentation and Data Analysis
  • - The Handbook of Flow Cytometry Methods - Current Protocols in Cytometry
Teaching methods
The course will be based mainly on lectures and discussions about them. The lectures will clarify the principles and methods of basic data analysis for individual methodologies.
Assessment methods
Exam Each student will be required to present a short seminar, the topic of which will be consulted with the lecturer and will relate to the focus of the course. Based on the evaluation of the seminar itself, it will also be reflected in the overall grade by 25%. The course will end with an exam in the form of a test summarizing the material for the whole semester. The result of the test will make up 75% of the total evaluation.
Náhradní absolvování
In the case of a study stay abroad, the course may be completed in an alternative form upon agreement with the course guarantor.
Language of instruction
Czech
Further comments (probably available only in Czech)
Study Materials
The course is taught annually.
Information on course enrolment limitations: Na předmět se vztahuje povinnost registrace, bez registrace může být znemožněn zápis předmětu!
Teacher's information
Klíčová literatura a přehledy Cossarizza A. et al. Guidelines for the use of flow cytometry and cell sorting in immunological studies (3rd Edition). Eur J Immunol. 2021. https://doi.org/10.1002/eji.202070126 Nolan J., Condello D. Spectral Flow Cytometry: The Current State and Future. Cytometry A. 2023. https://doi.org/10.1002/cyto.a.24682 Hennig C. et al. High-dimensional flow cytometry data: goldmine or fool’s gold? Cytometry A. 2024. https://doi.org/10.1002/cyto.a.24948 Barteneva N.S., Vorobjev I.A. Imaging Flow Cytometry: Development, Present and Future. Cytometry A. 2024. https://doi.org/10.1002/cyto.a.24840 Maecker H.T. et al. OMIP Collection (Optimized Multicolor Immunofluorescence Panels). Cytometry A. (průběžně aktualizované). https://onlinelibrary.wiley.com/journal/15524930 Standardy a metodiky MIFlowCyt: Minimum Information about a Flow Cytometry Experiment. ISAC Recommendation. https://isac-net.org/page/miflowcyt Welsh J.A. et al. MIFlowCyt-EV: Minimum Information for Reporting Extracellular Vesicle Flow Cytometry Experiments. J Extracell Vesicles. 2020. https://doi.org/10.1080/20013078.2020.1713526 ICCS Quality and Standards Committee – Flow Cytometry QC and Standardization Resources. https://www.cytometry.org/standards/ Profesní organizace a komunity ISAC – International Society for Advancement of Cytometry. https://isac-net.org CSAC – Česká společnost pro analytickou cytometrii. https://csac.cz
The course is also listed under the following terms Autumn 2007 - for the purpose of the accreditation, Autumn 2010 - only for the accreditation, Autumn 2006, Autumn 2007, Autumn 2008, Autumn 2009, Autumn 2010, Autumn 2011, Autumn 2011 - acreditation, Autumn 2012, Autumn 2013, Autumn 2014, Autumn 2015, Autumn 2016, autumn 2017, Autumn 2018, Autumn 2019, Autumn 2020, autumn 2021, Autumn 2022, Autumn 2023, Autumn 2024.
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