Course: Techniques of microscopy and image analysis for biologists

« Back
Course title Techniques of microscopy and image analysis for biologists
Course code KMB/223E
Organizational form of instruction Lecture + Lesson
Level of course Doctoral
Year of study not specified
Frequency of the course In academic years starting with an even year (e.g. 2018/2019), in the summer semester.
Semester Summer
Number of ECTS credits 5
Language of instruction English
Status of course Compulsory-optional
Form of instruction Face-to-face
Work placements This is not an internship
Recommended optional programme components None
Lecturer(s)
  • Lazar Josef, Mgr. Ph.D.
  • Vancová Marie, RNDr. Ph.D.
  • Weyda František, doc. RNDr. CSc.
  • Sehadová Hana, Mgr. Ph.D.
Course content
Content of lectures: 1) Introduction - history of microscopy, optic apparatus, types of objectives, types of microscopes 2) Classical light microscopy + Keller illumination and techniques of contrast - Nomarski contrast (DIC), Hoffman contrast (HMC), phase contrast, dark field 3) Fluorescence microscopy - principle, overview of fluorophores, types of microscopes, application 4) Confocal microscopy - principle, types of microscopes, application - FRAP, FRET, multiphotone and TIRF microscopy 5) Superresolution techniques - PALM, STORM, STED, SIM, Airy scan 6) Luminescence microscopy - principle, application 7) Detection of the light signal - CCD and EM-CCD cameras, photomultipliers, clarification of the HDR and deconvolution 8) Insight into the electron microscopy (Ing. Jana Nebesářová, CSc.) 9)Techniques of macro photography (Doc. RNDr. František Weyda, CSc.) 10) Image analysis_1 - software Adobe Photoshop 11) Image analysis_2 - software FIJI (ImageJ) 12) Image analysis_3 - software IMARIS a XuvStitch Content of practicals: 1) Practical demonstration of the microscope adjustment (Keller illumination, Nomarski contrast) - (Microscopy lecture room) 2) Demonstration of the fluorescence microscope - (Bioscience Imaging and Histology Unit) 3) Demonstration of the confocal microscope - (Bioscience Imaging and Histology Unit) 4) Excursion to the Olympus company (Prague) or demonstration of the microscopes in the University) 5) Demonstration of the luminescence microscope - (Bioscience Imaging and Histology Unit) 6) Excursion to the Laboratory of electron microscopy 7) Demonstration of macro photography taking 8) Image analysis in the Adobe Photoshop software_part 1 - (Computer lecture room) 9) Image analysis in the Adobe Photoshop software_part 2 - (Computer lecture room) 10) Image analysis in the Adobe Photoshop software_part 3 - (Computer lecture room) 11) Image analysis in the FIJI (ImageJ) software - (Computer lecture room) 12) Demonstration of the IMARIS software - (Bioscience Imaging and Histology Unit)

Learning activities and teaching methods
Monologic (reading, lecture, briefing), Dialogic (discussion, interview, brainstorming), Monitoring, Demonstration, Excursion, Work with multi-media resources (texts, internet, IT technologies), Practical training
  • Preparation for classes - 30 hours per semester
  • Class attendance - 50 hours per semester
  • Field trip - 4 hours per semester
  • Preparation for credit - 20 hours per semester
  • Preparation for exam - 20 hours per semester
Learning outcomes
Students will learn the principles of basic microscopy techniques and gain knowledge about the image analyses of biological material usable for scientific publication.
Students will learn who manipulate the bright-field, fluorescence, and confocal microscope, bioluminescence microscope and the principles of superresolution and electron microscopy. They become also acquainted with the less common microscopes by several excursion and thus they will obtain a comprehensive idea about the recent microscopy. They will be train how to adjust the light pathway in different types of microscopes to be able independently manipulate any type of bright-flied and fluorescence microscopes. Students should be able to choose the best method for visualization of variable biological objects. They will learn the basic common software for digital image analysis such are Adobe Photoshop and ImageJ.
Prerequisites
No special requirements.

Assessment methods and criteria
Oral examination, Student performance assessment, Systematic student observation, Test

Requirements for credit: 1) presence on the practical trainings (maximum one absence) 2) independent adjustment of the bright-field and fluorescence pathway in a microscope 3) successful passing of final test Requirements for oral exam: 1) obtaining of the credit
Recommended literature
  • http://olympus.magnet.fsu.edu/primer/techniques/confocal/applications/fretintro.html.
  • http://olympus.magnet.fsu.edu/primer/techniques/confocal/index.html.
  • http://olympus.magnet.fsu.edu/primer/techniques/fluorescence/fluorhome.html.
  • https://www.microscopyu.com/techniques/confocal.
  • https://www.microscopyu.com/techniques/fluorescence.
  • Nathan S. Claxton, Thomas J. Fellers, and Michael W. Davidson Laser Scanning Confocal Microscopy.


Study plans that include the course
Faculty Study plan (Version) Category of Branch/Specialization Recommended year of study Recommended semester
Faculty: Faculty of Science Study plan (Version): Infection Biology (1) Category: Biology courses - Recommended year of study:-, Recommended semester: Summer
Faculty: Faculty of Science Study plan (Version): Physiology and Developmental Biology (1) Category: Biology courses - Recommended year of study:-, Recommended semester: Summer
Faculty: Faculty of Science Study plan (Version): Physiology and Developmental Biology (1) Category: Biology courses - Recommended year of study:-, Recommended semester: Summer
Faculty: Faculty of Science Study plan (Version): Molecular and Cell Biology and Genetics (1) Category: Biology courses - Recommended year of study:-, Recommended semester: Summer
Faculty: Faculty of Science Study plan (Version): Molecular and Cell Biology and Genetics (1) Category: Biology courses - Recommended year of study:-, Recommended semester: Summer