Course detail
Microscopic Imaging Technology
FEKT-FMZTAcad. year: 2012/2013
The course will be a detailed overview of the principle and practice of light microscopy. The emphasis of the course will be on the correct and appropriate use of the light microscope. Course covers optical microscope theory and also advanced optical and imaging techniques.
Language of instruction
Czech
Number of ECTS credits
6
Mode of study
Not applicable.
Guarantor
Learning outcomes of the course unit
Practical knowledge of physical principle, microscopy design concept and microscopic image processing in the field of light microscopy.
Prerequisites
The subject knowledge on the Bachelor´s degree level is requested.
Co-requisites
Not applicable.
Planned learning activities and teaching methods
Teaching methods depend on the type of course unit as specified in the article 7 of BUT Rules for Studies and Examinations.
Assesment methods and criteria linked to learning outcomes
Requirements for completion of a course are specified by a regulation issued by the lecturer responsible for the course and updated for every year.
Course curriculum
Fundamentals of wave and geometry optic.
Eye as an optical system.
Quantitative description of the optical system.
Basic microscopy design concept.
CCD and CMOS sensors.
Dark field microscopy.
Phase contrast microscopy.
Stereomicroscopy.
Nomarsky differential interference contrast microscopy.
Hoffman modulation contrast microscopy.
Fluorescence microscopy.
Laser scanning (confocal) microscopy.
2-photon and multi-photon microscopy.
Optical coherent microscopy.
Application of light microscopic principles in ophthalmology, dermatology, endoscopy.
Basic techniques in microscopic image processing.
Eye as an optical system.
Quantitative description of the optical system.
Basic microscopy design concept.
CCD and CMOS sensors.
Dark field microscopy.
Phase contrast microscopy.
Stereomicroscopy.
Nomarsky differential interference contrast microscopy.
Hoffman modulation contrast microscopy.
Fluorescence microscopy.
Laser scanning (confocal) microscopy.
2-photon and multi-photon microscopy.
Optical coherent microscopy.
Application of light microscopic principles in ophthalmology, dermatology, endoscopy.
Basic techniques in microscopic image processing.
Work placements
Not applicable.
Aims
Knowledge of the light microscopy and its medical and biologic applications. Practical knowledge about microscopic image acquisition and processing.
Specification of controlled education, way of implementation and compensation for absences
Limitations of controlled teaching and its procedures are specified by a regulation issued by the lecturer responsible for the course and updated for every year.
Recommended optional programme components
Not applicable.
Prerequisites and corequisites
Not applicable.
Basic literature
D. B. Murphy Fundamentals of light microscopy and electronic imaging, Wiley-Liss, 2001
P. Mouroulis Visual Instrumentation, McGraw-Hill, 1999
P. Mouroulis Visual Instrumentation, McGraw-Hill, 1999
Recommended reading
Not applicable.
Classification of course in study plans
Type of course unit
Lecture
26 hod., optionally
Teacher / Lecturer
Syllabus
1. Wave and geometry optic - basic optical laws and phenomenon (interference, aberration, diffraction, polarization), optical components. Interaction of light with tissue - absorption, diffraction, attenuation, fluorescence, phosphorescence, autofluorescence.
2. Eye as an optical system, which participate on imaging process. Eye anatomy. Some rules connected to vision process (scotopic/photopic vision, Weber - Fencher law, Stiles - Crawford effect, darkness adaptation)
3. Description of the optical system. Quantitative evaluation of these systems (optical transfer function, modulation transfer function, Strehl ratio, wavefront aberration)
4. Basic microscopy design concept. Description and properties of particular components - holder, eyepiece, lens, condenser, light sources. Examples of microscopes.
5. Analog and digital microscopy. Light detection - CCD and CMOS sensors and their properties (signal-to-noise ratio, spatial resolution, temporal resolution). Videomicroscopy.
6. Upright and inverted microscopy - differences. Dark field microscopy - principle, design, applications. Phase contrast microscopy - physical and mathematic description, design, application.
7. Stereomicroscopy - principle, design, image processing. Nomarsky differential interference contrast (DIC) microscopy, Hoffman modulation contrast (HMC) microscope.
8. Fluorescence microscopy - description of fluorescence, fluorescence dyes, principles, microscope design.
9. Laser scanning microscopy, laser scanning confocal microscopy - principles, spatial resolution. Fluorescence scanning microscopy, 2-photon and mulit-photon microscopy.
10. Optical coherent microscopy and tomography - phenomenon of light interference for tomographic imaging. Systems working in temporal and frequency domain. Applications.
11.Application of light microscopic principles in ophthalmology, dermatology, endoscopy.
12. Basic techniques in microscopic image processing - disparity maps in steremince Energy Transfer (FRET), Stimulated Emission Depletion (STED), holographic microscopy.
12. Preparation of microscopic samples. Live cell imaging - heart cell contractility. Application of light microscopic principles in ophthalmology, dermatology, endoscopy.
13. Basic techniques in microscopic image processing - disparity maps in steremicroscopy, deconvolution, formation of focus image from different focus images sequence.
2. Eye as an optical system, which participate on imaging process. Eye anatomy. Some rules connected to vision process (scotopic/photopic vision, Weber - Fencher law, Stiles - Crawford effect, darkness adaptation)
3. Description of the optical system. Quantitative evaluation of these systems (optical transfer function, modulation transfer function, Strehl ratio, wavefront aberration)
4. Basic microscopy design concept. Description and properties of particular components - holder, eyepiece, lens, condenser, light sources. Examples of microscopes.
5. Analog and digital microscopy. Light detection - CCD and CMOS sensors and their properties (signal-to-noise ratio, spatial resolution, temporal resolution). Videomicroscopy.
6. Upright and inverted microscopy - differences. Dark field microscopy - principle, design, applications. Phase contrast microscopy - physical and mathematic description, design, application.
7. Stereomicroscopy - principle, design, image processing. Nomarsky differential interference contrast (DIC) microscopy, Hoffman modulation contrast (HMC) microscope.
8. Fluorescence microscopy - description of fluorescence, fluorescence dyes, principles, microscope design.
9. Laser scanning microscopy, laser scanning confocal microscopy - principles, spatial resolution. Fluorescence scanning microscopy, 2-photon and mulit-photon microscopy.
10. Optical coherent microscopy and tomography - phenomenon of light interference for tomographic imaging. Systems working in temporal and frequency domain. Applications.
11.Application of light microscopic principles in ophthalmology, dermatology, endoscopy.
12. Basic techniques in microscopic image processing - disparity maps in steremince Energy Transfer (FRET), Stimulated Emission Depletion (STED), holographic microscopy.
12. Preparation of microscopic samples. Live cell imaging - heart cell contractility. Application of light microscopic principles in ophthalmology, dermatology, endoscopy.
13. Basic techniques in microscopic image processing - disparity maps in steremicroscopy, deconvolution, formation of focus image from different focus images sequence.
Laboratory exercise
26 hod., compulsory
Teacher / Lecturer
Syllabus
1. Introductory laboratory - introduction to laboratory equipments, introduction to image acquisition and analysis software NIS - Elements.
2. Basic image operation in Matlab.
3. Stereomicroscopy, influence of illumination, disparity map.
4. Measurement of modulation transfer function using Nikon camera.
5. Image processing from confocal microscope.
6. Measurement of properties of fluorescent dye.
7. Microscopy with immerse objective, basic techniques in NIS-Elements.
8. Dark field and phase contrast microscopy.
9. Microscopy in polarization light, Malus law.
10. Measurement of light wavelength using microscope and interferometric approach.
11. Simulation in geometric optics.
12. Hartmann-Shack abberometry.
13. Free lab.
2. Basic image operation in Matlab.
3. Stereomicroscopy, influence of illumination, disparity map.
4. Measurement of modulation transfer function using Nikon camera.
5. Image processing from confocal microscope.
6. Measurement of properties of fluorescent dye.
7. Microscopy with immerse objective, basic techniques in NIS-Elements.
8. Dark field and phase contrast microscopy.
9. Microscopy in polarization light, Malus law.
10. Measurement of light wavelength using microscope and interferometric approach.
11. Simulation in geometric optics.
12. Hartmann-Shack abberometry.
13. Free lab.