Bi4170 Optical contrast and imaging methods

Faculty of Science
spring 2012 - acreditation

The information about the term spring 2012 - acreditation is not made public

Extent and Intensity
0/2. 2 credit(s) (plus extra credits for completion). Type of Completion: k (colloquium).
Teacher(s)
RNDr. Šárka Mašová, Ph.D. (seminar tutor)
Guaranteed by
RNDr. Božena Koubková, Ph.D.
Department of Botany and Zoology – Biology Section – Faculty of Science
Contact Person: RNDr. Šárka Mašová, Ph.D.
Supplier department: Department of Botany and Zoology – Biology Section – Faculty of Science
Prerequisites (in Czech)
Bi1050 Biological techniques || Bi2302 Zoological microtechnique || Bi1301 Microscopic Techniques
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
Course objectives
At the end of the course students should be able to individually choose an appropriate method for microscopic observation of different samples, document them using pen drawings and microphotographs and subsequently process these in a graphics editor.
Syllabus
  • Introduction to contrast-enhancing techniques for optical microscopy: Specimens types and applicable imaging techniques.
  • Darkfield contrast = Darkfield (or dark ground) microscopy: Alignment of a transmitted darkfield condenser; illustrations of the effects of darkfield and brightfield illumination of protozoan samples and in a whole mount metazoan specimens; advantages of darkfield microscopy in combination with fluorescence microscopy.
  • Phase contrast: Interaction of light waves with phase specimens, wave interactions in phase contrast microscopy, the phase contrast microscope, positive and negative phase contrast systems, interpretation of phase contrast images. Imaging of several specimens with both positive and negative phase contrast optical systems.
  • Differential Interference Contrast (DIC)= Nomarski Interference Contrast (NIC) or Nomarski microscopy: The light path, comparison of phase contrast and DIC microscopy, optical staining of transparent specimens, interpretation of DIC images, advantages and disadvantages. Set up of the transmitted DIC microscope (Olympus type). Imaging of several specimens with DIC optical systems. First acquaintance with microscopy image analysis (Stream Motion) - simple taking photos of specimens under DIC.
  • Photomicrography - digital imaging 1: Exposure, image contrast, brightness and color balance, ISO, filters, exposure characteristic curves, autofocus, dynamic range, Olympus DP-70 camera system, basic properties of digital images.
  • Photomicrography - digital imaging 2: Multiple Image Alignment (mia) and Extended Focal Imaging (efi) in digital image analysis (Stream Motion).
  • Fundamentals of video imaging: video signal generation, standard scanning rates, flicker.
  • Classical morphometry: Measurement of length, area, perimeter and numbering in digital image analysis (Stream Motion).
  • Digital image processing: Noise, blur, background intensity variations, brightness, contrast, general pixel value distribution (histogram profile), shadowed regions, bright features and areas of intermediate pixel intensity.
  • Scientific drawing 1: History of line drawings and scientific drawing, methods of ink drawings, drawing tube, appropriate tools.
  • Scientific drawing 2: Using software (Adobe Illustrator, Adobe Photoshop) and hardware (Tablet Pen) to modern scientific drawing and final processing.
  • Work on the plate for successful completion of the course.
Literature
    recommended literature
  • http://www.olympusmicro.com
  • http://micro.magnet.fsu.edu/
  • http://www.microscopyu.com/
  • http://resources.olympus-europa.com//micro/catalogs/C12570450051DE755F21AA2B8F00BA75C12571DA0047808A_Basics_of_Light_microscopy.pdf
  • http://www.physics.muni.cz/~kubena/PDF/Modmetv78.pdf
  • STEPHEN R. WILLIAMS: SCIENTIFIC DRAWING IN BIOLOGY (https://kb.osu.edu/dspace/bitstream/handle/1811/1947/V17N06_205.pdf?sequence=1)
  • Brian J. Ford 1993: Images of science: a history of scientific illustration. Oxford University Press, 208
  • Elaine R. S. Hodges,Guild of Natural Science Illustrators (U.S.) 2003: The Guild handbook of scientific illustration. John Wiley and Sons, 656
  • Mary Helen Briscoe 1996: Preparing scientific illustrations: a guide to better posters, presentations, and publications. Springer, 204
  • The microscope, and its revelations By William Benjamin Carpenter, Francis Gurney Smith 1856 http://books.google.com/books?vid=OCLC61578361&id=ZXMAAAAAMAAJ&pg
  • The Microscope and Its Revelations By William Benjamin Carpenter 1883 http://books.google.com/
  • KNOZ, Jan and Věra OPRAVILOVÁ. Základy mikroskopické techniky. 1. vyd. Brno: Masarykova univerzita, 1992, 195 s. ISBN 8021004738. info
  • Charles Oliver Coleman 2003: "Digital inking": How to make perfect line drawings on computers. Org. Divers. Evol. 3, Electr. Suppl. 14: 1 - 14 (http://senckenberg.de/odes/03-14.htm)
  • Jason D. Williams A short guide for production of line-drawings with Adobe Illustrator® (www.bio.net/bionet/mm/annelida/.../WilliamsIllustratorWorkshop.pdf)
Teaching methods
lectures and practical laboratory exercises
Assessment methods
For successful completion of the course, passing the final written test with 60% success rate is necessary. Electronic submission of prepared plate of pictures in A4 size, including numbering and scales bars. Each plate will contain from 5 to 10 microphotographs at 300 dpi or pen drawings at 1200 dpi. Images will be acquired at the exercises, photographed or drawn objects can be arbitrary, ideally the studied organism should be related to the student's final work, but it is not necessary. Unless stated otherwise, 80% attendance at the exercises is mandatory.
Language of instruction
Czech
Further Comments
The course is taught annually.
The course is taught: every week.
The course is also listed under the following terms Autumn 2012, Autumn 2013, Autumn 2014, Autumn 2015, autumn 2021, Autumn 2022.