Vurderingsordning

Faglig innhold

BI8060 gives an overview of bio-optical techniques and will be divided into 3 parts. Part 1: Starts with RGB photographic techniques to obtain information needed. To do so, we first go through photographic techniques such as exposure time, aperture settings (field of depth), camera sensitivity (ISO settings) and use of lenses for optimal information. This is followed by illumination techniques to obtain contrast, scattered light, even illumination etc. Further, we will proceed with underwater hyperspectral imaging to obtain optical finger prints of organisms (full reflectance spectrum per image pixel). Part 2 comprises bio-optical techniques such as spectral absorption, transmittance, reflectance, fluorescence and bioluminescence. This information can be derived from microscopes in the lab to remote sensing of habitats and ocean colour information from satellites. Part 3 focuses on pigment information from plants, algae and marine invertebrates.

Læringsutbytte

Imaging optics: We will go through photographic techniques, illumination and underwater hyperspectral imaging. Interpretation of this will be detailed in the bio-optical part and pigment part of the curriculum. Bio-optics: Light absorption- and utilization characteristics in microalgae, macroalgae and marine invertebrates. Chemo-taxonomically differences in pigmentation to elucidate taxonomical and functional differences between algal classes/pigment groups. This information will be put together in a taxonomic (chemotaxonomy), phylogenetic (different evolutionary routes, endosymbiosis), ecological (adjustments to different habitats) and physiological (adaptation and acclimation to key environmental variables) context. Demonstration of different bio-optical measuring techniques (spectroradiometer, spectrophotometer, spectrofluorometer) for the measurement of spectral absorption- and attenuation coefficients in organisms and in water (differentiation of water types and different optical components), light climate (irradiance, spectral irradiance, day length), in vivo absorption coefficients (to estimate absorbed quanta), photosystem II specific fluorescence excitation spectra (fraction of absorbed quanta reaching photosystem II), measurement of difference spectra. Pigments: The use of HPLC (high precision liquid chromatography) to isolate pigments will be demonstrated. Extraction, identification and quantification of these pigments will also be demonstrated and is an important part of the curriculum. Skills obtained: Understanding of the relationship between chemical composition in organisms and their bio-optical signature in Nature. Understanding basic optical principles. Understanding how to interpret bio-optical data & corresponding signatures. Understanding marine organism pigmentation routes & evolution.

Læringsformer og aktiviteter

The first week of lectures will be followed by 3 weeks were students go through lectures/demonstrations/reading the curriculum to provide 3 students reports (dependent of student numbers). There will be three groups (depend on how many students attending): A) Pigments, B) Under water bio-optics and C) Under water photographic techniques. The student’s reports will be presented by all students and should give an overview of the curriculum. Obligatory activities: Attending lectures, group work, workshops and presentations. Where and when: Auditorium/Gunnerus room at Trondhjem Biologiske Stasjon, Bynesveien 46. The course will be divided into theory, group work, presentations and demonstrations of selected methodology. The course is offered every alternate year in Oct-Nov (2021, 2023) Course duration: Week 44-46 (intensive course):

Obligatoriske aktiviteter

• Godkjent teori, øvinger og lab

Mer om vurdering

Oral exam with grade: Passed/not passed Details we be notified in Black Board 1 month before course start. Theory, teaching material and group presentations will be in English. The student group presentations will be presented, discussed and evaluated until accepted as part of the curriculum for all students (presentations will not be graded, just accepted/not accepted).

Spesielle vilkår

Kursmateriell

Geir Johnsen will hold the major lectures in bio-optics with basis of the two curriculum books Roy et al. (2011) & Watson & Zielinski (2013). Overview of which chapters in the books and selected papers will be added. Several scientific papers will also be part of the curriculum. Books in curriculum (students should have these in hand prior to course start): Watson J and Zielinski O (2013). Subsea Optics and Imaging. Woodhead Publ Ser in electronics and Optical materials 46. Woodhead Publishing Ltd., Cambridge, UK, 608 pp Roy S, Llewellyn C, Egeland ES, Johnsen G (2011). Phytoplankton pigments: Updates on Characterization, Chemotaxonomy and Applications in Oceanography. Cambridge University Press. Cambridge Environmental Chemistry Series. Cambridge, UK. Pp 845. ISBN: 978110700066-7 For those that will start reading prior to the course start: Read in Roy et al. (2011): Chapter 1, 11,13 & 14. Read in Watson & Zielinski: Chapter 1, 2, 3, 4 & 20.