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PhD Course, at Aarhus University Title: Zoological Imaging Purpose: To gain understanding and experience with principles and applications of different

imaging modalities and techniques in comparative physiology research. Time and location(s): Week 43 (24th – 28th October), 2016 First day: Please show up Monday 24th at 8:15am Building 1131, Room 127 (“Seminar room/Kaffestuen”) Zoophysiology, Department of Bioscience C. F. Møllers Allé 3 Aarhus University 8000 Aarhus C Denmark Different imaging systems used in the course are located at various university

departments in different parts of Aarhus. Please find map(s) of the University Campus and the University Hospital in Skejby

on the last pages. Practical information: Preparation before the course: Estimate total preparation time: 20-30 hours Course program and acquired data is available on: http://www.inside-zoo.com/401/login.php?redirect=/phd-course-2016-material.html

(password: Augustkrogh1929). Reading material: Text book: Smidt and Webb. 2010. Introduction to medical imaging. Physics,

engineering and clinical applications. Cambridge University Press (http://www.cambridge.org/us/academic/subjects/engineering/biomedical-engineering/introduction-medical-imaging-physics-engineering-and-clinical-applications?format=HB&isbn=9780521190657

Papers: We have collated a number of relevant reviews and primary articles (find

info in the program for the individual days). Software: Install ImageJ (https://imagej.nih.gov/ij/index.html) and try to become

somewhat acquainted (https://imagej.nih.gov/ij/docs/guide/index.html) with the software before the course

Introductory presentation: Participants are required to prepare a short talk (5 min)

to introduce their own work/projects on the first day of the course. Food: Coffee/Tea/Cake will be provided during the course. Lunch can be bought at

the university/hospital cafeterias.

Accommodation: See last page for info regarding accommodation

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Monday, 24th October 2016

Ultrasound (US) 8.15-9.00 Welcome, practical information, outline of the course 5 min participant project presentation Instructor(s): KH, HL, MP, TW Location: We will meet at Campus: Building 1131, Room 127 (“Seminar

room/Kaffestuen”) and then transfer together to Campus: Building 1222, Room 127 (“Biologiens Hus”)

9.00-9.45 Lecture: Ultrasound physics and technology Instructor: HL Location: Campus: Building 1222, Room 127 (“Biologiens Hus”) 10.00-10.45 Lecture: Introduction to Ultrasound imaging Instructor: HL Location: Campus: Building 1222, Room 127 (“Biologiens Hus”) 11.00- 11.45 Imaging for real (examples of imaging-research) Speaker: HL (Title: “Ultrasound in studies of Axolotl regeneration”) Location: Campus: Building 1222, Room 127 (“Biologiens Hus”) 12.00–13.00 Lunch break and transfer to Skejby hospital 13.00–14.45 Ultrasound: demonstration and exercises (Instructor: HL, KH) Instructor(s): HL, KH Location: Ultrasound lab at Skejby University Hospital 15.00–16.45 Ultrasound: Data analysis (Instructor: HL, KH) Instructor(s): HL, KH Location: Ultrasound lab at Skejby University Hospital 17.00–17.45 Imaging for real (examples of imaging-research) Speaker: TW (Title: “TW (Title: “How ultrasound techniques have helped to solve

cardiovascular problems in giraffes and snakes”) Location: Skejby University Hospital, “Konference rum” at Dept. of forensic

medicine (close to roof sign 5, 1st floor) 18.00-? Transfer back to the university – end of program Demonstration/exercises: Cardiac function is evaluated in Xenopus laevis during propofol and benzocaine anaesthesia. The use of M-mode, B-mode, Colour Doppler mode, Power Doppler mode and Pulsed-wave Doppler mode is covered. Acquisition of heart rate, flow velocity, pulse wave velocity, stroke volume and cardiac output is demonstrated in the software of the ultrasound machine (Vevo2100). The effect of the two applied anaesthetics is compared in terms of effect on cardiac function and how this may affect functional measurements. In the data analysis section acquisition of physiological parameters is demonstrated in freeware (ImageJ), and macro-based spatial and temporal sampling to increase tissue to blood contrast in animals with nucleated red blood cells is demonstrated.

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Reading for ultrasound session: Ultrasound background material: Smith and Webb. 2010. Introduction to medical imaging. Chap. 1 - General image characteristics, data acquisition and image reconstruction. p. 1-33. Smith and Webb. 2010. Introduction to medical imaging. Chap. 4 – Ultrasound Imaging. p 145- 203. Useful techniques in ultrasound studies: Tan et al. 2015. 3D Reconstruction of Chick Embryo Vascular Geometries Using Non-invasive High-Frequency Ultrasound for Computational Fluid Dynamics Studies. Ann Biomed Eng. 43:2780-93. https://www.ncbi.nlm.nih.gov/pubmed/?term=3D+Reconstruction+of+Chick+Embryo+Vascular+Geometries+Using+Non-invasive+High-Frequency+Ultrasound+for+Computational+Fluid+Dynamics+Studies Wasmeir et al. 2007. Reproducibility of transthoracic echocardiography in small animals using clinical equipment. Coron Artery Dis. 18: 283-91. https://www.ncbi.nlm.nih.gov/pubmed/17496492 TW Lecture (Mon 17-17.45): Jensen et al. 2010. How the python heart separates pulmonary and systemic blood pressures and blood flows. J Exp Biol 213: 1611-1617. https://www.ncbi.nlm.nih.gov/pubmed/?term=How+the+python+heart+separates+pulmonary+and+systemic+blood+pressures+and+blood+flows

Smerup, et al. 2016. The thick left ventricular wall of the giraffe heart normalises wall tension, but limits stroke volume and cardiac output. J Exp Biol 219: 457-463.

https://www.ncbi.nlm.nih.gov/pubmed/?term=The+thick+left+ventricular+wall+of+the+giraffe+heart+normalises+wall+tension%2C+but+limits+stroke+volume+and+cardiac+output

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Tuesday, 25th October 2016 Positron Emission Tomography (PET) 9.00-9.45 Lecture: PET principles and technology Instructor(s): AKOA Location: We will meet in Building 1131, Room 127 (“Seminar room/Kaffestuen”)

and walk together to Campus: 1540-K20 (the basement under Microbiology) 10.00-10.45 Lecture: Practical PET imaging Instructor(s): AKOA Location: Campus: 1540-K20 (the basement under Microbiology) 11.00- 11.45 Imaging for real (examples of imaging-research) Speaker: AKOA (Title: “Scanning in translational brain research on laboratory

animals”) Location: Campus: 1540-K20 (the basement under Microbiology) 12.00–13.00 Lunch break and transfer to PET-centre, Aarhus University Hospital,

Nørrebrogade 44 (A 10-15 min walk, guides: AKOA, KH) 13.00–13.45 PET-group1: Workshop: Radiochemistry (Instructor: SJ) 13.00–13.45 PET-group2: Workshop: The Cyclotron and related physics (Instructor: OLM) 14.00–15.00 PET-group 1 & 2: µPET/MR, demonstration (Instructor: MITS, KH) 15.00–15.15 Transfer to Campus (A 10-15 min walk, guide: KH) 15.30–16.45 PET: Data analysis Instructor(s): KH, HL Location: Campus: 1540-K20 (the basement under Microbiology) 17.00–17.45 Imaging for real (examples of imaging-research) Speaker: MB (Title: “PET in comparative physiology and medicine”) Location: Campus: 1540-K20 (the basement under Microbiology) 17.45 End of program Demonstration/exercises: Cerebral 18F-FDG-imaging of anaesthetised Wistar rat using a pre-clinical MR/PET system will be demonstrated. In the data analysis section the visualisation of the spatial distribution of 18F-FDG will be demonstrated, including measurements of standard uptake values (SUV) in the brain using ImageJ freeware. Reading for PET-session: Smith and Webb. 2010. Introduction to medical imaging. Chap. 3 – Nuclear medicine: Planar scintigraphy, SPECT and PET/CT. p 89 - 144. Phelps. 2000. Positron emission tomography provides molecular imaging of biological processes. -Proc Natl Acad Sci USA. 1;97(16):9226-33. https://www.ncbi.nlm.nih.gov/pubmed/10922074 Alstrup AKO and Winterdahl M. 2009. Imaging techniques in large animals. Scand J Lab Anim Sci 36(1):55–66.

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Wednesday, 26th October 2016 Computed Tomography (CT) 8.15-9.00 “Catch-up morning”: PET analysis continued Instructor(s): KH, HL Location: Campus: Building 1222, Room 127 (“Biologiens Hus”) 9.00-9.45 Lecture: CT physics and technology Instructor(s): KH Location: Campus: Building 1222, Room 127 (“Biologiens Hus”) 10.00-10.45 Lecture: Practical CT imaging Instructor(s): KH Location: Campus: Building 1222, Room 127 (“Biologiens Hus”) 11.00- 11.45 Imaging for real (examples of imaging-research) Speaker: KH (Title: “Zoological Imaging using CT (& MRI)”) Location Campus: Building 1222, Room 127 (“Biologiens Hus”) 12.00–13.00 Lunch break and transfer to Skejby hospital 13.00–14.45 CT: demonstration and exercises Instructor(s): KH, HL Location: Skejby University Hospital, “Konference rum, Afdl. C” (close to roof

sign 12, ground level) 15.00–16.20 CT: data analysis Instructor(s): KH, HL Location: Skejby University Hospital, “Konference rum” at Dept. of forensic

medicine (close to roof sign 5, 1st floor) 16.30–17.15 Imaging for real (examples of imaging-research) Speaker: TW (Title: “Flow separation in the anuran Conus”) Location: Skejby University Hospital, “Konference rum” at Dept. of forensic

medicine (close to roof sign 5, 1st floor) 18.00-? Transfer back to the university - end of program Demonstration/exercises: Anatomical imaging will be demonstrated using non-contrasted and contrast agent perfused freshwater turtles. The advantages of energy switching and dual energy procedures will be demonstrated using fossil samples. In the data analysis section the extraction of volumetric and density measurements will be demonstrated using freeware (ImageJ). The application of stereological techniques to CT data to acquire three-dimensional measurements of complex structures will also be demonstrated. Finally, basis material decomposition from dual energy data will be demonstrated. Reading for CT-session: CT background: Smith and Webb 2010. Introduction to medical imaging. Chap. 2 – X-ray planar radiography and computed tomography. p 34 - 88.

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Useful techniques in CT studies: Metscher. 2009. MicroCT for comparative morphology: simple staining methods allow high-contrast 3D imaging of diverse non-mineralized animal tissues. BMC Physiology 9:11 doi:10.1186/1472-6793-9-11. https://www.ncbi.nlm.nih.gov/pubmed/?term=MicroCT+for+comparative+morphology%3A+simple+staining+methods+allow+high-contrast+3D+imaging+of+diverse+non-mineralized+animal+tissues Pauwels et al. 2013. An exploratory study of contrast agents for soft tissue visualization by means of high resolution X-ray computed tomography imaging. J Microsc. 250: 21-31. https://www.ncbi.nlm.nih.gov/pubmed/?term=An+exploratory+study+of+contrast+agents+for+soft+tissue+visualization+by+means+of+high+resolution+X-ray+computed+tomography+imaging McCollough et al. 2011. Dual-energy algorithms and postprocessing techniques. In: T.R.C. Johnson et al. (eds.). Dual Energy CT in Clinical Practice, Medical Radiology. Springer-Verlag Berlin Heidelberg 2011. http://link.springer.com/chapter/10.1007%2F174_2010_36

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Thursday, 27th October 2016 Magnetic Resonance Imaging (MRI) 8.15-9.00 “Catch-up morning”: CT analysis continued Instructor(s): KH, HL Location: Campus: Building 1222, Room 127 (“Biologiens Hus”) 9.00-9.45 Lecture: MRI physics and technology Instructor: MCK Location: Campus: Building 1222, Room 127 (“Biologiens Hus”) 10.00-10.45 Lecture: MRI and safety Instructor: MCK Location: Campus: Building 1222, Room 127 (“Biologiens Hus”) 11.00- 11.45 Lecture: Hyperpolarized MRI Instructor: CL Location: Campus: Building 1222, Room 127 (“Biologiens Hus”) 12.00–13.00 Lunch break and transfer to Skejby hospital 13.00–13.45 MRI: demonstration of clinical 3T-MRI system (room t.b.a., Instructor: MCK, MP,

HL, KH) Instructor(s): MCK, MP, HL, KH Location: MR5: MR Research Centre, Skejby University Hospital 14.00–14.45 MRI: Demonstration of Hyperpolarized MRI Instructor(s): CL, MP, HL, KH Location: Basement: MR Research Centre, Skejby University Hospital 15.00–16.45 MRI: data analysis Instructor(s): MP, HL, KH Location: Skejby University Hospital, “Konference rum” at Dept. of forensic

medicine (close to roof sign 5, 1st floor) 17.00–17.45 Imaging for real (examples of imaging-research) Speaker: AH (Title: “Ultrasound in comparative physiology and medicine”) Location: Skejby University Hospital, “Konference rum” at Dept. of forensic

medicine (close to roof sign 5, 1st floor) 18.00-? Transfer back to the university - end of program Demonstration/exercises: Anatomical MRI (T1-, T2-, and proton weighted) will be demonstrated on a clinical 3T system on non-contrasted and contrast agent perfused turtles. Hyperpolarized MRI is demonstrated on a high-field 9.4 T system using hyperpolarized pyruvate in anaesthetised pythons; one fasting and one digesting ca. 48 h following after feeding (app. 25% of own body mass). In the data analysis section the extraction of volumetric measurements will be demonstrated using freeware (ImageJ) with particular focus on the soft tissue. The application of stereological techniques to MRI data to acquire three-dimensional measurements of complex structures will also be demonstrated.

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Reading for MRI-session: MRI background: Smith and Webb. 2010. Introduction to medical imaging. Chap. 5 – Magnetic resonance imaging (MRI). p 204 - 281. Plewes and Kucharczyk. 2012. Physics of MRI: A primer. J Magn Reson Imaging. 35(5):1038–54. https://www.ncbi.nlm.nih.gov/pubmed/?term=Plewes+DB%2C+Kucharczyk+W+(2012).+Physics+of+MRI Useful techniques in MRI studies: Ralph et al. 2012. Hyperpolarized 13C metabolic imaging using dissolution dynamic nuclear polarization. J Magn Reson Imaging. 36:1314-28. https://www.ncbi.nlm.nih.gov/pubmed/23165733

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Friday, 28th October 2016 Interactive PDF and 3D printing (US, CT, MRI, and PET-analysis continued) 8.15-9.00 “Catch-up morning”: MRI analysis continued Instructors: KH, HL Location: Campus: Building 1222, Room 127 (“Biologiens Hus”) 9.00-9.45 Interactive PDF’s Instructor: HL Location: Campus: Building 1222, Room 127 (“Biologiens Hus”) 10.00-10.45 3D-printing Instructor: MØN Location: Campus: Building 1222, Room 127 (“Biologiens Hus”) 11.00- 11.45 Lecture: Imaging for real (examples of imaging-research) Imaging for real (examples of imaging-research) Speaker: HL (Title: “Examples of the use of interactive PDF’s and 3D-printing in

various projects) Location: Campus: Building 1222, Room 127 (“Biologiens Hus”) 12.00–13.00 Lunch break 13.00–14.15 Visit to “The 3D printing lab” at the Architect School Instructor: MØN Location: Arkitektskolen (Transfer to Arkitektskolen, a 10-15 min walk, guide:

MØN, HL, KH) 14.30–16.30 Data analysis: Preparing interactive PDF’s and 3D print-files from CT-data Instructors: HL, KH Location: Campus: Building 1222, Room 127 (“Biologiens Hus”) 16.30–17.30 Closing remarks and feedback from participants Instructors: HL, KH, MP, TW Location: Campus: Building 1222, Room 127 (“Biologiens Hus”) Reading for interactive PDF/3D-printing session: Ruthensteiner and Hess. 2008. Embedding 3D models of biological specimens in PDF publications. Microsc Res Tech. 71:778-86. https://www.ncbi.nlm.nih.gov/pubmed/?term=Embedding+3D+models+of+biological+specimens+in+PDF+publications Lauridsen et al. 2011. Inside out: modern imaging techniques to reveal animal anatomy. PLoS One. 2011 Mar 22;6(3):e17879. https://www.ncbi.nlm.nih.gov/pubmed/?term=lauridsen+inside+out Lauridsen et al. 2016. From tissue to silicon to plastic: three-dimensional printing in comparative anatomy and physiology. R Soc open sci. 2016 Mar 2;3(3):150643. https://www.ncbi.nlm.nih.gov/pubmed/?term=From+tissue+to+silicon+to+plastic%3A+three-dimensional+printing+in+comparative+anatomy+and+physiology

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Instructors: KH: Kasper Hansen, PhD Zoophysiology, Department of Bioscience Aarhus University 8000 Aarhus C, Denmark E-mail: kasperhansen@bios.au.dk HL: Henrik Lauridsen, PhD Comparative Medicine Lab, Department of Clinical Medicine, Aarhus University (Denmark) and Butcher Lab, Department of Biomedical Engineering, Cornell University (USA) E-mail: henrik@clin.au.dk MP: Michael Pedersen, PhD Comparative Medicine Lab, Department of Clinical Medicine, Aarhus University (Denmark) E-mail: michael@clin.au.dk TW: Tobias Wang, PhD Zoophysiology, Department of Bioscience Aarhus University 8000 Aarhus C, Denmark E-mail: tobias.wang@bios.au.dk AKOA: Aage Kristian Olsen Alstrup, PhD (cand.med.vet.) Nuklearmedicinsk Afdeling & PET-Centret, forskningsafdeling Nørrebrogade 44 8000, Aarhus C, Danmark SJ: Steen Jakobsen, PhD Institut for Klinisk Medicin - PET-Centret, forskningsafdeling Nørrebrogade 44 8000 Aarhus C, Danmark OLM: Ole Lajord Munk, PhD Department of Nuclear Medicine & PET Center Aarhus University Hospital Nørrebrogade 44 8000 Aarhus C, Danmark MITS: Mette Irene Theilgaard Simonsen Department of Nuclear Medicine & PET Center Aarhus University Hospital Nørrebrogade 44 8000 Aarhus C, Danmark MB: Morten Busk, PhD Institut for Klinisk Medicin - Afdeling for Eksperimentel Klinisk Onkologi, NBG Nørrebrogade 44 8000 Aarhus C, Danmark

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MCK: Martin Colliander Kristensen, MR-physicist Department of Procurement & Clinical Engineering, Central Denmark Region, Oluf Palmes Allé 15, DK-8200 Aarhus N, Denmark. E-mail: Martin.Kristensen@stab.rm.dk AH: Arne Hørlyck, Chief Physician Department of Clinical Medicine - Røntgen og Skanning, Skejby University Hospital Palle Juul-Jensens Boulevard 99 8200 Aarhus N, Denmark E-mail: hoerlyck@clin.au.dk CL: Christoffer Laustsen, PhD Department of Clinical Medicine - The MR Research Centre Aarhus University Palle Juul-Jensens Boulevard 99 8200 Aarhus N, Danmark E-mail: cl@clin.au.dk MØN: Mathias Ørum Nørgård, Cand Arch Aarhus School of Architecture

Nørreport 20, 8000 Aarhus C, Denmark Addresses and maps: Campus (and Section for Zoophysiology) Building 1131 – Room 127 (“Seminar room/Kaffestuen” on the ground floor) Aarhus University, Institut for Bioscience C.F.Møllers Allé 3 8000 Aarhus C, Denmark GoogleMaps-link: https://goo.gl/maps/kz5kaohqQGG2 (or see Maps below) Comparative Medicine Lab, at the University Hospital in Skejby Look for: “MR Research Centre” Main entrance 6, ground floor, roof sign 14 Aarhus University Hospital, Skejby Palle Juul-Jensens Boulevard 99 8200 Aarhus N, Denmark GoogleMaps-link: https://goo.gl/maps/JjaxRUUEnnm (or see Maps below)

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Zoophysiology (In Danish “Zoofysiologi”) :

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Comparative Medicine Lab (MR Research Centre):

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Accommodation: There are many different hotels and possibilities for accommodation in Aarhus. Some examples are listed here: Cabin Aarhus CABINN Aarhus Kannikegade 14 8000 Aarhus C Phone: +45 86 75 70 00

E-mail: aarhus@cabinn.com

Hotel La Tour Randersvej 139 8200 Aarhus N Phone: +45 86 16 78 88

We also strongly recommend searching via AirBnB, Hotels.com and/or

expedia.com