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Bio 219 Biomedical Imaging and Scientific Visualization

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Bio 219 Biomedical Imaging and Scientific Visualization Bio 219 Biomedical Imaging and Scientific Visualization Ch. Zollikofer M. Ponce de León Organization • OLAT: – course scripts (pdf) • website: www.aim.uzh.ch/morpho/wiki/Teaching/SciVis – course scripts (pdf); passwd: scivisdocs – link collection (tutorials, applets, software/data downloads, ...) • book (background information): Zollikofer & Ponce de León, Virtual Reconstruction. A Primer in Computer-assisted Paleontology and Biomedicine (NY: Wiley, 2005) CHF 55 • final exam – Monday, 26. May 2014, 1015-1100 BioMedImg & SciVis • at the intersection between – theory/practice of image data acquisition – computer graphics – medical diagnostics – computer-assisted paleoanthropology Grotte Chauvet, France Biomedical Imaging • acquisition • processing • analysis • visualization ... of biomedical data Scientific Visualization visual... • representation (cf. data presentation) • exploration • analysis ...of scientific data aims of this course • provide theoretical (and practical) foundations of – image data acquisition, storage, retrieval – image data processing and analysis – image data visualization/rendering • establish links between – real-life vision and computer vision – computer science and biomedical sciences – theory and practice of handling biomedical data contents • real-life vision • computers and data representation • 2D image data acquisition • 3D image data acquisition • biomedical image processing in 2D and 3D • biomedical image data visualization and interaction biomedical data types of data data flow humans and computers facts and data • facts exist by definition (±independent of the observer): – females and males – humans and Neanderthals – dogs and wolves • data are generated through observation: – number of living human species: 1 – proportion of females to males at birth: 49/51 – nr. of wolves per square km biomedical data: general • physical/physiological data about the human body: – density – temperature – pressure – mass – chemical composition biomedical data: space and time • spatial – 1D – 2D – 3D • temporal • spatiotemporal (4D) ... distribution of physical/physiological data biomedical data: modes of representation and perception • text • image: visual – 1D – 2D – 3D • temporal • auditory • haptic • • and combinations crossed stereo pictures biomedical data: logical (digital) representation • binary representation – text data formats – image data formats – audio data formats – object surface/volume data formats – data flow object data acquisition data storage data processing data representation subject input-output chain: object to subject object input device:data acquisition memory: data storage CPU: data processing output device: data presentation (rendering) subject input-output chain: within subject output device, e.g. computer screen eyes, ears, ...: input device, data acquisition brain: data storage data processing data representation data analysis motor output parallels input sensory devices organs computer (CPU) brain (CNS) feedback feedback output motor devices system computers and users patient, feedback biomedical object user input computer output ? • congruence between computer output and sensory input? • continuous feedback? input-output: data flow indirect: virtual/enhanced reality BioMedImg SciVis object subject direct input-output: feedback loop indirect: virtual/enhanced reality with feedback BioMedImg SciVis object subject direct open-loop and closed-loop systems perception action reaction interaction Galileo’s Drawing hands telescope M.C. Escher (1948) .
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