Bio 219 Biomedical Imaging and Scientific Visualization

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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 devices sensory organs

computer (CPU)
brain (CNS)

output
motor

devices
system

computers and users

feedback

patient, biomedical object

user

computer
?

•ꢀ congruence between computer output and sensory input? •ꢀ continuous feedback?

input-output: data flow

indirect:

virtual/enhanced reality
BioMedImg
SciVis

subject
object

direct

input-output: feedback loop

indirect:

virtual/enhanced reality with feedback
BioMedImg
SciVis

subject
object

direct

open-loop and closed-loop systems

perception action reaction interaction

Galileo’s
Drawing hands

telescope
M.C. Escher (1948)

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