the state of the art
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UCIrvineDEPARTMENT OFBIOMEDICAL ENGINEERING
The State of the ArtThe State of the ArtThe State of the ArtThe State of the Art
Joerg MeyerJoerg Meyerjmeyer@uci.edujmeyer@uci.edu
April 19, 2023April 19, 2023
Joerg MeyerJoerg Meyerjmeyer@uci.edujmeyer@uci.edu
April 19, 2023April 19, 2023
Biomedical Image ProcessingBiomedical Image ProcessingBiomedical Image ProcessingBiomedical Image Processing
1500 ||||||||||||||||||||||||||||||||| 2003
UCIrvineBiomedical Image Processing – The State of the Art
Joerg Meyer - jmeyer@uci.edu
DEPARTMENT OF BIOMEDICAL ENGINEERING
Biomedical Image ProcessingBiomedical Image ProcessingBiomedical Image ProcessingBiomedical Image Processing
UCIrvineBiomedical Image Processing – The State of the Art
Joerg Meyer - jmeyer@uci.edu
DEPARTMENT OF BIOMEDICAL ENGINEERING
Biomedical Image ProcessingBiomedical Image ProcessingBiomedical Image ProcessingBiomedical Image Processing
UCIrvineBiomedical Image Processing – The State of the Art
Joerg Meyer - jmeyer@uci.edu
DEPARTMENT OF BIOMEDICAL ENGINEERING
Biomedical Image ProcessingBiomedical Image ProcessingBiomedical Image ProcessingBiomedical Image Processing
X-RayX-RayX-RayX-Ray
(Eberhart’s Manual of High Frequncy Currents, Ch. 10, 1911)(Eberhart’s Manual of High Frequncy Currents, Ch. 10, 1911)(Eberhart’s Manual of High Frequncy Currents, Ch. 10, 1911)(Eberhart’s Manual of High Frequncy Currents, Ch. 10, 1911)
(Gundelach Tube, 1898 – 1905)(Gundelach Tube, 1898 – 1905)
Oak Ridge Associated UniversitiesOak Ridge Associated Universities
Health PhysicsHealth PhysicsInstrumentation MuseumInstrumentation Museum
(Gundelach Tube, 1898 – 1905)(Gundelach Tube, 1898 – 1905)
Oak Ridge Associated UniversitiesOak Ridge Associated Universities
Health PhysicsHealth PhysicsInstrumentation MuseumInstrumentation Museum
UCIrvineBiomedical Image Processing – The State of the Art
Joerg Meyer - jmeyer@uci.edu
DEPARTMENT OF BIOMEDICAL ENGINEERING
Biomedical Image ProcessingBiomedical Image ProcessingBiomedical Image ProcessingBiomedical Image Processing
Week 0 Week 4Week 0 Week 4Week 0 Week 4Week 0 Week 4
UCIrvineBiomedical Image Processing – The State of the Art
Joerg Meyer - jmeyer@uci.edu
DEPARTMENT OF BIOMEDICAL ENGINEERING
Biomedical Image ProcessingBiomedical Image ProcessingBiomedical Image ProcessingBiomedical Image Processing
Scaphoid BoneScaphoid BoneScaphoid BoneScaphoid Bone
Week 0 Week 4Week 0 Week 4Week 0 Week 4Week 0 Week 4
UCIrvineBiomedical Image Processing – The State of the Art
Joerg Meyer - jmeyer@uci.edu
DEPARTMENT OF BIOMEDICAL ENGINEERING
Biomedical Image ProcessingBiomedical Image ProcessingBiomedical Image ProcessingBiomedical Image Processing
Step 1: Incision MarkingStep 1: Incision MarkingStep 1: Incision MarkingStep 1: Incision Marking
UCIrvineBiomedical Image Processing – The State of the Art
Joerg Meyer - jmeyer@uci.edu
DEPARTMENT OF BIOMEDICAL ENGINEERING
Biomedical Image ProcessingBiomedical Image ProcessingBiomedical Image ProcessingBiomedical Image Processing
Step 2: Exposure of Fracture LineStep 2: Exposure of Fracture LineStep 2: Exposure of Fracture LineStep 2: Exposure of Fracture Line
UCIrvineBiomedical Image Processing – The State of the Art
Joerg Meyer - jmeyer@uci.edu
DEPARTMENT OF BIOMEDICAL ENGINEERING
Biomedical Image ProcessingBiomedical Image ProcessingBiomedical Image ProcessingBiomedical Image Processing
Step 3: Screw Insertion SiteStep 3: Screw Insertion SiteStep 3: Screw Insertion SiteStep 3: Screw Insertion Site
UCIrvineBiomedical Image Processing – The State of the Art
Joerg Meyer - jmeyer@uci.edu
DEPARTMENT OF BIOMEDICAL ENGINEERING
Biomedical Image ProcessingBiomedical Image ProcessingBiomedical Image ProcessingBiomedical Image Processing
Step 4: X-RayStep 4: X-RayStep 4: X-RayStep 4: X-Ray
Before 2 months postopBefore 2 months postop Before 2 months postopBefore 2 months postop
(Images courtesy of: Electronic Textbook of Hand Surgery, http://www.eatonhand.com)(Images courtesy of: Electronic Textbook of Hand Surgery, http://www.eatonhand.com)(Images courtesy of: Electronic Textbook of Hand Surgery, http://www.eatonhand.com)(Images courtesy of: Electronic Textbook of Hand Surgery, http://www.eatonhand.com)
UCIrvineBiomedical Image Processing – The State of the Art
Joerg Meyer - jmeyer@uci.edu
DEPARTMENT OF BIOMEDICAL ENGINEERING
Biomedical Image ProcessingBiomedical Image ProcessingBiomedical Image ProcessingBiomedical Image Processing
High FrequencyHigh FrequencyX-Ray TubeX-Ray Tube
High FrequencyHigh FrequencyX-Ray TubeX-Ray Tube
(Eberhart’s Manual of High Frequncy Currents, Chap. 10, 1911)(Eberhart’s Manual of High Frequncy Currents, Chap. 10, 1911)(Eberhart’s Manual of High Frequncy Currents, Chap. 10, 1911)(Eberhart’s Manual of High Frequncy Currents, Chap. 10, 1911)
Portable SystemPortable SystemPortable SystemPortable System
UCIrvineBiomedical Image Processing – The State of the Art
Joerg Meyer - jmeyer@uci.edu
DEPARTMENT OF BIOMEDICAL ENGINEERING
Biomedical Image ProcessingBiomedical Image ProcessingBiomedical Image ProcessingBiomedical Image Processing
Scaphoids Scaphoids (1mm)(1mm)
Scaphoids Scaphoids (1mm)(1mm)
MagneVu 1000MagneVu 1000(MRI)(MRI)
MagneVu 1000MagneVu 1000(MRI)(MRI)
UCIrvineBiomedical Image Processing – The State of the Art
Joerg Meyer - jmeyer@uci.edu
DEPARTMENT OF BIOMEDICAL ENGINEERING
Biomedical Image ProcessingBiomedical Image ProcessingBiomedical Image ProcessingBiomedical Image Processing
UCIrvineBiomedical Image Processing – The State of the Art
Joerg Meyer - jmeyer@uci.edu
DEPARTMENT OF BIOMEDICAL ENGINEERING
Biomedical Image ProcessingBiomedical Image ProcessingBiomedical Image ProcessingBiomedical Image Processing
• Problems:Problems:– TimeTime– Cost factorCost factor
• Solution:Solution:– Correlate X-ray images with 3-D modelsCorrelate X-ray images with 3-D models– Database (typical bones)Database (typical bones)
• Problems:Problems:– TimeTime– Cost factorCost factor
• Solution:Solution:– Correlate X-ray images with 3-D modelsCorrelate X-ray images with 3-D models– Database (typical bones)Database (typical bones)
UCIrvineBiomedical Image Processing – The State of the Art
Joerg Meyer - jmeyer@uci.edu
DEPARTMENT OF BIOMEDICAL ENGINEERING
Biomedical Image ProcessingBiomedical Image ProcessingBiomedical Image ProcessingBiomedical Image Processing
Various shapes and sizes (Zimmer, 1968)Various shapes and sizes (Zimmer, 1968)Various shapes and sizes (Zimmer, 1968)Various shapes and sizes (Zimmer, 1968)
Scaphoid BonesScaphoid BonesScaphoid BonesScaphoid Bones
UCIrvineBiomedical Image Processing – The State of the Art
Joerg Meyer - jmeyer@uci.edu
DEPARTMENT OF BIOMEDICAL ENGINEERING
Biomedical Image ProcessingBiomedical Image ProcessingBiomedical Image ProcessingBiomedical Image Processing
Classification (Herbert)Classification (Herbert)Classification (Herbert)Classification (Herbert)
Scaphoid Bone FracturesScaphoid Bone FracturesScaphoid Bone FracturesScaphoid Bone Fractures
UCIrvineBiomedical Image Processing – The State of the Art
Joerg Meyer - jmeyer@uci.edu
DEPARTMENT OF BIOMEDICAL ENGINEERING
Biomedical Image ProcessingBiomedical Image ProcessingBiomedical Image ProcessingBiomedical Image Processing
A - C: Scaphoid view 1 - with forearm pronated 45deg. to view profile of scaphoid & STT joint
D - Scaphoid view 2 (ulnar oblique view) showing radioscaphoid joint (from Rockwood & Green)
A - C: Scaphoid view 1 - with forearm pronated 45deg. to view profile of scaphoid & STT joint
D - Scaphoid view 2 (ulnar oblique view) showing radioscaphoid joint (from Rockwood & Green)
AA BB
CC DD
UCIrvineBiomedical Image Processing – The State of the Art
Joerg Meyer - jmeyer@uci.edu
DEPARTMENT OF BIOMEDICAL ENGINEERING
Biomedical Image ProcessingBiomedical Image ProcessingBiomedical Image ProcessingBiomedical Image Processing
• Solution:Solution:– SuperimposeSuperimpose
radiographicradiographic
scan andscan and
3-D model3-D model
– Select bestSelect best
model frommodel from
databasedatabase
• Solution:Solution:– SuperimposeSuperimpose
radiographicradiographic
scan andscan and
3-D model3-D model
– Select bestSelect best
model frommodel from
databasedatabase
UCIrvineBiomedical Image Processing – The State of the Art
Joerg Meyer - jmeyer@uci.edu
DEPARTMENT OF BIOMEDICAL ENGINEERING
Biomedical Image ProcessingBiomedical Image ProcessingBiomedical Image ProcessingBiomedical Image Processing
• General General Question:Question:
– How to combineHow to combine
differentdifferent
modalities?modalities?
• General General Question:Question:
– How to combineHow to combine
differentdifferent
modalities?modalities?
UCIrvineBiomedical Image Processing – The State of the Art
Joerg Meyer - jmeyer@uci.edu
DEPARTMENT OF BIOMEDICAL ENGINEERING
Visible Human (CT, frozen)Visible Human (CT, frozen)Visible Human (CT, frozen)Visible Human (CT, frozen)
Joseph Paul JerniganJoseph Paul JerniganJoseph Paul JerniganJoseph Paul Jernigan
UCIrvineBiomedical Image Processing – The State of the Art
Joerg Meyer - jmeyer@uci.edu
DEPARTMENT OF BIOMEDICAL ENGINEERING
Visible Human (CT, frozen)Visible Human (CT, frozen)Visible Human (CT, frozen)Visible Human (CT, frozen)
Slice 1125Slice 1125Slice 1125Slice 1125
UCIrvineBiomedical Image Processing – The State of the Art
Joerg Meyer - jmeyer@uci.edu
DEPARTMENT OF BIOMEDICAL ENGINEERING
Visible Human (MRI)Visible Human (MRI)Visible Human (MRI)Visible Human (MRI)
Slice 1125Slice 1125Slice 1125Slice 1125
UCIrvineBiomedical Image Processing – The State of the Art
Joerg Meyer - jmeyer@uci.edu
DEPARTMENT OF BIOMEDICAL ENGINEERING
Visible Human (RGB color)Visible Human (RGB color)Visible Human (RGB color)Visible Human (RGB color)
Slice 1125Slice 1125Slice 1125Slice 1125
UCIrvineBiomedical Image Processing – The State of the Art
Joerg Meyer - jmeyer@uci.edu
DEPARTMENT OF BIOMEDICAL ENGINEERING
Visible Human (RGB color)Visible Human (RGB color)Visible Human (RGB color)Visible Human (RGB color)
UCIrvineBiomedical Image Processing – The State of the Art
Joerg Meyer - jmeyer@uci.edu
DEPARTMENT OF BIOMEDICAL ENGINEERING
Visible Human Visible Human (3-D Reconstruction)(3-D Reconstruction)Visible Human Visible Human (3-D Reconstruction)(3-D Reconstruction)
UCIrvineBiomedical Image Processing – The State of the Art
Joerg Meyer - jmeyer@uci.edu
DEPARTMENT OF BIOMEDICAL ENGINEERING
CT ScannerCT ScannerCT ScannerCT Scanner
UCIrvineBiomedical Image Processing – The State of the Art
Joerg Meyer - jmeyer@uci.edu
DEPARTMENT OF BIOMEDICAL ENGINEERING
CT ScannerCT ScannerCT ScannerCT Scanner
UCIrvineBiomedical Image Processing – The State of the Art
Joerg Meyer - jmeyer@uci.edu
DEPARTMENT OF BIOMEDICAL ENGINEERING
CT ScannerCT ScannerCT ScannerCT Scanner
UCIrvineBiomedical Image Processing – The State of the Art
Joerg Meyer - jmeyer@uci.edu
DEPARTMENT OF BIOMEDICAL ENGINEERING
CT ScannerCT ScannerCT ScannerCT Scanner
UCIrvineBiomedical Image Processing – The State of the Art
Joerg Meyer - jmeyer@uci.edu
DEPARTMENT OF BIOMEDICAL ENGINEERING
CT ScannerCT ScannerCT ScannerCT Scanner
UCIrvineBiomedical Image Processing – The State of the Art
Joerg Meyer - jmeyer@uci.edu
DEPARTMENT OF BIOMEDICAL ENGINEERING
CT ScannerCT ScannerCT ScannerCT Scanner
UCIrvineBiomedical Image Processing – The State of the Art
Joerg Meyer - jmeyer@uci.edu
DEPARTMENT OF BIOMEDICAL ENGINEERING
CT ScannerCT ScannerCT ScannerCT Scanner
UCIrvineBiomedical Image Processing – The State of the Art
Joerg Meyer - jmeyer@uci.edu
DEPARTMENT OF BIOMEDICAL ENGINEERING
CT ScannerCT ScannerCT ScannerCT Scanner
UCIrvineBiomedical Image Processing – The State of the Art
Joerg Meyer - jmeyer@uci.edu
DEPARTMENT OF BIOMEDICAL ENGINEERING
CT ScannerCT ScannerCT ScannerCT Scanner
UCIrvineBiomedical Image Processing – The State of the Art
Joerg Meyer - jmeyer@uci.edu
DEPARTMENT OF BIOMEDICAL ENGINEERING
CT ScannerCT ScannerCT ScannerCT Scanner
UCIrvineBiomedical Image Processing – The State of the Art
Joerg Meyer - jmeyer@uci.edu
DEPARTMENT OF BIOMEDICAL ENGINEERING
CT ScannerCT ScannerCT ScannerCT Scanner
UCIrvineBiomedical Image Processing – The State of the Art
Joerg Meyer - jmeyer@uci.edu
DEPARTMENT OF BIOMEDICAL ENGINEERING
Image AcquisitionImage AcquisitionImage AcquisitionImage Acquisition
UCIrvineBiomedical Image Processing – The State of the Art
Joerg Meyer - jmeyer@uci.edu
DEPARTMENT OF BIOMEDICAL ENGINEERING
CT ScannerCT ScannerCT ScannerCT Scanner
UCIrvineBiomedical Image Processing – The State of the Art
Joerg Meyer - jmeyer@uci.edu
DEPARTMENT OF BIOMEDICAL ENGINEERING
Image AcquisitionImage AcquisitionImage AcquisitionImage Acquisition
UCIrvineBiomedical Image Processing – The State of the Art
Joerg Meyer - jmeyer@uci.edu
DEPARTMENT OF BIOMEDICAL ENGINEERING
Image AcquisitionImage AcquisitionImage AcquisitionImage Acquisition
UCIrvineBiomedical Image Processing – The State of the Art
Joerg Meyer - jmeyer@uci.edu
DEPARTMENT OF BIOMEDICAL ENGINEERING
Image AcquisitionImage AcquisitionImage AcquisitionImage Acquisition
UCIrvineBiomedical Image Processing – The State of the Art
Joerg Meyer - jmeyer@uci.edu
DEPARTMENT OF BIOMEDICAL ENGINEERING
Image AcquisitionImage AcquisitionImage AcquisitionImage Acquisition
UCIrvineBiomedical Image Processing – The State of the Art
Joerg Meyer - jmeyer@uci.edu
DEPARTMENT OF BIOMEDICAL ENGINEERING
Image AcquisitionImage AcquisitionImage AcquisitionImage Acquisition
UCIrvineBiomedical Image Processing – The State of the Art
Joerg Meyer - jmeyer@uci.edu
DEPARTMENT OF BIOMEDICAL ENGINEERING
Principle of a CT ScannerPrinciple of a CT ScannerPrinciple of a CT ScannerPrinciple of a CT Scanner
ObjectTranslation
Rotation
X-Ray Source
Detector
Object
X-Ray Source
Detector
a) Translation b) Rotation
Image AcquisitionImage AcquisitionImage AcquisitionImage Acquisition
UCIrvineBiomedical Image Processing – The State of the Art
Joerg Meyer - jmeyer@uci.edu
DEPARTMENT OF BIOMEDICAL ENGINEERING
Principle of an MRI ScannerPrinciple of an MRI ScannerPrinciple of an MRI ScannerPrinciple of an MRI Scanner
a) Random Spin b) directional magnetic field
Image AcquisitionImage AcquisitionImage AcquisitionImage Acquisition
UCIrvineBiomedical Image Processing – The State of the Art
Joerg Meyer - jmeyer@uci.edu
DEPARTMENT OF BIOMEDICAL ENGINEERING
a) Directional Puls (orthogonal) b) Relaxation
Image AcquisitionImage AcquisitionImage AcquisitionImage Acquisition
Principle of an MRI ScannerPrinciple of an MRI ScannerPrinciple of an MRI ScannerPrinciple of an MRI Scanner
UCIrvineBiomedical Image Processing – The State of the Art
Joerg Meyer - jmeyer@uci.edu
DEPARTMENT OF BIOMEDICAL ENGINEERING
Image AcquisitionImage AcquisitionImage AcquisitionImage Acquisition
UCIrvineBiomedical Image Processing – The State of the Art
Joerg Meyer - jmeyer@uci.edu
DEPARTMENT OF BIOMEDICAL ENGINEERING
Rhesus Monkey BrainRhesus Monkey BrainRhesus Monkey BrainRhesus Monkey Brain
• High-resolution large-scale image dataHigh-resolution large-scale image data
RGB image series (real-color, dyed), 5037 x 3871 x 1400, 76 GBRGB image series (real-color, dyed), 5037 x 3871 x 1400, 76 GB(data courtesy of Edward G. Jones, Center for Neuroscience, UC Davis)(data courtesy of Edward G. Jones, Center for Neuroscience, UC Davis)
• High-resolution large-scale image dataHigh-resolution large-scale image data
RGB image series (real-color, dyed), 5037 x 3871 x 1400, 76 GBRGB image series (real-color, dyed), 5037 x 3871 x 1400, 76 GB(data courtesy of Edward G. Jones, Center for Neuroscience, UC Davis)(data courtesy of Edward G. Jones, Center for Neuroscience, UC Davis)
• Resolution: 2666dpi Resolution: 2666dpi
Pixel spacing: 9 Pixel spacing: 9 mm
• Enables zoomingEnables zooming
down to the cell down to the cell
level.level.
• Total data size:Total data size:76 GB76 GB
UCIrvineBiomedical Image Processing – The State of the Art
Joerg Meyer - jmeyer@uci.edu
DEPARTMENT OF BIOMEDICAL ENGINEERING
Image AcquisitionImage AcquisitionImage AcquisitionImage Acquisition
UCIrvineBiomedical Image Processing – The State of the Art
Joerg Meyer - jmeyer@uci.edu
DEPARTMENT OF BIOMEDICAL ENGINEERING
3-D Reconstruction3-D Reconstruction3-D Reconstruction3-D Reconstruction
UCIrvineBiomedical Image Processing – The State of the Art
Joerg Meyer - jmeyer@uci.edu
DEPARTMENT OF BIOMEDICAL ENGINEERING
Image AcquisitionImage AcquisitionImage AcquisitionImage Acquisition
UCIrvineBiomedical Image Processing – The State of the Art
Joerg Meyer - jmeyer@uci.edu
DEPARTMENT OF BIOMEDICAL ENGINEERING
From 2-D Cross-sections to 3-DFrom 2-D Cross-sections to 3-DFrom 2-D Cross-sections to 3-DFrom 2-D Cross-sections to 3-D
RGB image series (real-color, human brain), 1472 x 1152 x 753, 3.57 GBRGB image series (real-color, human brain), 1472 x 1152 x 753, 3.57 GB(data courtesy of Arthur W. Toga, Dept. of Neurology, UCLA School of Medicine)(data courtesy of Arthur W. Toga, Dept. of Neurology, UCLA School of Medicine)
RGB image series (real-color, human brain), 1472 x 1152 x 753, 3.57 GBRGB image series (real-color, human brain), 1472 x 1152 x 753, 3.57 GB(data courtesy of Arthur W. Toga, Dept. of Neurology, UCLA School of Medicine)(data courtesy of Arthur W. Toga, Dept. of Neurology, UCLA School of Medicine)
UCIrvineBiomedical Image Processing – The State of the Art
Joerg Meyer - jmeyer@uci.edu
DEPARTMENT OF BIOMEDICAL ENGINEERING
3-D Reconstruction3-D Reconstruction3-D Reconstruction3-D Reconstruction
• 3-D Volume Rendering of a Human Brain3-D Volume Rendering of a Human Brain• 3-D Volume Rendering of a Human Brain3-D Volume Rendering of a Human Brain
RGB image series (real-color, human brain), 1472 x 1152 x 753, 3.57 GB(data courtesy of Arthur W. Toga, Dept. of Neurology, UCLA School of Medicine,
image courtesy of Eric B. Lum, Ikuko Takanashi, CIPIC, UC Davis)
RGB image series (real-color, human brain), 1472 x 1152 x 753, 3.57 GB(data courtesy of Arthur W. Toga, Dept. of Neurology, UCLA School of Medicine,
image courtesy of Eric B. Lum, Ikuko Takanashi, CIPIC, UC Davis)
UCIrvineBiomedical Image Processing – The State of the Art
Joerg Meyer - jmeyer@uci.edu
DEPARTMENT OF BIOMEDICAL ENGINEERING
From 2-D Cross-sections to 3-DFrom 2-D Cross-sections to 3-DFrom 2-D Cross-sections to 3-DFrom 2-D Cross-sections to 3-D
??
UCIrvineBiomedical Image Processing – The State of the Art
Joerg Meyer - jmeyer@uci.edu
DEPARTMENT OF BIOMEDICAL ENGINEERING
From 2-D Cross-sections to 3-DFrom 2-D Cross-sections to 3-DFrom 2-D Cross-sections to 3-DFrom 2-D Cross-sections to 3-D
UCIrvineBiomedical Image Processing – The State of the Art
Joerg Meyer - jmeyer@uci.edu
DEPARTMENT OF BIOMEDICAL ENGINEERING
From 2-D Cross-sections to 3-DFrom 2-D Cross-sections to 3-DFrom 2-D Cross-sections to 3-DFrom 2-D Cross-sections to 3-D
UCIrvineBiomedical Image Processing – The State of the Art
Joerg Meyer - jmeyer@uci.edu
DEPARTMENT OF BIOMEDICAL ENGINEERING
3-D Reconstruction3-D Reconstruction3-D Reconstruction3-D Reconstruction
CT head (CT head (512 cross-sections, 1024 planes512 cross-sections, 1024 planes))rendered with different transparency transfer functions rendered with different transparency transfer functions
UCIrvineBiomedical Image Processing – The State of the Art
Joerg Meyer - jmeyer@uci.edu
DEPARTMENT OF BIOMEDICAL ENGINEERING
Human brainHuman brain((128 cross-sections,128 cross-sections,
220 planes220 planes))
Cancer cell Cancer cell ((256 cross-sections,256 cross-sections,
512 planes512 planes))
Ice BlockIce Block(Human brain)(Human brain)
((128 cryo-sections,128 cryo-sections,256 planes256 planes))
3-D Reconstruction3-D Reconstruction
UCIrvineBiomedical Image Processing – The State of the Art
Joerg Meyer - jmeyer@uci.edu
DEPARTMENT OF BIOMEDICAL ENGINEERING
3-D Reconstruction3-D Reconstruction3-D Reconstruction3-D Reconstruction
MRI scan of a human skullMRI scan of a human skull
UCIrvineBiomedical Image Processing – The State of the Art
Joerg Meyer - jmeyer@uci.edu
DEPARTMENT OF BIOMEDICAL ENGINEERING
3-D Reconstruction3-D Reconstruction3-D Reconstruction3-D Reconstruction
CT scan of a human skullCT scan of a human skull
UCIrvineBiomedical Image Processing – The State of the Art
Joerg Meyer - jmeyer@uci.edu
DEPARTMENT OF BIOMEDICAL ENGINEERING
3-D Reconstruction3-D Reconstruction3-D Reconstruction3-D Reconstruction
CT scan of a human skullCT scan of a human skull
UCIrvineBiomedical Image Processing – The State of the Art
Joerg Meyer - jmeyer@uci.edu
DEPARTMENT OF BIOMEDICAL ENGINEERING
How to scale down large-scale data?How to scale down large-scale data?How to scale down large-scale data?How to scale down large-scale data?
MM
120 CD-ROMs120 CD-ROMs 100k polygons100k polygons
UCIrvineBiomedical Image Processing – The State of the Art
Joerg Meyer - jmeyer@uci.edu
DEPARTMENT OF BIOMEDICAL ENGINEERING
Space DecompositionSpace DecompositionSpace DecompositionSpace Decomposition• Data arrangedData arranged
in slicesin slices• Data arrangedData arranged
in slicesin slices
UCIrvineBiomedical Image Processing – The State of the Art
Joerg Meyer - jmeyer@uci.edu
DEPARTMENT OF BIOMEDICAL ENGINEERING
Space DecompositionSpace DecompositionSpace DecompositionSpace Decomposition• Goal: extract subvolumeGoal: extract subvolume• Problem: data arranged in slices orProblem: data arranged in slices or
unstructured gridsunstructured grids• Necessity to touch a lot of files or dataNecessity to touch a lot of files or data• Solution: breaking up the data set into Solution: breaking up the data set into
bricksbricks• Data in bricks still too big for transmission/Data in bricks still too big for transmission/
interactive renderinginteractive rendering• Solution: multiresolution representationSolution: multiresolution representation idea: combination of octree/waveletidea: combination of octree/wavelet
• Goal: extract subvolumeGoal: extract subvolume• Problem: data arranged in slices orProblem: data arranged in slices or
unstructured gridsunstructured grids• Necessity to touch a lot of files or dataNecessity to touch a lot of files or data• Solution: breaking up the data set into Solution: breaking up the data set into
bricksbricks• Data in bricks still too big for transmission/Data in bricks still too big for transmission/
interactive renderinginteractive rendering• Solution: multiresolution representationSolution: multiresolution representation idea: combination of octree/waveletidea: combination of octree/wavelet
UCIrvineBiomedical Image Processing – The State of the Art
Joerg Meyer - jmeyer@uci.edu
DEPARTMENT OF BIOMEDICAL ENGINEERING
Space DecompositionSpace DecompositionSpace DecompositionSpace Decomposition• Data arrangedData arranged
in slicesin slices• Data arrangedData arranged
in slicesin slices
UCIrvineBiomedical Image Processing – The State of the Art
Joerg Meyer - jmeyer@uci.edu
DEPARTMENT OF BIOMEDICAL ENGINEERING
Space DecompositionSpace DecompositionSpace DecompositionSpace Decomposition• Data arrangedData arranged
in slicesin slices• Data arrangedData arranged
in slicesin slices
UCIrvineBiomedical Image Processing – The State of the Art
Joerg Meyer - jmeyer@uci.edu
DEPARTMENT OF BIOMEDICAL ENGINEERING
Space DecompositionSpace DecompositionSpace DecompositionSpace Decomposition• Breaking up theBreaking up the
data into bricksdata into bricks• Breaking up theBreaking up the
data into bricksdata into bricks
UCIrvineBiomedical Image Processing – The State of the Art
Joerg Meyer - jmeyer@uci.edu
DEPARTMENT OF BIOMEDICAL ENGINEERING
Space DecompositionSpace DecompositionSpace DecompositionSpace Decomposition• Breaking up theBreaking up the
data into bricksdata into bricks• Breaking up theBreaking up the
data into bricksdata into bricks
UCIrvineBiomedical Image Processing – The State of the Art
Joerg Meyer - jmeyer@uci.edu
DEPARTMENT OF BIOMEDICAL ENGINEERING
Space DecompositionSpace DecompositionSpace DecompositionSpace Decomposition• Breaking up theBreaking up the
data into bricksdata into bricks• Breaking up theBreaking up the
data into bricksdata into bricks
......
UCIrvineBiomedical Image Processing – The State of the Art
Joerg Meyer - jmeyer@uci.edu
DEPARTMENT OF BIOMEDICAL ENGINEERING
Space DecompositionSpace DecompositionSpace DecompositionSpace Decomposition• Breaking up theBreaking up the
data into bricksdata into bricks• Breaking up theBreaking up the
data into bricksdata into bricks
......
UCIrvineBiomedical Image Processing – The State of the Art
Joerg Meyer - jmeyer@uci.edu
DEPARTMENT OF BIOMEDICAL ENGINEERING
Space DecompositionSpace DecompositionSpace DecompositionSpace Decomposition• Breaking up theBreaking up the
data into bricksdata into bricks• Breaking up theBreaking up the
data into bricksdata into bricks
......
UCIrvineBiomedical Image Processing – The State of the Art
Joerg Meyer - jmeyer@uci.edu
DEPARTMENT OF BIOMEDICAL ENGINEERING
Space DecompositionSpace DecompositionSpace DecompositionSpace Decomposition• Breaking up theBreaking up the
data into bricksdata into bricks• Breaking up theBreaking up the
data into bricksdata into bricks
ROIROI......
UCIrvineBiomedical Image Processing – The State of the Art
Joerg Meyer - jmeyer@uci.edu
DEPARTMENT OF BIOMEDICAL ENGINEERING
Combination: Octree/WaveletCombination: Octree/WaveletCombination: Octree/WaveletCombination: Octree/Wavelet• Leaf encodingLeaf encoding• Leaf encodingLeaf encoding
UCIrvineBiomedical Image Processing – The State of the Art
Joerg Meyer - jmeyer@uci.edu
DEPARTMENT OF BIOMEDICAL ENGINEERING
Wavelet CompressionWavelet CompressionWavelet CompressionWavelet Compression
image pyramidimage pyramid
original (256 x 256)original (256 x 256) step 1step 1 step 2step 2
......
UCIrvineBiomedical Image Processing – The State of the Art
Joerg Meyer - jmeyer@uci.edu
DEPARTMENT OF BIOMEDICAL ENGINEERING
Wavelet CompressionWavelet CompressionWavelet CompressionWavelet Compression
MRI scanMRI scan
original (256 x 256)original (256 x 256) n = 8n = 8
n = 2n = 2n = 3n = 3n = 4n = 4n = 5n = 5
n = 7n = 7 n = 6n = 6
UCIrvineBiomedical Image Processing – The State of the Art
Joerg Meyer - jmeyer@uci.edu
DEPARTMENT OF BIOMEDICAL ENGINEERING
Wavelet CompressionWavelet CompressionWavelet CompressionWavelet Compression
Original image array
Original image array
Original VolumeOriginal Volume
L H L H
First run: x-directionFirst run: x-direction First run: x-directionFirst run: x-direction
HL HL LL LL
LH LH HL HL
HLLHLLLLLLLL
LHLLHL HLLHLL
LLH LLH
LHH LHH
HLHHLH
HHHHHH
Second run: y-directionSecond run: y-direction Third run: z-direction Third run: z-direction
UCIrvineBiomedical Image Processing – The State of the Art
Joerg Meyer - jmeyer@uci.edu
DEPARTMENT OF BIOMEDICAL ENGINEERING
Progressive ReconstructionProgressive ReconstructionProgressive ReconstructionProgressive Reconstruction
Initial stage Second level of detailInitial stage Second level of detail
Third level of detail Final reconstructed imageThird level of detail Final reconstructed image
UCIrvineBiomedical Image Processing – The State of the Art
Joerg Meyer - jmeyer@uci.edu
DEPARTMENT OF BIOMEDICAL ENGINEERING
• Cancer ResearchCancer Research
– Image processing (segmentation, classification)Image processing (segmentation, classification)
– Multi-modal imaging (CT/MRI/cryosection/confocal)Multi-modal imaging (CT/MRI/cryosection/confocal)
• NeuroscienceNeuroscience
– Rhesus Macaque Monkey Brain Atlas (NIMH)Rhesus Macaque Monkey Brain Atlas (NIMH)
– Scalable Visualization Toolkits for Bays to Brains (NPACI)Scalable Visualization Toolkits for Bays to Brains (NPACI)
• Cell PhysiologyCell Physiology
– Connectivity in Leech Giant Glial CellsConnectivity in Leech Giant Glial Cells
– Correspondence Analysis in Time-variant MicroscopicCorrespondence Analysis in Time-variant Microscopic3D Image Data3D Image Data
• Molecular DiagnosticsMolecular Diagnostics
– Genomics, Proteomics, Phylogenetic TreesGenomics, Proteomics, Phylogenetic Trees
• Cancer ResearchCancer Research
– Image processing (segmentation, classification)Image processing (segmentation, classification)
– Multi-modal imaging (CT/MRI/cryosection/confocal)Multi-modal imaging (CT/MRI/cryosection/confocal)
• NeuroscienceNeuroscience
– Rhesus Macaque Monkey Brain Atlas (NIMH)Rhesus Macaque Monkey Brain Atlas (NIMH)
– Scalable Visualization Toolkits for Bays to Brains (NPACI)Scalable Visualization Toolkits for Bays to Brains (NPACI)
• Cell PhysiologyCell Physiology
– Connectivity in Leech Giant Glial CellsConnectivity in Leech Giant Glial Cells
– Correspondence Analysis in Time-variant MicroscopicCorrespondence Analysis in Time-variant Microscopic3D Image Data3D Image Data
• Molecular DiagnosticsMolecular Diagnostics
– Genomics, Proteomics, Phylogenetic TreesGenomics, Proteomics, Phylogenetic Trees
Application AreasApplication AreasApplication AreasApplication Areas
UCIrvineBiomedical Image Processing – The State of the Art
Joerg Meyer - jmeyer@uci.edu
DEPARTMENT OF BIOMEDICAL ENGINEERING
• Projection SystemsProjection Systems– Concave Reality Projection SystemConcave Reality Projection System– RealityCenterRealityCenter– Interactive White BoardsInteractive White Boards– Active/Passive Stereo ProjectorsActive/Passive Stereo Projectors
• Spatial Tracking HardwareSpatial Tracking Hardware– Nest-of-Birds (electro-magnetic)Nest-of-Birds (electro-magnetic)– VICON Motion Tracking SystemVICON Motion Tracking System
(vision)(vision)
• Interaction HardwareInteraction Hardware– PinchGloves (data gloves)PinchGloves (data gloves)– Stylus (6dof pointing device)Stylus (6dof pointing device)
• Projection SystemsProjection Systems– Concave Reality Projection SystemConcave Reality Projection System– RealityCenterRealityCenter– Interactive White BoardsInteractive White Boards– Active/Passive Stereo ProjectorsActive/Passive Stereo Projectors
• Spatial Tracking HardwareSpatial Tracking Hardware– Nest-of-Birds (electro-magnetic)Nest-of-Birds (electro-magnetic)– VICON Motion Tracking SystemVICON Motion Tracking System
(vision)(vision)
• Interaction HardwareInteraction Hardware– PinchGloves (data gloves)PinchGloves (data gloves)– Stylus (6dof pointing device)Stylus (6dof pointing device)
InfrastructureInfrastructureInfrastructureInfrastructure
UCIrvineBiomedical Image Processing – The State of the Art
Joerg Meyer - jmeyer@uci.edu
DEPARTMENT OF BIOMEDICAL ENGINEERING
ConclusionsConclusionsConclusionsConclusions
• Engineering solutions can helpEngineering solutions can help
to make health care affordableto make health care affordable• Economic feasibilityEconomic feasibility• Data set size andData set size and
image quality increasesimage quality increases• Scalable solutionsScalable solutions
UCIrvineBiomedical Image Processing – The State of the Art
Joerg Meyer - jmeyer@uci.edu
DEPARTMENT OF BIOMEDICAL ENGINEERING
AcknowledgementsAcknowledgementsAcknowledgementsAcknowledgements• Center for Neuroscience,UC DavisCenter for Neuroscience,UC Davis
• Engineering Research Center, Mississippi State UniversityEngineering Research Center, Mississippi State University
• Center for Image Processing and Integrated ComputingCenter for Image Processing and Integrated Computing
(CIPIC), UC Davis(CIPIC), UC Davis
• The Scripps Research Institute (TSRI), La Jolla, CAThe Scripps Research Institute (TSRI), La Jolla, CA
• San Diego Supercomputer CenterSan Diego Supercomputer Center
• These projects are funded in part by the National Institute These projects are funded in part by the National Institute
of Mental Health (NIMH) through the Center for of Mental Health (NIMH) through the Center for
Neuroscience at UC Davis, and the National Partnership Neuroscience at UC Davis, and the National Partnership
for Advanced Computational Infrastructure (NPACI)for Advanced Computational Infrastructure (NPACI)
(award #10195430 00120410).(award #10195430 00120410).
• Center for Neuroscience,UC DavisCenter for Neuroscience,UC Davis
• Engineering Research Center, Mississippi State UniversityEngineering Research Center, Mississippi State University
• Center for Image Processing and Integrated ComputingCenter for Image Processing and Integrated Computing
(CIPIC), UC Davis(CIPIC), UC Davis
• The Scripps Research Institute (TSRI), La Jolla, CAThe Scripps Research Institute (TSRI), La Jolla, CA
• San Diego Supercomputer CenterSan Diego Supercomputer Center
• These projects are funded in part by the National Institute These projects are funded in part by the National Institute
of Mental Health (NIMH) through the Center for of Mental Health (NIMH) through the Center for
Neuroscience at UC Davis, and the National Partnership Neuroscience at UC Davis, and the National Partnership
for Advanced Computational Infrastructure (NPACI)for Advanced Computational Infrastructure (NPACI)
(award #10195430 00120410).(award #10195430 00120410).
UCIrvineBiomedical Image Processing – The State of the Art
Joerg Meyer - jmeyer@uci.edu
DEPARTMENT OF BIOMEDICAL ENGINEERING
That‘s all, folks!That‘s all, folks!That‘s all, folks!That‘s all, folks!
Joerg MeyerUniversity of California, IrvineBME/EECS Department644E Engineering TowerIrvine, CA 92697-2625
jmeyer@uci.eduhttp://www.eng.uci.edu/~jmeyer
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