Lecture Physiotherapy2017 PDF

Image Processing and Analysis
in Biomechanics
João Manuel R. S. Tavares
tavares@fe.up.pt www.fe.up.pt/~tavares
March 24, 2017

Outline
•  Introduction
•  Segmentation
•  Motion Tracking
•  Analysis of Objects: Matching, Morphing and
Registration
•  3D Reconstruction
•  Conclusions and Future Directions
•  Research Team
•  Publications & Events
@2017 João Manuel R.S. Tavares Image Processing and Analysis in Biomechanics 2
Introduction
Presentation
•  Associate Professor at FEUP (DEMec)
•  Senior Research and Projects Coordinator of the
Institute of Science and Innovation in Mechanical
and Industrial Engineering (INEGI)
•  Habilitation in Mechanical Engineering from the
University of Porto
•  PhD and MSc degrees in Electrical and Computer
Engineering from FEUP
•  BSc degree in Mechanical Engineering from FEUP
•  Research Areas: Image Processing and Analysis,
Medical Imaging, Biomechanics, Human Posture
and Control, Product Development
Introduction
•  The researchers of Image Processing and
Analysis aim the development of algorithms to
perform fully or semi-automatically tasks
performed by the (quite complex) human vision
system
Original images Computational 3D voxelized and

poligonized models built
Azevedo et al. (2010) Computer Methods in Biomechanics and Biomedical Engineering 13(3):359-369
Introduction
•  Image processing and analysis are topics of the
most importance for our Society
•  Algorithms of image processing and analysis are
frequently used, for example, in:
–  Natural Sciences
–  Sports
–  Biology
–  Industry
–  Engineering
–  Medicine
Introduction
•  Examples of common tasks involving algorithms
of image processing and analysis:
–  Noise removal
–  Geometric correction
–  Segmentation, recognition (2D-4D)
–  Motion and deformation tracking and analysis,
including matching, registration and morphing
–  3D reconstruction
–  Assisted medical diagnosis and intervention
Introduction
•  Image Acquisition: a sensor captures the
energy reflected or emitted by the imaged object
http://what-when-how.com/introduction-to-video-and-image-processing/image-acquisition-introduction-to-
video-and-image-processing-part-1
Introduction
•  Image: a matrix with n rows and m columns (and l
slices in 3D), being each basic element known as
pixel (or voxel in 3D)
Introduction
•  Image Processing: by applying mathematical
operations/rules using the values of the image
pixels (or voxels in 3D) in the Cartesian or in other
domain
⎡ −1 0 +1 ⎤ Sobel operator
⎢ ⎥
∗ ⎢ −2 0 2 ⎥ = Gx
⎢⎣ −1 0 +1 ⎥⎦
Gx 2 + Gy 2 = G
⎡ −1 −2 −1 ⎤
⎢ ⎥
∗ ⎢ 0 0 0 ⎥ = Gy
⎢⎣ +1 +2 +1 ⎥⎦
( ∗ denotes convolution)
Introduction
•  Difficulties: noise, artifacts, occlusion, poor
illumination, reflections, complex objects and
backgrounds
https://rahaddadi.files.wordpress.com/2011/05/face_black_and_white_optical_illusion_cool-s453x562-92306-5803.jpg
http://s1.cdn.autoevolution.com/images/news/the-longest-traffic-jam-in-history-12-days-62-mile-long-47237_1.jpg
Introduction
Usual Pipeline
Image(s) Image(s) segmentation /
enhancement / features extraction
Image(s)
correction
image (pre)processing
tracking 3D vision
computer vision
matching
motion
analysis
registration
image analysis /
computational morphing
vision
Introduction
•  (Pre)processing of noisy images using an
intelligent worm
Original images (a), noisy corrupted images (b) and

smoothed images using different smoothing methods (c-h)
Araujo et al. (2014) Expert Systems with Applications 41(13):5892-5906
Segmentation
Segmentation
•  It is intended to identify in a fully or semi-
automatically manner objects (2D/3D) presented
in static images or in image sequences
•  The most usual methodologies are based on
thresholding, region growing, template
matching, statistical, geometric or physical
modeling, or artificial classifiers
•  It is one of the most usual operations involved in
the computational analysis of objects in images
•  Frequent problems: noise, artifacts, low resolution,
reduced contrast, shapes not previously known,
occlusion, multiple objects, etc.
Segmentation
•  Image segmentation by threshold (binarization)
Ma et al. (2010) Computer Methods in Biomechanics and Biomedical Engineering 13(2):235-246

Segmentation
•  Example: segmentation of contours in dynamic
pedobarography (Otsu’s method, morphologic dilation,
xor operation)
pressure
opaque layer
lamp transparent
layer
lamp
reflected light glass
contact layer
+ glass
mirror
camera
Original images Segmented images
Bastos & Tavares (2004) Lecture Notes in Computer Science 3179:39-50

Segmentation
•  Image segmentation by region growing

Segmentation
•  Example: segmentation of ear structures (region
growing)
Region Growing, x=215; y=254
X: 254 Y: 214
Index: 116.7
RGB: 0.459, 0.459, 0.459
Original Image Segmentation obtained

(bony labyrinth)
Barroso et al. (2011) CNME 2011
Ferreira et al. (2014) Computer Methods in Biomechanics and Biomedical Engineering 17(8):888-904
Segmentation
•  Segmentation based on neuronal networks
Original metallographic After segmentation

images (material microstructures )
Albuquerque et al. (2008) Nondestructive Testing and Evaluation 23(4):273-283
Albuquerque et al. (2009) NDT & E International 42(7):644-651
Segmentation
•  Segmentation of objects based on deformable
templates
Example of a
deformable template
(for the eye)
Carvalho & Tavares (2006) CompIMAGE 2006, 129-134

Carvalho & Tavares (2007) VipIMAGE 2007, 209-215
Segmentation
•  Example: segmentation of eye
features (deformable geometric template)
Original image and associated Segmentation of the iris using a

force (or energy) fields deformable template (a circle)
Segmentation of an
Carvalho & Tavares (2006) CompIMAGE 2006, 129-134 eye using an
Carvalho & Tavares (2007) VipIMAGE 2007, 209-215 deformable template
Segmentation
•  Statistical modeling of objects (point distribution
models)
Vasconcelos & Tavares (2008) Computer Modeling in Engineering & Sciences 36(3):213-241
Segmentation
•  Segmentation of based on active shape models
(point distribution models, optimization)
Vasconcelos & Tavares (2008) Computer Modeling in Engineering & Sciences 36(3):213-241
Segmentation
•  Example: analysis of the vocal tract during
speech production from MR images (active shape model)
Original
image
Final
segmentation
Vasconcelos et al. (2011) Journal of Voice 25(6):732-742

Segmentation
•  Segmentation of objects based on active
contours (i.e. snakes – parametric models)
Esnake = ∫E
s=0
int (v(s)) + Eext (v(s))ds
2 2 2
dv(s) d v(s)
Eint = α (s) + β (s)
ds ds 2
Tavares et al. (2009) International Journal for Computational Vision and Biomechanics 2(2):209-220
Segmentation
•  Example: segmentation of medical images
(active contours - snakes)
Initial contour Final contour
Tavares et al. (2009) International Journal for Computational Vision and Biomechanics 2(2):209-220
Gonçalves et al. (2008) Computer Modeling in Engineering & Sciences 32(1):45-55
Segmentation
•  Segmentation of objects based on the level-set
method (geometrical models)
Typical form of the motion

equation:
∂φ
+ F Δφ = 0
∂t
Ma et al. (2010) Medical Engineering & Physics 32(7):766-774
Segmentation
•  Example: segmentation of the carotid
bifurcation in a Doppler image (active contour / level-
set model)
Segmentation using the contour Segmentation using the level-set

active method (Yessi’s model) method (Chan-Vese’s model)
Silva et al. (2011) VipIMAGE 2011, 117-122
Santos et al. (2013) Expert Systems with Applications 40(16):6570-6579
Jodas et al. (2016) Expert Systems with Applications 46:1-14
Segmentation
•  Example: segmentation of skin pigmented
lesions in dermoscopic images (color spaces, level-
set model)
Illustration of the
segmentation process
Segmentation examples under different imaging conditions
and different types of skin pigmented lesions
Filho et al. (2015) Journal of Medical Systems 39(11):177
Ma & Tavares (2016) IEEE Journal of Biomedical and Health Informatics 20(2):615-623
Oliveira et al. (2016) Expert Systems with Applications 61:53-63
Segmentation
•  Example: segmentation
of 3D CT lung images
(3D level-set model)
Filho et al. (2017) Medical Image Analysis 35:503-516

Segmentation
•  Segmentation of objects based on the level set
method with a prior knowledge

Segmentation
•  Example: segmentation simultaneously of three
organs of the female pelvic cavity in MRI
images (level-set method, a prior knowledge)
Segmentation of the bladder, vagina and rectum in pelvic cavity images

(3 examples)
Ma et al. (2013) Computers in Biology and Medicine 43(4):248-258

Ma et al. (2012) The Int. Journal for Numerical Methods in Biomedical Engineering 28(6-7):714-726
Segmentation
•  Example: segmentation of the bladder walls in
MR images (level-set method, a prior knowledge)
Segmentation of the interior and external walls of the bladder (3 examples)
Ma et al. (2011) Annals of Biomedical Engineering 39(8):2287-2297

Segmentation
•  Example: segmentation of the carotid artery
lumen in MR images (K-means, classification indexes, active
contour model)
3. Cluster with low
1. Original image 2. K-means intensity pixels (inverted) Pre-processing
Noise reduction Contrast improvement
Median filter Adaptive Gamma

Correction
Segmentation
K-means clustering
Obtain pixels Region
with subtractive
with low values growing
clustering
4. Lumen identification To obtain all regions
separately
(classification indexes) 5. Final result
Lumen identification
Calculate Select the region
Extraction of the
classification with maximum Active contour
contour pixels
indexes roundness
Mean roundness, Refinement of the
irregularity and contour
centre indexes
Jodas et al. (2016) Computers in Biology and Medicine 79(1):233-242

Motion Tracking
Motion Tracking
•  It is intended to track the motion (and/or the
deformation) of objects in image sequences
•  In this area, the methodologies based on optical
flow, block matching and stochastic methods
are widespread
•  Usually, it concerns the estimation of the
motion involved, the management of the
features being tracked, the analysis of the
motion tracked and its quantification
•  Usual problems: non-rigid motions, geometric
distortion, non-constant illumination, occlusion,
noise, multiple objects, etc.
Motion Tracking
•  Computational framework
to track features in image
sequences (Kalman Filter or
Unscented Kalman Filter,
optimization, Mahalanobis
distance, management model)
Pinho et al. (2007) Int. Journal of Simulation Modelling 6(2):84-92

Pinho & Tavares (2009) VipIMAGE 2009, 299-304
Pinho & Tavares (2009) Computer Modeling in Engineering &
Sciences 46(1):51-75
Motion Tracking
•  Example: tracking marks in gait analysis (Kalman
filter, Mahalanobis distance, optimization, management
model)
(5 frames)
Prediction Uncertainty Area Measurement Correspondence Result

Pinho et al. (2005) ICCB 2005, 915-926
Pinho & Tavares (2009) Computer Modeling in Engineering & Sciences 46(1):51-75
Motion Tracking
•  Example: tracking marks in order to detect gait
events (Kalman filter, Mahalanobis
distance, optimization)
Sousa et al. (2007) ISHF2007, 331-340

Sousa et al. (2007) ICCB2007, 291-296
Motion Tracking
•  Example: tracking mice in long image
sequences (Kalman filter, Mahalanobis distance,
optimization, management model)
(547 frames)
Pinho et al. (2005) LSCCS, Vol. 4A:463-466

Pinho et al. (2007) International Journal of Simulation Modelling 6(2):84-92
Analysis of Objects:
Matching
Matching
•  The goal is to establish correspondence
between image features
•  It is regularly used in the computational analysis of
objects in images, for example, to register (i.e.
align) objects, recognize objects, attain 3D
information, analyze tracked motion, etc.
•  Generally, it is achieved by considering
invariant characteristics, as curvature, or
displacements in a global/eigen spaces (like in
modal space)
•  Common problems: occlusion, non-rigid
deformations, high shape variations, etc.
Matching
•  Based on physical or geometrical modeling and
modal matching
Modeling Eigenvalues /
(physical or eigenvectors
Contour 1 geometrical) computation
Matching
matrix
assembly
Modeling Eigenvalues /
(physical or eigenvectors
geometrical) computation
Contour 2
Matches
achievement
Bastos & Tavares (2006) Inverse Problems in Science and Engineering 14(5):529-541 (optimization)
Tavares & Bastos (2010) Progress in Computer Vision and Image Analysis 339-368
Matching
•  Example: matching contours in dynamic
pedobarography (FEM modeling, modal matching,
optimization)
pressure
opaque layer
lamp transparent
layer
lamp
reflected light glass
contact layer
+ glass
mirror
camera
Original images Matched contours
Bastos & Tavares (2004) LNCS 3179:39-50

Tavares & Bastos (2010) Progress in Computer Vision and Image Analysis, 339-368
Matching
•  Example: matching contours and surfaces in
dynamic pedobarography (FEM modeling, modal
analysis, optimization)
Matching found Matching found between iso-contours (2 views)

between two contours
Image of dynamic
pedobarography
Matching found between two intensity (pressure) surfaces (2 views)

Tavares & Bastos (2005) Electronic Letters on Computer Vision and Image Analysis 5(3):1-20
Morphing
Morphing (i.e. simulation)
•  It is an especially used in Computer Graphics, but
also very useful in the analysis of objects in images,
for example, to estimate the deformation involved
between objects or between configurations of an
object, to simulate the transitions between shapes
acquired with a high temporal gap, etc.
•  Normally, it is attained by considering simple
geometric transformations
•  However, when it must be considered the real
behavior of the objects, physical based
methodologies and modeling as, for example, FEM,
should be considered
–  Common difficulties are related to the estimation of the
involved forces and with the properties of the adopted
(virtual) material
–  The adequate matching of the objects is crucial
Morphing
•  Physical morphing/simulation of contours (FEM
modeling, modal analysis, optimization, Lagrange’s eq.)
Morphing
•  Example: morphing contours (FEM modeling, modal
analysis, optimization, Lagrange’s equation)
Deformations
estimated
Original images Matching

found
Gonçalves et al. (2008) Computer Modeling in Engineering & Sciences 32(1):45-55

Registration
Registration
•  It is commonly required in order to compare
objects acquired at different time instants or
according to distinct conditions
•  It is essential, for example, in Medicine to follow up
the evaluation of diseases
•  Usually, it is achieved by considering characteristic
features, as points of high curvature, and their
matching, or by minimization of a similarity
measure, followed by the estimation of the
involved transformation
•  Common problems: key and invariant features not
easily detected, occlusion, non-rigid deformations,
severe shape variations, etc.
Registration
•  Registration based on contours matching,
optimization and dynamic programming
The cost matrix is built

based on geometric or
physical principles
The matching is found
based on the minimization
of the sum of the costs
associated to the possible
correspondences
To search for the best
matching is used an
optimization assignment
algorithm
Bastos & Tavares (2006) Inverse Problems in Science and Engineering 14(5):529-541
Oliveira & Tavares (2009) Computer Modeling in Engineering & Sciences 43(1):91-110
Oliveira, Tavares, Pataky (2009) Journal of Biomechanics 42(15):2620-2623
Registration
•  Example: registration of pedobarography
images (geometrical modeling, matching, optimization,
dynamic programming)
Original images and contours Contours and images before and

Oliveira et al. (2009) Journal of Biomechanics 42(15):2620-2623
after the registration
Registration
•  Example: registration of brain MR images
(geometrical modeling, matching, optimization, dynamic
programming)
Correspondences found
Fixed image and Moving image and between the Corpus
contour (MRI) contour (MRI) Callosum contours
Registration: 2D,
monomodal,
intrasubject
Processing time:
0.5 s (AMD
Turion64, 2.0 GHz,
1.0 GB of RAM)
Images dimension:
217x140 pixels
Overlapped images Overlapped images Difference between the

before the registration after the registration images after the registration
Oliveira & Tavares (2014) Computer Methods in Biomechanics and Biomedical Engineering 17(2):73-93
Registration
•  Registration of images based on Fourier transf.
Original images Images before and

Oliveira, Pataky, Tavares (2010) Computer Methods in Biomechanics and Biomedical Engineering 13(6):731-740
Registration
•  Example: registration of brain MR images
(Fourier transform)
Registration: 2D,
monomodal,
intrasubject
Processing time: 2.1 s
(AMD Turion64, 2.0
GHz, 1.0 GB of RAM)
Images dimension:
221x257 pixels
Registration
•  Registration based on the iterative search for the
parameters of the transformation that optimizes a
similarity measure between the input images
Fixed image Moving image
Pre-registration
Similarity measure Interpolator transformation
(optional)
Optimizer Geometric transformation
The optimization algorithm stops when a similarity criterion is achieved
Registration
•  Example: registration of pedobarography
images (Hybrid method: Fourier transform based
registration + optimization of a similarity measure)
Original images Images before and

Oliveira & Tavares (2012) Medical & Biological Engineering & Computing 49,(3):313-323
Registration
•  Example: registration/fusion of head CT/MR
images (optimization of a similarity measure)
Registration: 2D,
multimodal,
intrasubject (without
pre-registration)
Similarity measure: MI
Processing time: 4.6 s
(AMD Turion64, 2.0
GHz, 1.0 GB of RAM)
Images dimension:
246x234 pixels
Registration
•  Example: applications in plantar pressure
image studies
A computational platform was
developed to assist biomechanical
studies that can be used for:
-  Foot segmentation
-  Foot classification: left/right,
high arched, flat, normal, …
-  Foot axis computation
-  Footprint indices
computation
-  Posterior statistical analysis
Oliveira, Sousa, Santos, Tavares (2012) Computer Methods in
Biomechanics and Biomedical Engineering 15(11):1181-1188
Registration
•  Example: registration/fusion using iterative optimization
“Checkerboard” of the slices before the registration (CT/MRI-PD, brain)
F M F M
M F M F
F M F M
M F M F
(The “checkerboard” slice is built by interchanging square patches of both slices and preserving
their original spatial position in the fixed (F) and moving (M) slices)
Registration
•  Example: registration/fusion using iterative opt. (cont.)
Checkerboard of the slices after the registration (CT/MRI-PD, brain)
Registration: 3D, multimodal, intrasubject; Similarity measure: MI
Registration
•  Example: application on brain DaTSCAN SPECT
images
Brain DaTSCAN SPECT images are used to assist the diagnosis of
the Parkinson’s disease and to distinguish it from other degenerative
diseases. The solution developed is able to:
–  Segment the relevant areas and perform dimensional analysis
–  Quantify the binding potential of the basal ganglia
–  Computation of statistical data relatively to a reference population
–  Image classification for diagnosis purposes
Normal Alzheimer Idiopathic Essential

Parkinsonism tremor
Registration
images
3D volume images are automatically registered and statistical
analysis relatively to a reference population can be attained
Mean slice from the Corresponding Difference of Z-scores mapping over

population used as slice of a patient intensities the slice (red – high Z-
reference scores)
(The blue rectangles represent the 3D ROIs used
to compute the binding potentials)
Oliveira et al. (2014) The Quarterly Journal of Nuclear Medicine and Molecular Imaging 58(1):74-84
Registration
images
Basal ganglia 3D shape reconstruction and quantification
Basal ganglia Basal ganglia Basal ganglia

from a mean from a patient from a patient
image of a normal with idiopathic with vascular
population Parkinson’s disease Parkinson’s disease
Oliveira et al. (2014) The Quarterly Journal of Nuclear Medicine and

Molecular Imaging 58(1):74-84
Registration
•  Example: application on brain DaTSCAN
SPECT/CT fusion
3D visualization after CT/SPECT fusion

(the lesion identified in the SPECT
Three slices (coronal, sagittal and axial) after slices is indicated)
registration and identification of the potential lesion
Registration
•  Registration of image sequences: spatial &
temporal registration
Fixed sequence Moving sequence
Apply the spatio & Build the temporal Estimate the linear
Compute the
temporal representative temporal
similarity measure
transformation images registration
Build the spatio & Search for the transformation

Optimizer temporal that register the temporal
transformation representative images
Registration optimization Pre-registration
Oliveira, Sousa, Santos, Tavares (2011) Medical & Biological Engineering & Computing 49(7):843-850
Oliveira & Tavares (2013) Medical & Biological Engineering & Computing 51(3):267-276
Registration
•  Example: registration of image sequences in
dynamic pedobarography (spatial & temporal registration)
Device: Light reflection
(25 fps, resolution 30
pixels/cm2)
Before the
Image similarity
registration
measure: MSD
Sequences dimension:
160x288x22,
160x288x25
Processing time: 1 min
(using an AMD
After the
Turion64, 2.0 GHz, 1.0
registration
GB of RAM)
Template Source Overlapped

sequence sequence sequences
3D Reconstruction
3D Reconstruction
•  It is intended to accomplish the 3D reconstruction of
objects or scenes from images
•  In this area, the following methodologies are common:
external shapes – active techniques (with energy projection
or relative motion), passive techniques (without energy projection
nor relative motion) and of space carving; inner shapes – 2D
segmentation (contours, for example) and data interpolation,
3D segmentation or deformation of 3D deformable
models prebuilt
•  Usually, it involves tasks of camera calibration, data
segmentation, matching, triangulation, registration and
fusion
•  Common problems: geometric distortion, insufficient or
unstable illumination, occlusion, noise, multiple objects,
complex shapes and topologies, etc.
3D Reconstruction
•  3D reconstruction of organs from medical images
based on 2D segmentation, loft (marching
cubes) and smooth
Pimenta et al. (2006) CompIMAGE 2006, 343-348 Reconstructed organs

Alexandre et al. (2007) VipIMAGE 2007, 359-362 from pelvic cavity
3D Reconstruction
•  3D reconstruction of scenes using techniques of
active vision (dense
stereo vision)
Original image pair Disparity map

obtained
Azevedo et al. (2006) VISAPP 2006, 383-388
3D Reconstruction
•  3D reconstruction of objects by space carving
Pattern image Pattern and object turntable

sequence image sequence
Camera Background/object
calibration segmentation
Volumetric 3D
reconstruction
3D model
polygonization
Azevedo et al. (2008) Advances in Computational Vision and Medical Image Processing: Methods and
Applications, 117-136
3D Reconstruction
•  Example: 3D reconstruction of objects by space
carving
Original images Computational 3D models built voxelized

and poligonized
Azevedo et al. (2008) Advances in Computational Vision and Medical Image Processing: Methods and
Applications, 117-136
3D Reconstruction
•  Example: 3D reconstruction of objects by space
carving
Original images Computational 3D models built voxelized

and poligonized
3D Reconstruction
•  Example: 3D reconstruction from multiple views
(registration/fusion)
Axial and sagittal T2-weighted MR images
3D Reconstruction of the bladder by fusion data

from the axial and sagittal images (2 views)

Conclusions and Future
Directions
Conclusions
•  The area of image processing and analysis is very
complex and demand, but of raised importance in many
domains
•  Numerous hard challenges exist, as for example, adverse
conditions in the image acquisition process, occlusion,
objects with complicate shapes, with topological variations
or undergoing complex motion or deformation
•  Considerable work has already been developed, but
important and complex goals still to be reached
•  Methods and methodologies of other research areas,
as of Mathematics, Computational Mechanics, Medicine
and Biology, can contribute significantly for their
reaching
Future Directions
•  Applications involving image registration and fusion
in space and time, particularly with 4D data
•  Applications with images acquired by different imaging
modalities, mainly by ultrasound and microscopic
imaging
•  Reconstruction of more realistic 3D models by
fusion the data acquired from different views and
imaging modalities
•  Integration of advanced physical modeling
principles into algorithms of image analysis
•  Application cases: nuclear medicine, assisted medical
diagnosis and intervention, cells imaging
•  …
Acknowledgments
The work presented has been done with the
funding of the research projects and Institutions:
–  NORTE-01-0145-FEDER-000022
–  PTDC/BBB-BMD/3088/2012
–  PTDC/SAU-BEB/102547/2008
–  PTDC/SAU-BEB/104992/2008
–  PTDC/EEA-CRO/103320/2008
–  UTAustin/CA/0047/2008
–  UTAustin/MAT/0009/2008
–  PDTC/EME-PME/81229/2006
–  PDTC/SAU-BEB/71459/2006
–  POSC/EEA-SRI/55386/2004
Research Team
(Image Processing and Analysis)
Research Team (Image Processing and Analysis)
•  Post-Doc students (5):
–  Finished: Alexandre Carvalho, Simone Prado, Mercedes Filho, Pedro Predosa
–  In course: Zhen Ma
•  PhD students (15):
–  Finished: Zhen Ma, Francisco Oliveira, Teresa Azevedo, Daniel Moura, Sandra Rua,
Maria Vasconcelos, Roberta Oliveira
–  In course: João Nunes, Alex Araujo, Carlos Gulo, Danilo Jodas, Pedro Morais, Andre
Pilastri, Domingos Vieira, Jessica Delmoral
•  MSc students (33):
–  Finished: Raquel Alves, Carolina Tabuas, Jorge Pereira, Luis Ribeiro, Luis Ferro,
Rita Teixeira, Liliana Azevedo, Diana Cidre, Célia Cruz, Priscila Alves, Pedro
Gomes, Nuno Sousa, Diogo Faria, Elisa Barroso, Ana Jesus, Frederico Jacobs,
Gabriela Queirós, Daniela Sousa, Francisco Oliveira, Teresa Azevedo, Maria
Vasconcelos, Raquel Pinho, Luísa Bastos, Cândida Coelho, Jorge Gonçalves,
Frederico Junqueira, Jessica Delmoral, Ricardo Le
–  In course: Bruna Pires, Diogo Correia, Rafaela Pinto
•  BSc students (2)
–  Finished: Ricardo Ferreira, Soraia Pimenta
Publications & Events
Taylor & Francis journal “Computer Methods in
Biomechanics and Biomedical Engineering:
Imaging & Visualization”
Indexed in:
Scopus, DBLP and Thomson Reuters
Emerging Sources Index ©
www.tandfonline.com/tciv
Springer book series “Lecture Notes in
Computational Vision and Biomechanics (LNCV&B)”
Editors: João Manuel R. S. Tavares, Renato Natal Jorge
Indexed in
www.springer.com/series/8910
Events
Thank You!
(authenticus.up.pt)
Image Processing and Analysis
in Biomechanics
João Manuel R. S. Tavares
tavares@fe.up.pt www.fe.up.pt/~tavares
March 24, 2017

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Image Processing and Analysis

March 24, 2017

Original images Computational 3D voxelized and

Original images (a), noisy corrupted images (b) and

Ma et al. (2010) Computer Methods in Biomechanics and Biomedical Engineering 13(2):235-246

Original images Segmented images

Bastos & Tavares (2004) Lecture Notes in Computer Science 3179:39-50

Ma et al. (2010) Computer Methods in Biomechanics and Biomedical Engineering 13(2):235-246

Original Image Segmentation obtained

Original metallographic After segmentation

Carvalho & Tavares (2006) CompIMAGE 2006, 129-134

Original image and associated Segmentation of the iris using a

Vasconcelos et al. (2011) Journal of Voice 25(6):732-742

Initial contour Final contour

Typical form of the motion

Segmentation using the contour Segmentation using the level-set

Filho et al. (2017) Medical Image Analysis 35:503-516

Ma et al. (2010) Medical Engineering & Physics 32(7):766-774

Segmentation of the bladder, vagina and rectum in pelvic cavity images

Ma et al. (2013) Computers in Biology and Medicine 43(4):248-258

Segmentation of the interior and external walls of the bladder (3 examples)

Ma et al. (2011) Annals of Biomedical Engineering 39(8):2287-2297

Noise reduction Contrast improvement

Median filter Adaptive Gamma

Jodas et al. (2016) Computers in Biology and Medicine 79(1):233-242

Pinho et al. (2007) Int. Journal of Simulation Modelling 6(2):84-92

Prediction Uncertainty Area Measurement Correspondence Result

Sousa et al. (2007) ISHF2007, 331-340

Pinho et al. (2005) LSCCS, Vol. 4A:463-466

Bastos & Tavares (2004) LNCS 3179:39-50

Matching found Matching found between iso-contours (2 views)

Matching found between two intensity (pressure) surfaces (2 views)

Original images Matching

Gonçalves et al. (2008) Computer Modeling in Engineering & Sciences 32(1):45-55

The cost matrix is built

Original images and contours Contours and images before and

Overlapped images Overlapped images Difference between the

Original images Images before and

Fixed image Moving image

Optimizer Geometric transformation

The optimization algorithm stops when a similarity criterion is achieved

Original images Images before and

“Checkerboard” of the slices before the registration (CT/MRI-PD, brain)

Checkerboard of the slices after the registration (CT/MRI-PD, brain)

Registration: 3D, multimodal, intrasubject; Similarity measure: MI

Normal Alzheimer Idiopathic Essential

Mean slice from the Corresponding Difference of Z-scores mapping over

Basal ganglia Basal ganglia Basal ganglia

Oliveira et al. (2014) The Quarterly Journal of Nuclear Medicine and

3D visualization after CT/SPECT fusion

Fixed sequence Moving sequence

Build the spatio & Search for the transformation

Registration optimization Pre-registration

Template Source Overlapped

Pimenta et al. (2006) CompIMAGE 2006, 343-348 Reconstructed organs

Original image pair Disparity map

Pattern image Pattern and object turntable

Original images Computational 3D models built voxelized