Ghassan Hamarneh
 Professor
 School of Computing Science
 Faculty of Applied Science
 Simon Fraser University

 ACM Senior Member & IEEE Senior Member
 BRC RAMP NeuroDevNet NeuroScience
 CDIRE BIONF MICCAI BCNI CFRI PHP

 
Medical Image Analysis Lab

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Software Download (software provided "as is")

* names of students leading the code development appear between parentheses
dMRIGraphEmbed
Take a field of diffusion orientation distribution functions (ODF) and map them  to a graph representation
(Brian Booth)
DijkstraTract
 Take a diffusion MRI scan and generate a graph representation, combined with Dijkstra’s algorithm to perform minimal path tractography.
(Brian Booth)
DT-ICE
MATLAB tool to generate information content measures (e.g. entropy and joint entropy) from tensor-valued data.
(Brian Booth)
WalkTract
MATLAB tool for competitive, multi-region, probabilistic tractography.
(Brian Booth)
DT-STRUCT
MATLAB toolbox to highlight corners, tubular structures, and sheet-like structures in diffusion tensor images.
(Brian Booth & Krishna Nand)
DT-Frenet
MATLAB tool to segment highly-curved fiber bundles from DTI
(Brian Booth)

STEAM

Statistical Template Estimation for Abnormality Mapping
(Brian Booth)
CervCellSeg
MATLAB code for segmenting cervical cells, based on "A Variational Approach for Overlapping Cell Segmentation" (Overlapping Cervical Cytology Image Segmentation Challenge, ISBI 2014)
(Masoud Nosrati)

DeformIt 2.0

Image Data Augmentation Tool: Simulate novel images with ground truth segmentations from a single  image-segmentation pair, now with support for scalar, vector, and tensor-valued 2D and 3D images
(Brian Booth)
 
View3D
MATLAB viewer for 3D scalar, vector, and tensor-valued medical images 
(Hossein Badakhshannoory)
 
CudaFitKMdPET
CUDA code for Fast GPU Fitting of Kinetic Models for Dynamic PET
(Ben Smith)
DT-MRI Bilateral Filtering
(Judith Hradsky & Brian Booth)
MRF Scale Selection
MRF based method for vessel scale selection
(Hengameh Mirzaliian)
 
HairSim
Software for simulating hair on skin images for dermatology studies
(Hengameh Mirzaliian)
 
ILR Toolkit
Software library for manipulating multi-region, probabilistic shapes using Aitchison geometry
(Shawn Andrews)
Out of date.
Refer to
DeformIt 2.0 instead.
DeformIt

Image Data Augmentation Tool: Simulate novel images with ground truth segmentations from a single  image-segmentation pair
(Preet Jassi and Lisa Tang)
 
TongueTrack
Software for tracking the movement of the tongue in ultrasound sequences
(Lisa Tang)
 
VascuSynth
Simulate 3D images of vascular trees based on oxygen demand maps and physical parameters
(Preet Jassi)
  
TurtleSeg
Interactive 3D image segmentation software with a unique "spotlight" feature
(Andrew Top)
PerceptVis
Perception-based visualization of manifold-valued medical images using distance preserving dimensionality reduction
(Chris McIntosh)
FastRW
Fast version of random walker with priors
(Shawn Andrews)
ITK on Apple iOS
Documentation and code for running ITK on iOS devices (iPod touch, iPhone, iPad)
(Boris Shabash & Zhi Feng Huang)
LiveVessel
Intuitive and efficient vessel segmentation tool, finds centre-line and boundaries simultaneously
(Miranda Poon and Ryan Dickie)
NMQC on FlintBox  (License Extension)
scintillation camera quality control tests following NEMA procedures
(Andy Rova)
ACO Shape Correspondence  [on TMW]
Ant Colony Optimization for Shape Correspondence
(Olive van Kaick)
n-SIFT
n-dimensional SIFT
(scale invariant feature transform)
(Warren Cheung)
I-DO
ITK Deformable Organisms framework
(Chris McIntosh)
MATITK
MATLAB-ITK interface for calling ITK filters from MATLAB
(Vincent Chu)
Livewire
Matlab program for interactive 2D segmentation
Out-of-date. Refer to View3D instead
OrthoView

Matlab GUI for interactive viewing of 3D volumes
Active Contour Models (Snakes)
Matlab program for interactive 2D segmentation
Active Shape Models
Matlab program for 2D segmentation  of known shapes
Spring-Mass Mesh Model
Matlab Physics-based implementation of a spring-mass mesh model
Medial Shape Profiles
Matlab GUI demo for shape representation & (statistics- and operator-based) deformations
 
Synthetic Sequence Generator
Matlab GUI for generating synthetic sequences (shapes and images)
Hough Transform
Matlab GUI  for line detection
Digital Oscilloscope
Displaying digital signals
 
 
 
back© 2003-2015 G. Hamarneh Contact Email [replace (at) with @] Home  Last update: 29-Dec-2014top