Software

Names of students leading the code development appear between parentheses

HistoGlimpseRNN

Recurrent Visual Attention Model for Analyzing Histopathology Whole Slide Images

(Aïcha Bentaieb)

UncertaintyGuidedFCN

Uncertainty-guided Multi-loss Functions

(Aïcha Bentaieb)

StainTransferNet

Transferring Stains Across Histopathology Images and Datasets

(Aïcha Bentaieb)

BrainNetCNN

Convolutional neural networks for connectomes

(Jeremy Kawahara and Colin Brown)

PulsatileVascuSeg

Highlight vascular structures exhibiting radial distension pulsatile motions

(Alborz Amir-Khalili)

TopoFCN

Topology-Aware Fully Convolutional Network for Image Segmentation

(Aïcha Bentaieb)

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 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"

(Masoud Nosrati)

DeformIt 2.0

Image Data Augmentation Tool: Simulate novel images with ground truth segmentations from a single image-segmentation pair

(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)

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 and ITK Image IO 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

(3D SIFT, 4D SIFT, etc.)

(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

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)