Code supporting our IEEE TMI paper: ERGO: efficient recurrent graph optimized emitter density estimation in single molecule localization microscopy.

(Ben Cardoen)

Learning-to-Augment Noisy & Denoised Data

Code supporting our paper Computers in Biology and Medicine 2021 paper: Learning-to-Augment Strategy using Noisy and Denoised Data: Improving Generalizability of Deep CNN for the Detection of COVID-19 in X-ray Images

(Mohammad Momeny)


Code supporting our papers CMIG2021, MICCAI2019, MICCAI MLMI 2019 for 2D ImHistNet and 3D ImHistNet - Learnable Image Histogram-based DNN.

(Arafat Hussain)

Generalizable Feature Learning with Class Imbalance

Code supporting our MICCAI 2019 paper: Generalizable Feature Learning in the Presence of Data Bias and Domain Class Imbalance: Application to Skin Lesion Classification

(Chris Yoon)

MCC Loss for Segmentation

A loss function for training deep segmentation models based on the Matthews Correlation Coefficient (supporting our ISBI 2021 paper)

(Kumar Abhishek)


Super-Resolution NETwork Analysis, SuperResNET, is an integrated software for the analysis of 3D single molecule localization microscopy (SMLM) point cloud data. It consists of computational modules to read, pre-process, post-process, quantify, and visualize 3D SMLM data. SuperResNET allows the user to extract, visualize, and analyze biological clusters. SuperResNET is largely based on the original Scientific Reports 2018 and Scientific Reports 2019 works.

(Ismail Khater)


Missing MRI Pulse Sequence Synthesis using Multi-Modal Generative Adversarial Network

(Anmol Sharma)

Illumination-based Transformations for Skin Lesion Images

Generating transformations based on illumination information and color imaging of the skin for RGB skin lesion images.

(Kumar Abhishek)


Superresolution visualization of 3D protein localization data from a range of super-resolution microscopes

(Ben Cardoen)

GAN Skin Lesion Segmentation

Code for ISBI 2018 paper: Generative adversarial networks to segment skin lesions
(Saeed Izadi)

Super-Resolution via Bilinear Pooling

Code for MICCAI 2019 MLMIR: Image Super Resolution via Bilinear Pooling: Application to Confocal Endomicroscopy

(Saeed Izadi)

Super-Resolution (Confocal Laser Endomicroscopy)

Code for MICCAI 2018: Can Deep Learning Relax Endomicroscopy Hardware Miniaturization Requirements?

(Saeed Izadi)


Trained CNN to detect four types of dermoscopic criteria based on our winning entry for Part 2 of the 2017 ISIC Skin Challenge

(Jeremy Kawahara)

SMLM PC3 Cav1/CAVIN1 Point Cloud Data

3D point clouds of super resolution molecule localization microscopy (SMLM) of Cav1 protein in prostate cancer (PC3) and CAVIN1/PTRF transfected PC3 (PC3-PTRF) cells

(Ismail Khater)

Melanoma Recognition via Visual Attention

Attention-based method for melanoma recognition, with attention map regularization

(Yiqi Yan and Jeremy Kawahara)

Local Synthetic Instances (LSI)

An oversampling method for synthetic data generation or similar tasks. It is designed for the challenging case of high-dimensional, non-gaussian data with low sample size

(Colin Brown)


Recurrent Visual Attention Model for Analyzing Histopathology Whole Slide Images

(Aïcha Bentaieb)


Uncertainty-guided Multi-loss Functions

(Aïcha Bentaieb)


Transferring Stains Across Histopathology Images and Datasets

(Aïcha Bentaieb)


Convolutional neural networks for connectomes

(Jeremy Kawahara and Colin Brown)


Highlight vascular structures exhibiting radial distension pulsatile motions

(Alborz Amir-Khalili)


Topology-Aware Fully Convolutional Network for Image Segmentation

(Aïcha Bentaieb)


Take a field of diffusion orientation distribution functions (ODF) and map them to a graph representation

(Brian Booth)


Take a diffusion MRI scan and generate a graph representation, combined with Dijkstra’s algorithm to perform minimal path tractography.

(Brian Booth)


MATLAB tool to generate information content measures from tensor-valued data.

(Brian Booth)


MATLAB tool for competitive, multi-region, probabilistic tractography.

(Brian Booth)


MATLAB toolbox to highlight corners, tubular structures, and sheet-like structures in diffusion tensor images.

(Brian Booth & Krishna Nand)


MATLAB tool to segment highly-curved fiber bundles from DTI

(Brian Booth)


Statistical Template Estimation for Abnormality Mapping

(Brian Booth)


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)


MATLAB viewer for 3D scalar, vector, and tensor-valued medical images

(Hossein Badakhshannoory)


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)


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)


Software for tracking the movement of the tongue in ultrasound sequences

(Lisa Tang)


Simulate 3D images of vascular trees based on oxygen demand maps and physical parameters

(Preet Jassi)


Interactive 3D image segmentation software with a unique "spotlight" feature

(Andrew Top)


Perception-based visualization of manifold-valued medical images using distance preserving dimensionality reduction

(Chris McIntosh)


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)


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-dimensional scale invariant feature transform (SIFT)(3D SIFT, 4D SIFT, etc.)

(Warren Cheung)


ITK Deformable Organisms framework

(Chris McIntosh)


MATLAB-ITK interface for calling ITK filters from MATLAB

(Vincent Chu)


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)