Primary software developer named between parentheses

Code supporting our work on SLiMe: Segment-Like-Me paper

(Aliasghar Khani)

Code supporting our work on SYRAC: Synthesize, Rank, and Count

(Adriano D’Alessandro) 

SubPrecisionContactDetection (MCS-DETECT)

Code supporting our Journal of Cell Biology paper on automatic sub-precision membrane contact site detection, in our paper: Membrane contact site detection (MCS-DETECT) reveals dual control of rough mitochondria-ER contacts

(Ben Cardoen)


Code supporting our 2023 paper: Orthogonal Multi-frequency Fusion Based Image Reconstruction and Diagnosis in Diffuse Optical Tomography.

(Hanene Ben Yedder and Ben Cardoen) 


Code supporting our 2022 IEEE TMI paper: Multitask Deep Learning Reconstruction and Localization of Lesions in Limited Angle Diffuse Optical Tomography

(Hanene Ben Yedder and Ben Cardoen) 


Code supporting our MICCAI 2019 paper: Limited-angle diffuse optical tomography image reconstruction using deep learning.

(Hanene Ben Yedder and Ben Cardoen) 


Code supporting our MICCAI MLMIR 2018 paper: Deep Learning based Image Reconstruction for Diffuse Optical Tomography.

(Hanene Ben Yedder and Aïcha Bentaieb) 


Code supporting our MICCAI 2023 paper: Multi-domain Vision Transformer for Small Medical Image Segmentation Datasets

(Siyi Du) 


Code supporting our paper: DermSynth3D: Synthesis of in-the-wild annotated dermatology images

(Ashish Sinha, Jeremy Kawahara, Arezou Pakzad, Kumar Abhishek) 


Code supporting our CRV 2023 paper: Learning-to-Count by Learning-to-Rank

(Adriano D’Alessandro) 


Code supporting our paper DataCurator.jl: Efficient, portable, and reproducible validation, curation, and transformation of large heterogeneous datasets using human-readable recipes compiled into machine verifiable templates

(Ben Cardoen) 


Reference Julia implementation of colocalization metrics for 2D and 3D (microscopy) images



Code supporting our paper Log-Paradox: Necessary and sufficient conditions for confounding statistically significant pattern reversal under the log-transform  

(Ben Cardoen) 

Multi-Modal AI Explanation

Code supporting our two papers: MedIA - Guidelines and evaluation of clinical explainable AI in medical image analysis; and AAAI: Evaluating Explainable AI on a Multi-Modal Medical Imaging Task: Can Existing Algorithms Fulfill Clinical Requirements?

(Weina Jin) 


Code supporting our paper: Mouth2audio: Intelligible Audio Synthesis from Videos with Distinctive Vowel Articulation

(Saurabh Garg

Active Learning from Noisy Teacher 

Code supporting our CMIG paper: Active Deep Learning from a Noisy Teacher for Semi-supervised 3D Image Segmentation: Application to COVID-19 Pneumonia Infection in CT

(Arafat Hussain) 


Code supporting our NeurIPS paper MaskTune: Mitigating Spurious Correlations by Forcing to Explore

(Saeid Asgari, Aliasghar Khani) 

Learning to Segment from Noisy Annotations

Code supporting our MICCAI MIL3ID paper on Learning to Segment Skin Lesions from Noisy Annotations

(Zahra Mirikharaji)

Star Shape Segmentation Loss

Code supporting our MICCAI 2018 paper on star shape prior for CNN based image segmentation

(Zahra Mirikharaji)


Code supporting our work on SPECHT: Self-tuning Plausibility Based Object Detection Enables Quantification of Conflict in Heterogeneous Multi-scale Microscopy

(Ben Cardoen)

Code supporting our ECCV ISIC paper CIRCLe: Color Invariant Representation Learning for Unbiased Classification of Skin Lesions

(Arezou Pakzad)

Code supporting our ECCV ISIC paper, FairDisCo: Fairer AI in Dermatology via Disentanglement Contrastive Learning

(Siyi Du)

Code supporting our ICCV VRMI paper on WhiteNNer-Blind Image Denoising via Noise Whiteness Priors

(Saeed Izadi)

Multimodal XAI

Code supporting our AAAI paper on Evaluating Explainable AI on Multi-Modal Medical Imaging Task

(Weina Jin)


Code supporting our Medical Image Analysis paper: Skin3D: Detection and Longitudinal Tracking of Pigmented Skin Lesions in 3D Total-Body Textured Meshes

(Mengliu Zhao, Jeremy Kawahara, Kumar Abhishek, and Sajjad Shamanian)


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) 


Code for AECNN: Adversarial and Enhanced CNN for data-efficient segmentation of gastrointestinal polyps from colonoscopy images

(Saeed Izadi)

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) 


This minimal path tractography toolbox is a MATLAB tool to take a diffusion MRI (dMRI) scan and generate a graph representation where a each node is a voxel in the dMRI and graph edges are weighted by the diffusion measurements. This graph is then combined with Dijkstra's algorithm to perform minimal path tractography

(Brian Booth)



MATLAB tool to generate information content measures from tensor-valued data.  Estimators are provided for entropy, joint entropy, conditional entropy, mutual information, and variation of information. Both Shannon and Renyi-based information content estimators are implemented.

(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. In particular, DT-STRUCT can highlight corners, tubular structures, and sheet-like structures. Each structure detector can be run at multiple spatial scales.

(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", which was submitted to the "Overlapping Cervical Cytology Image Segmentation Challenge", held in conjunction with IEEE International Symposium on Biomedical Imaging (IEEE 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)  

Note:  Download this file for sample code and modifications to simplify running DeformIt on 2D colour images.



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

(Hossein Badakhshannoory) 

Documentation (PDF file)


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)


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)