SFU Medical Image Analysis Lab

DermSynth3D

Official code for "DermSynth3D: Synthesis of in-the-wild Annotated Dermatology Images". A data generation pipeline for creating photorealistic in-the-wild synthetic dermatalogical data with rich multi-task annotations for various skin-analysis tasks.

awesome-skin-image-analysis-datasets

Datasets for skin image analysis

FuseNet

Repository for our deep multi-frequency fusion paper in DOT imaging.

CIRCLe

CIRCLe: Color Invariant Representation Learning for Unbiased Classification of Skin Lesions. Mirror of https://github.com/arezou-pakzad/CIRCLe

mial-hamarneh-repository-template

A template to accelerate the release of state of the art software accompanying papers released at Prof. Hamarneh's medicalimageanalysis.com

skin-lesion-segmentation-survey

DOTNet

Addresses the problem of reconstructing images acquired by diffuse optical tomography using deep learning.

Rank2Count

The official repository for the paper "Learning-to-Count by Learning-to-Rank", accepted as an oral presentation at CRV2023

LADOTNet

Repository for our limited angle deep learning based DOT image reconstruction

MultiNet

Repository for our deep multitask paper in DOT imaging.

SLiMe

Segment-Like-Me: 1-shot image segmentation using Stable Diffusion

SubPrecisionContactDetection.jl

A Julia package to detect contacts below the precision of a superresolution microscope between 2 subcellular organelles in 2-channel superresolution (STED) microscopy. Mirror of https://github.com/bencardoen/SubPrecisionContactDetection.jl

SYRAC

Synthesize, Rank, Count; A Method for unsupervised crowd counting using latent diffusion models

TreeDiffusion

Official Code for "Representing Anatomical Trees by Denoising Diffusion of Implicit Neural Fields"

ERGO.jl

Object / density detection in astigmatic superresolution dSTORM microscopy. Mirror of https://github.com/bencardoen/ERGO.jl

ERGO.py

Mirror of https://github.com/bencardoen/ERGO.py

labtools

A set of scripts to streamline remote working with clusters. Mirror of https://github.com/bencardoen/labtools

singularity_slurm_cuda

Example on how to leverage Singularity on HPC. Mirror of https://github.com/bencardoen/singularity_slurm_cuda

skin3d

Mirror of https://github.com/jeremykawahara/skin3d

SlurmMonitor.jl

SLURM Monitor to detect node health and notify Slack in case of events. Mirror of https://github.com/bencardoen/SlurmMonitor.jl

SPECHT.jl

SPECHT is a Julia implementation of a contrastive weakly supervised object detection and identification method for fluorescence microscopy. Mirror of https://github.com/bencardoen/SPECHT.jl

Colocalization.jl

Colocalization metrics and distances for images or their sparse representations. Mirror of https://github.com/bencardoen/Colocalization.jl

DataCurator.jl

A scalable Julia package to transparently validate and transform large biomedical datasets using human readable recipes that are translated to machine verifiable templates. Mirror of https://github.com/bencardoen/DataCurator.jl

DEEMD

Treatment efficacy estimation based on microscopy images on RxRx19a

IDE-tips-tricks

Gist to collect urls/tips/tricks/configs for setup of IDEs (VSCode, vi, neovim, cgpt, copilot, ...)

LogParadox.jl

Detects sufficient and necessary conditions for pattern inversion conditional on log transform Mirror of https://github.com/bencardoen/LogParadox.jl

MaskTune

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

nERdy

This repository provides code for training, inference of endoplasmic reticulum segmentation method nERdy+, and the analysis of the dynamics presented in the paper nERdy: network analysis of endoplasmic reticulum dynamics

SmlmTools.jl

Computational tools for single molecule localization / superresolution microscopy (point clouds). Mirror of https://github.com/bencardoen/SmlmTools.jl

VascuSynth

VascuSynth is short for Vascular Synthesizer: An algorithm and accompanying software for synthesizing vascular or other tubular, tree-like structures