SFU Medical Image Analysis Lab

All

35 repositories

SubPrecisionContactDetection.jl
Public
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
julia contact interaction superresolution sted-microscopy subprecision
Julia
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GNU Affero General Public License v3.0
•0•1•0•0•Updated Sep 19, 2024Sep 19, 2024
AFreeCA
Public
Python
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Other
•0•0•0•0•Updated Sep 4, 2024Sep 4, 2024
LesionElevation
Public
[MICCAI ISIC 2024] Code for "Lesion Elevation Prediction from Skin Images Improves Diagnosis"
MIT License
•0•1•0•0•Updated Jul 30, 2024Jul 30, 2024
StyleSeg
Public
[MICCAI ISIC 2024] Code for "Segmentation Style Discovery: Application to Skin Lesion Images"
MIT License
•0•3•0•0•Updated Jul 30, 2024Jul 30, 2024
DermSynth3D
Public
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.
medical-imaging body-parser synthesis deeplearning skin-segmentation dermatology 3d-graphics image-blending synthetic-dataset-generation skin-images
Jupyter Notebook
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GNU Affero General Public License v3.0
•3•23•0•0•Updated Jul 28, 2024Jul 28, 2024
nERdy
Public
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
Python
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GNU Affero General Public License v3.0
•0•0•0•0•Updated Jul 19, 2024Jul 19, 2024
TreeDiffusion
Public
Official Code for "Representing Anatomical Trees by Denoising Diffusion of Implicit Neural Fields"
tree-structure vessel-segmentation occupancy-modeling neural-fields implicit-surfaces diffusion-models vasculature implicit-neural-representation miccai2024
Python
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MIT License
•0•2•0•0•Updated Jul 4, 2024Jul 4, 2024
awesome-skin-image-analysis-datasets
Public
Datasets for skin image analysis
machine-learning deep-learning datasets medical-image-analysis melanoma skin-lesion-classification skin-lesion-segmentation dataset-collection
MIT License
•6•23•0•0•Updated Jun 19, 2024Jun 19, 2024
VascuSynth
Public
VascuSynth is short for Vascular Synthesizer: An algorithm and accompanying software for synthesizing vascular or other tubular, tree-like structures
C++
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Apache License 2.0
•0•0•1•0•Updated Apr 10, 2024Apr 10, 2024
MaskTune
Public
Code supporting our NeurIPS paper MaskTune: Mitigating Spurious Correlations by Forcing to Explore
Python
•0•0•0•0•Updated Apr 10, 2024Apr 10, 2024
DEEMD
Public
Treatment efficacy estimation based on microscopy images on RxRx19a
Python
•0•0•0•0•Updated Oct 18, 2023Oct 18, 2023
SYRAC
Public
Synthesize, Rank, Count; A Method for unsupervised crowd counting using latent diffusion models
Python
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Other
•0•1•0•0•Updated Oct 6, 2023Oct 6, 2023
FuseNet
Public
Repository for our deep multi-frequency fusion paper in DOT imaging.
frequency deep-learning cancer fusion direct-imaging medical-image-analysis diffuse-optical-tomography
Python
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GNU Affero General Public License v3.0
•0•4•0•0•Updated Oct 4, 2023Oct 4, 2023
DOTNet
Public
Addresses the problem of reconstructing images acquired by diffuse optical tomography using deep learning.
deep-learning image-reconstruction probe breast-cancer early-detection diffuse-optical-tomography
Python
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MIT License
•0•2•0•0•Updated Oct 4, 2023Oct 4, 2023
LADOTNet
Public
Repository for our limited angle deep learning based DOT image reconstruction
deep-learning image-reconstruction probe artifacts transfer-learning breast-cancer diffuse-optical-tomography
Python
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GNU Affero General Public License v3.0
•0•1•0•0•Updated Oct 4, 2023Oct 4, 2023
MultiNet
Public
Repository for our deep multitask paper in DOT imaging.
real-time localization deep-learning cancer image-reconstruction probe breast-cancer multitask-learning lesion-detection reconstruction-algorithm
Python
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GNU Affero General Public License v3.0
•0•1•0•0•Updated Oct 4, 2023Oct 4, 2023
SLiMe
Public
Segment-Like-Me: 1-shot image segmentation using Stable Diffusion
python pytorch image-segmentation self-attention few-shot-segmentation cross-attention stable-diffusion 1-shot-segmentation was-attention
Python
•0•2•0•0•Updated Sep 27, 2023Sep 27, 2023
skin3d
Public
Mirror of https://github.com/jeremykawahara/skin3d
Jupyter Notebook
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Other
•0•0•0•0•Updated Jul 31, 2023Jul 31, 2023
IDE-tips-tricks
Public
Gist to collect urls/tips/tricks/configs for setup of IDEs (VSCode, vi, neovim, cgpt, copilot, ...)
MIT License
•1•0•0•0•Updated Jul 4, 2023Jul 4, 2023
skin-lesion-segmentation-survey
Public
dermatology medical-image-analysis skin-lesion skin-lesion-segmentation deep-learning segmentation
MIT License
•0•4•0•0•Updated Jun 16, 2023Jun 16, 2023
DataCurator.jl
Public
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
Julia
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GNU Affero General Public License v3.0
•0•0•0•0•Updated Jun 12, 2023Jun 12, 2023
Rank2Count
Public
The official repository for the paper "Learning-to-Count by Learning-to-Rank", accepted as an oral presentation at CRV2023
Jupyter Notebook
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GNU Affero General Public License v3.0
•0•2•0•0•Updated May 13, 2023May 13, 2023
CIRCLe
Public
CIRCLe: Color Invariant Representation Learning for Unbiased Classification of Skin Lesions. Mirror of https://github.com/arezou-pakzad/CIRCLe
gan classification representation-learning dermatology fairness-ai skin-lesion-classification fairness-ml bias-mitigation skin-type-bias
Python
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GNU Affero General Public License v3.0
•2•3•0•0•Updated Apr 18, 2023Apr 18, 2023
Colocalization.jl
Public
Colocalization metrics and distances for images or their sparse representations. Mirror of https://github.com/bencardoen/Colocalization.jl
Julia
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GNU Affero General Public License v3.0
•0•0•0•0•Updated Feb 20, 2023Feb 20, 2023
SPECHT.jl
Public
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
Julia
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GNU Affero General Public License v3.0
•0•0•0•0•Updated Feb 11, 2023Feb 11, 2023
SmlmTools.jl
Public
Computational tools for single molecule localization / superresolution microscopy (point clouds). Mirror of https://github.com/bencardoen/SmlmTools.jl
Julia
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Other
•0•0•0•0•Updated Feb 11, 2023Feb 11, 2023
LogParadox.jl
Public
Detects sufficient and necessary conditions for pattern inversion conditional on log transform Mirror of https://github.com/bencardoen/LogParadox.jl
Julia
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GNU Affero General Public License v3.0
•0•0•0•0•Updated Jan 18, 2023Jan 18, 2023
labtools
Public
A set of scripts to streamline remote working with clusters. Mirror of https://github.com/bencardoen/labtools
bash ssh sshfs
Shell
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GNU General Public License v3.0
•0•0•0•0•Updated Dec 26, 2022Dec 26, 2022
SlurmMonitor.jl
Public
SLURM Monitor to detect node health and notify Slack in case of events. Mirror of https://github.com/bencardoen/SlurmMonitor.jl
julia slurm-workload-manager
Julia
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GNU Affero General Public License v3.0
•0•0•0•0•Updated Sep 22, 2022Sep 22, 2022
singularity_slurm_cuda
Public
Example on how to leverage Singularity on HPC. Mirror of https://github.com/bencardoen/singularity_slurm_cuda
cuda singularity hpc-clusters slurm-workload-manager apptainer
Shell
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GNU Affero General Public License v3.0
•0•0•0•0•Updated Sep 13, 2022Sep 13, 2022