Simon Lysdahlgaard

AI · Radiology · Research

A simple hub for useful AI and research links.

A curated homepage for GitHub repositories, AI tools, datasets, radiology resources, writing tools, and other links relevant to medical imaging research.

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nnU-Net

Self-configuring framework for biomedical image segmentation.

GitHubMedical imaging

nnInteractive

Interactive medical image segmentation with human-in-the-loop correction.

GitHubAnnotation

VoxTell

MIC-DKFZ GitHub repository for medical image segmentation and voxel-level annotation/research workflows.

GitHubSegmentation

napari-voxtell

Napari plugin that integrates VoxTell for text-prompted volumetric medical image segmentation.

GitHubSegmentation

Chest DR

Ark

Fully open AI foundation model for chest radiography, trained to accrue and reuse knowledge from heterogeneous public expert labels.

CT

Merlin

StanfordMIMI 3D vision-language foundation model for computed tomography, with CT representation learning and downstream segmentation research workflows.

GitHubCTSegmentation

CT

TotalSegmentator

Automatic segmentation of anatomical structures in CT.

MRI/QSM

QSMxT

Quantitative susceptibility mapping toolbox for reproducible MRI workflows.

Imaging

3D Slicer

Open-source platform for medical image visualization, segmentation, registration, and quantitative analysis.

Open sourceMedical imaging

ITK-SNAP

Software for manual and semi-automatic segmentation of 3D medical images.

Open sourceAnnotation

Neurodesk

Portable environment for reproducible neuroimaging with many tools available through containers.

NeuroimagingContainers

FreeSurfer stable

Stable FreeSurfer release for cortical reconstruction, anatomical segmentation, and structural MRI analysis.

FastSurfer

Deep learning-based neuroimaging pipeline for fast cortical reconstruction and brain segmentation.

Brain MRI

BrainIAC

Foundation model for generalized structural brain MRI analysis, with downstream tasks such as brain age prediction, sequence classification, tumor segmentation, and stroke-related prediction.

GitHubNeuroimagingMRI

DICOM

MicroDicom

Lightweight DICOM viewer useful for viewing and inspecting medical image files.

Spinal cord

Spinal Cord Toolbox

Open-source toolbox for processing and analyzing spinal cord MRI data.

Challenges

Grand Challenge

Medical imaging challenges, datasets, and benchmarking platform.

DatasetsBenchmarks

Datasets

TCIA

Public cancer imaging archive for AI, radiomics, and reproducibility studies.

Public dataDICOM

Writing

Overleaf

Collaborative LaTeX editor for manuscripts, theses, and papers.

ManuscriptsLaTeX

References

Zotero

Reference manager for papers, systematic reviews, and citation libraries.

CitationsResearch

Reviews

LatteReview

Tool for literature review and systematic review workflows.

Reviews

litsearchr

Tool for developing search strategies and search terms for systematic review workflows.

Reviews

ASReview

AI-assisted screening tool for systematic reviews using active learning.

Statistics

RStudio

Integrated development environment for R, statistics, reproducible analysis, and research workflows.

References

EndNote

Reference manager for manuscript writing, citation handling, and publication workflows.

CitationsWriting

References

Mendeley

Reference manager and PDF library for organizing papers, citations, and academic reading.

Nomad

Workload orchestrator for running containers, batch jobs, and services across compute infrastructure.

Dataflow

Apache NiFi

Open-source system for automating data movement, routing, transformation, and workflow pipelines.

Open sourceData

AssemblyNet

Whole-brain MRI segmentation pipeline using an ensemble of convolutional neural networks.

MONAI

Open-source PyTorch-based framework for deep learning in medical imaging.

Open sourcePyTorch

Muscle MRI

MuscleMap

Open-source community project for whole-body quantitative MRI of muscle morphometry and composition.

Synthesis

SuperSynth

FreeSurfer resource collecting synthesis-based neuroimaging tools such as SynthSeg and SynthSR.

Histology

HistoAtlasSegmentation

FreeSurfer resource for histology-based atlas segmentation workflows.

FreeSurferSegmentation

Brain tumor

TumorSynth

Tool for segmenting healthy brain tissue and tumor in multi-sequence brain MRI.

SAMSEG

Sequence-adaptive multimodal segmentation tool for robust brain MRI structure segmentation.

MS lesions

LST-AI

Deep learning ensemble for multiple sclerosis lesion segmentation in MRI.

Dataset

Open MS Dataset

Open multiple sclerosis MRI data with lesion annotations for segmentation and benchmarking.

Repository

Zenodo

Open repository for research data, software, preprints, datasets, and DOI-based archiving.

Stroke

DeepISLES

Out-of-the-box tool for ischemic stroke lesion segmentation in MRI.

Lung CT

LungSCAPE

HRCT lung segmentation pipeline for pulmonary structures and abnormalities.

Fetal MRI

FetalSynthSeg

Domain randomization method for fetal brain MRI segmentation across variable acquisition settings.

Dataset

CTSpine1K

Large-scale CT dataset for vertebrae segmentation and spine imaging research.

SPM

Statistical Parametric Mapping software for analysis of functional and structural brain imaging data.

MATLABBrain imaging

PET/MRI

OPETIA

Odense-Oxford PET Image Analysis toolbox for PET/MRI preprocessing and quantitative analysis.

Computer vision

YOLO

Ultralytics YOLO repository for object detection, segmentation, pose, and vision AI workflows.

GitHubVision AI

Datasets

Kaggle

Platform for datasets, notebooks, machine learning competitions, and practical AI experimentation.

AI models

Hugging Face

Platform for AI models, datasets, demos, transformers, and machine learning community resources.

Repository

NITRC

Neuroimaging Tools and Resources Collaboratory for imaging tools, datasets, and research resources.

NeuroimagingTools

Stroke

Acute stroke detection/segmentation

Repository for acute stroke detection and segmentation in medical imaging.

Dataset

CheXpert

Large public chest radiograph dataset for automated interpretation and machine learning research.

Chest X-rayDataset

Dataset

OASIS

Open Access Series of Imaging Studies with brain MRI data for neuroimaging and aging research.

Brain MRIDataset

Fetal MRI

FeTA dataset

Fetal Tissue Annotation resource for fetal brain MRI segmentation and benchmarking.

Head CT

RSNA-ICH

RSNA Intracranial Hemorrhage Detection challenge dataset for head CT classification research.

Radiomics

PyRadiomics

Open-source Python package for extracting radiomics features from medical images.

PythonRadiomics

MATLAB

MATLAB

Numerical computing environment used for image processing, statistics, signal processing, and research workflows.

Notebook

Jupyter Notebook

Interactive notebook environment for Python, data analysis, visualization, and reproducible computational research.

Programming

Python

General-purpose programming language widely used for AI, medical imaging, data science, and automation.

Speech AI

OpenAI Whisper

Open-source automatic speech recognition system useful for transcription and audio-to-text workflows.

GitHub

CompositIA

GitHub repository for the CompositIA project.

GitHub

SPEKTR

Open-source software for x-ray spectral modeling and related imaging research workflows.

Annotation

Label Studio

Flexible data-labeling platform for images, text, audio, video, and machine learning workflows.

CT

WCHN/CTseg

GitHub repository for CT segmentation workflows and related medical imaging research.

X-ray

X-ray image enhancement

GitHub repository for enhancement methods applied to X-ray images.

Knee X-ray

KNEEL

GitHub repository from iMEDSLab related to knee imaging and AI-based analysis.

Wrist X-ray

DeepWrist

GitHub repository from iMEDSLab related to wrist X-ray analysis with deep learning.

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Current research topics

Stable segmentation pipeline for infarct lesions on DWI/ADC MRI
Radiography-assisted AI tools for better positioning
Creation of QSM images with deep learning tools

About me

I am a radiography and radiology researcher with an interest in artificial intelligence, medical image analysis, segmentation, radiomics, quantitative MRI/CT, and practical tools that improve research workflows.

Google Scholar ResearchGate SDU research profile

Research themes

AI-based segmentation in CT and MRI
Radiography, positioning, image quality, and workflow optimization
Stroke imaging, DWI lesion segmentation, and infarct volumetry
Radiomics, reproducibility, and quantitative imaging methods
Open-source tools, GitHub workflows, and research automation

Videos & webinars

Selected talks, demonstrations, and learning material worth revisiting.

EuSoMII Webinar Series 2025–2026

Webinars on medical imaging informatics, artificial intelligence, and digital imaging research.

Quantitative Susceptibility Mapping

Lectures, presentations, and tutorials about QSM methods and applications.

YOUTUBE · SEGMENTATION

Deep learning segmentation in ITK-SNAP 4.4

Demonstration of promptable deep-learning segmentation integrated into ITK-SNAP.

YOUTUBE · ANNOTATION

Medical image annotation

Tutorial on medical image annotation using CVAT and Makesense AI.