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@KatherLab Kather Lab at EKFZ / TU Dresden

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    66 repositories

    • MediSwarm

      Public
      MediSwarm is an open-source project for advancing medical deep learning using swarm intelligence and NVFlare. Developed by the Odelia consortium, it ensures data privacy through federated learning, enabling collaborative, decentralized model training across institutions for improved medical research and applications.
      Python
      •
      MIT License
      •2•12•20•3•Updated Jan 1, 2026Jan 1, 2026

    • swarm-learning-hpe

      Public
      Experimental repo for Odelia project based on HPE platform. This repo contains multiple models for histopathology and radiology training.
      distributed-systemsdeep-learningblockchain
      Jupyter Notebook
      •
      MIT License
      •2•13•29•13•Updated Dec 16, 2025Dec 16, 2025

    • STAMP

      Public
      Solid Tumor Associative Modeling in Pathology
      bioinformaticsresearchdeep-learningmcpsurvival-analysisagentstcga-dataweakly-supervised-learningdigital-pathologypathology
      Python
      •
      MIT License
      •46•103•12•3•Updated Dec 4, 2025Dec 4, 2025

    • llmaixweb

      Public
      A web interface for the LLMAIx framework. Information Extraction.
      Vue
      •
      GNU Affero General Public License v3.0
      •0•12•1•10•Updated Nov 24, 2025Nov 24, 2025

    • 3DAnnotationSimSAM2

      Public
      SAM 2 - assisted annotation simulation of 3D radiology imaging
      Python
      •
      Apache License 2.0
      •0•0•0•0•Updated Nov 10, 2025Nov 10, 2025

    • PathPrism

      Public
      Jupyter Notebook
      •
      Other
      •0•3•0•0•Updated Nov 5, 2025Nov 5, 2025

    • llmaixlib

      Public
      Python library for document preprocessing and information extraction
      Python
      •
      MIT License
      •0•6•0•5•Updated Oct 27, 2025Oct 27, 2025

    • mopadi

      Public
      MOrphing histoPAthology DIffusion models for explainability of AI pipelines in medical image analysis.
      Python
      •
      Other
      •2•11•0•0•Updated Oct 21, 2025Oct 21, 2025

    • workspaces

      Public
      A tool to manage ephemeral data
      Rust
      •
      GNU General Public License v3.0
      •2•0•0•0•Updated Oct 15, 2025Oct 15, 2025

    • HepatoSageCT

      Public
      Repository of code for experiments in the paper "Detection of Esophageal Varices and Prediction of Liver Decompensation in Unresectable Hepatocellular Carcinoma using Artificial Intelligence"
      Python
      •
      MIT License
      •1•0•0•0•Updated Oct 9, 2025Oct 9, 2025

    • COBRA

      Public
      COntrastive Biomarker Representation Alignment (COBRA) [CVPR25]
      Python
      •
      GNU General Public License v3.0
      •3•22•1•0•Updated Oct 1, 2025Oct 1, 2025

    • wsi-viewer

      Public
      HTML
      •
      MIT License
      •1•0•0•0•Updated Oct 1, 2025Oct 1, 2025

    • CLEAR

      Public
      Python
      •
      GNU General Public License v3.0
      •0•2•0•0•Updated Oct 1, 2025Oct 1, 2025

    • mamba

      Public
      Mamba SSM architecture
      Python
      •
      Apache License 2.0
      •1.6k•0•0•0•Updated Sep 23, 2025Sep 23, 2025

    • causal-conv1d

      Public
      Causal depthwise conv1d in CUDA, with a PyTorch interface
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •147•0•0•0•Updated Sep 23, 2025Sep 23, 2025

    • pathoMozhi

      Public
      PathoMozhi is a Flamingo-style vision-language model for computational pathology. Checkpoint available on Hugging Face: oyemainhun/pathoMozhi
      Python
      •
      Other
      •0•0•0•0•Updated Sep 8, 2025Sep 8, 2025

    • LLMAIx

      Public
      Document Information Extraction & Anonymization using local LLMs
      Python
      •
      GNU Affero General Public License v3.0
      •19•131•1•0•Updated Aug 28, 2025Aug 28, 2025

    • GraDaCu

      Public
      Grammar-based Data Curation
      Python
      •
      MIT License
      •0•2•0•0•Updated Aug 21, 2025Aug 21, 2025

    • prov-gigapath

      Public
      Prov-GigaPath: A whole-slide foundation model for digital pathology from real-world data
      Python
      •
      Apache License 2.0
      •89•0•0•0•Updated Aug 6, 2025Aug 6, 2025

    • HIBRID

      Public
      HIBRID: Histology and ct-DNA based Risk-stratification with Deep Learning
      Python
      •
      MIT License
      •0•5•0•0•Updated Jul 31, 2025Jul 31, 2025

    • NVFlare_MediSwarm

      Public
      NVIDIA Federated Learning Application Runtime Environment
      Python
      •
      Apache License 2.0
      •228•1•0•0•Updated Jul 22, 2025Jul 22, 2025

    • HNSCC_FM_MIL_study

      Public
      Repository for data extraction and model extraction alongside model objects for the paper "End-to-end prediction of clinical outcomes in head and neck squamous cell carcinoma with foundation model-based multiple instance learning" by Meneghetti et al. 2025 in BMC Artificial Intelligence
      Python
      •
      MIT License
      •0•7•1•0•Updated Jul 22, 2025Jul 22, 2025

    • CONCH

      Public
      Vision-Language Pathology Foundation Model - Nature Medicine
      Python
      •
      Other
      •43•0•0•0•Updated Jul 18, 2025Jul 18, 2025

    • flash-attention

      Public
      Fast and memory-efficient exact attention
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •2.3k•0•0•0•Updated Jul 18, 2025Jul 18, 2025

    • STAMP-Benchmark

      Public
      Solid Tumor Associative Modeling in Pathology
      Python
      •
      MIT License
      •46•10•0•0•Updated Jun 26, 2025Jun 26, 2025

    • cbioportal-studyparser

      Public
      Python
      •1•0•0•1•Updated Jun 13, 2025Jun 13, 2025

    • MultiTargetCRC

      Public
      Repository for our research paper "Assessing Genotype-Phenotype Correlations with Deep Learning in Colorectal Cancer: A Multi-Centric Study"
      Python
      •
      GNU General Public License v3.0
      •0•2•0•0•Updated May 22, 2025May 22, 2025

    • ToolArena

      Public
      A benchmark for agentic tool creation.
      benchmarkingtoolsagentsllmsllm-toolsllm-agents
      Python
      •10•5•0•1•Updated May 17, 2025May 17, 2025

    • ToolMaker

      Public
      Turn GitHub repositories into LLM tools. (ACL 2025)
      medicineagentsradiologypathologytool-usefunction-callingllm-agentstool-creation
      Python
      •8•64•1•0•Updated May 16, 2025May 16, 2025

    • EAGLE

      Public
      Efficient Approach for Guided Local Examination in Digital Pathology
      Python
      •
      GNU General Public License v3.0
      •1•32•0•0•Updated May 4, 2025May 4, 2025