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@KatherLab Kather Lab at EKFZ / TU Dresden

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    48 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
      •1•8•10•5•Updated Mar 7, 2025Mar 7, 2025

    • LLMAIx

      Public
      Document Information Extraction & Anonymization using local LLMs
      Python
      •
      GNU Affero General Public License v3.0
      •8•40•1•0•Updated Mar 7, 2025Mar 7, 2025

    • NVFlare_MediSwarm

      Public
      NVIDIA Federated Learning Application Runtime Environment
      Python
      •
      Apache License 2.0
      •188•0•0•2•Updated Mar 6, 2025Mar 6, 2025

    • EAGLE

      Public
      Efficient Approach for Guided Local Examination in Digital Pathology
      Python
      •
      GNU General Public License v3.0
      •0•10•0•0•Updated Mar 5, 2025Mar 5, 2025

    • liverMRI

      Public
      Liver MRI pretraining pipeline
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Feb 25, 2025Feb 25, 2025

    • ToolMaker

      Public
      LLM Agents Making Agent Tools
      medicineagentsradiologypathologytool-usefunction-callingllm-agentstool-creation
      Python
      •4•12•1•1•Updated Feb 19, 2025Feb 19, 2025

    • COBRA

      Public
      COntrastive Biomarker Representation Alignment (COBRA)
      Python
      •
      GNU General Public License v3.0
      •0•9•0•0•Updated Feb 18, 2025Feb 18, 2025

    • STAMP

      Public
      Solid Tumor Associative Modeling in Pathology
      Python
      •
      MIT License
      •26•63•9•7•Updated Feb 15, 2025Feb 15, 2025

    • mopadi

      Public
      MOrphing histoPAthology DIffusion models for explainability of AI pipelines in medical image analysis.
      Python
      •
      Other
      •0•5•0•0•Updated Feb 7, 2025Feb 7, 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
      Python
      •
      MIT License
      •0•0•0•0•Updated Feb 2, 2025Feb 2, 2025

    • crc_single_cell_stromal

      Public
      Jupyter Notebook
      •
      MIT License
      •1•0•0•0•Updated Jan 22, 2025Jan 22, 2025

    • HIBRID

      Public
      HIBRID: Histology and ct-DNA based Risk-stratification with Deep Learning
      Python
      •0•0•0•0•Updated Jan 14, 2025Jan 14, 2025

    • uni

      Public
      Towards a general-purpose foundation model for computational pathology - Nature Medicine
      Jupyter Notebook
      •
      Other
      •58•0•0•0•Updated Jan 6, 2025Jan 6, 2025

    • prompt_injection_attacks

      Public
      Python
      •
      Other
      •2•4•0•0•Updated Dec 28, 2024Dec 28, 2024

    • patho_prompt_injection

      Public
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •0•1•0•0•Updated Dec 28, 2024Dec 28, 2024

    • 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
      Python
      •
      MIT License
      •1•12•29•1•Updated Dec 9, 2024Dec 9, 2024

    • genml

      Public
      This is a pipeline of feature extraction for genomics mutation using foundation models.
      Python
      •0•2•0•0•Updated Dec 5, 2024Dec 5, 2024

    • STAMP-Benchmark

      Public
      Solid Tumor Associative Modeling in Pathology
      Python
      •
      MIT License
      •26•2•0•0•Updated Dec 2, 2024Dec 2, 2024

    • GraDaCu

      Public
      Grammar-based Data Curation
      Python
      •0•2•0•0•Updated Nov 13, 2024Nov 13, 2024

    • marugoto

      Public
      Tools to build deep learning pipelines.
      Python
      •
      MIT License
      •31•93•1•0•Updated Nov 12, 2024Nov 12, 2024

    • LLMAnonymizer-Publication

      Public
      Anonymize Medical Documents using LLMs
      Python
      •
      Other
      •2•9•0•0•Updated Sep 2, 2024Sep 2, 2024

    • highres-WSI-heatmaps

      Public
      Python
      •
      GNU General Public License v3.0
      •5•8•0•0•Updated Jul 9, 2024Jul 9, 2024

    • joint-mtl-cpath

      Public
      Python
      •
      MIT License
      •0•6•0•0•Updated Jul 8, 2024Jul 8, 2024

    • llm-agent

      Public
      LLM agents in medicine
      Python
      •
      Other
      •3•10•0•0•Updated Jun 24, 2024Jun 24, 2024

    • Medical_LLM

      Public
      Welcome to the Medical LLM repository, your premier gateway to a structured and meticulously designed pipeline exclusively crafted for large language models (LLMs) based medical projects.
      Python
      •
      MIT License
      •2•14•3•0•Updated Apr 10, 2024Apr 10, 2024

    • end2end-WSI-preprocessing

      Public
      End-to-end pipeline to go from raw H&E slides to normalised extracted features for training
      Python
      •
      MIT License
      •6•25•2•0•Updated Mar 20, 2024Mar 20, 2024

    • crc-models-2022

      Public
      trained deep learning models for biomarker prediction from colorectal cancer pathology slides, 2022 edition
      MIT License
      •0•4•1•0•Updated Mar 8, 2024Mar 8, 2024

    • barspoon-transformer

      Public
      A transformer architecture for pathological whole slide images.
      Python
      •
      GNU General Public License v3.0
      •5•6•0•2•Updated Feb 6, 2024Feb 6, 2024

    • wanshi-utils

      Public
      Ultilities repo for visualizations and result assesments
      visualizationutilities
      Python
      •
      MIT License
      •1•4•5•0•Updated Dec 13, 2023Dec 13, 2023

    • heterogeneity-targeted

      Public
      Python
      •0•0•0•0•Updated Oct 24, 2023Oct 24, 2023