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    114 repositories

    • preprocessing

      Public
      `preprocessing` is a python library and CLI tool designed for the purpose of preprocessing MRI data for Deep Learning at QTIM.
      Python
      •
      MIT License
      •0•1•0•0•Updated Feb 21, 2025Feb 21, 2025

    • CorisDB_Curation

      Public
      Repo for organizing the db scheme of our coris_db
      Jupyter Notebook
      •
      MIT License
      •1•0•0•0•Updated Feb 17, 2025Feb 17, 2025

    • Chronicle

      Public
      An ordered record of events and data
      Python
      •
      Other
      •6•0•0•0•Updated Feb 17, 2025Feb 17, 2025

    • dl-prediction-brca-tiph-ext

      Public
      Implementation of the paper "Deep Learning-based Prediction of Breast Cancer Tumor and Immune Phenotypes from Histopathology" by Tiago Gonçalves, Dagoberto Pulido-Arias, Julian Willett, Katharina V. Hoebel, Mason Cleveland, Syed Rakin Ahmed, Elizabeth Gerstner, Jayashree Kalpathy-Cramer, Jaime S. Cardoso, Christopher P. Bridge and Albert E. Kim.
      Python
      •
      MIT License
      •1•1•0•0•Updated Feb 17, 2025Feb 17, 2025

    • Hereditary_glaucoma

      Public
      Code to download publicly available datasets on disc and cup segmentation from Color Fundus Photos and to train a segmentation model.
      Python
      •0•0•0•0•Updated Jan 30, 2025Jan 30, 2025

    • Hereditary_FeTS22

      Public
      Python
      •0•0•0•0•Updated Jan 30, 2025Jan 30, 2025

    • codabench

      Public
      Codabench is a flexible, easy-to-use and reproducible benchmarking platform. Check our paper at Patterns Cell Press https://hubs.li/Q01fwRWB0
      Python
      •
      Apache License 2.0
      •31•0•0•0•Updated Jan 13, 2025Jan 13, 2025

    • EyeLiner

      Public
      Automatic Longitudinal Image Registration using Fundus Landmarks (ARVO 2024)
      Python
      •
      Apache License 2.0
      •377•3•0•0•Updated Dec 20, 2024Dec 20, 2024

    • fundus_detection_segmentation_pipeline

      Public
      For fundus photography to obtain segmentation-based clinical metrics using a 2-step detection and segmentation pipeline
      Jupyter Notebook
      •0•0•0•0•Updated Dec 13, 2024Dec 13, 2024

    • OPTIMEyes

      Public
      Updated Image Comparator and Classifier
      Jupyter Notebook
      •1•2•3•0•Updated Dec 12, 2024Dec 12, 2024

    • segmentationMonaiLabel

      Public
      Python
      •1•0•0•0•Updated Dec 12, 2024Dec 12, 2024

    • NVFlare

      Public
      NVIDIA Federated Learning Application Runtime Environment
      Python
      •
      Apache License 2.0
      •185•0•0•0•Updated Nov 28, 2024Nov 28, 2024

    • Challenges

      Public
      Machine Learning Challenges hosted on Codabench
      Python
      •2•0•0•0•Updated Nov 9, 2024Nov 9, 2024

    • GA_Prospective_Study

      Public
      Python
      •1•0•0•0•Updated Nov 4, 2024Nov 4, 2024

    • wandb-deploy-example

      Public
      A guide to using the free tier of wandb
      Other
      •0•0•0•0•Updated Oct 31, 2024Oct 31, 2024

    • segmentation_generic

      Public
      Segmentation of images
      Python
      •1•0•0•1•Updated Oct 28, 2024Oct 28, 2024

    • OptimEYES-Anaylsis

      Public
      For pulling and analyzing data from the Image-Comparator app.
      Jupyter Notebook
      •1•0•0•0•Updated Oct 22, 2024Oct 22, 2024

    • model_conversion

      Public
      For cervical cancer model conversion to tflite and executorch for use on edge (android) devices
      Jupyter Notebook
      •0•1•0•0•Updated Oct 15, 2024Oct 15, 2024

    • FL_ViT_pretraining

      Public
      Python
      •0•2•0•0•Updated Sep 16, 2024Sep 16, 2024

    • trame_optimeyes

      Public
      trame tools and visualizations
      Python
      •
      Other
      •2•2•1•0•Updated Sep 12, 2024Sep 12, 2024

    • video_action_annotation

      Public
      JavaScript
      •0•0•0•0•Updated Sep 3, 2024Sep 3, 2024

    • video_action_annotator

      Public
      0•0•0•0•Updated Sep 3, 2024Sep 3, 2024

    • MedSAM

      Public
      Intro to MedSAM Model
      Jupyter Notebook
      •1•1•0•0•Updated Aug 30, 2024Aug 30, 2024

    • federatedLearning_glaucoma_segmentation

      Public
      Federated Learning Optic Disc and Cup Segmentation Model for Glaucoma Monitoring in Color Fundus Photographs(CFPs)
      Python
      •0•1•0•0•Updated Aug 20, 2024Aug 20, 2024

    • Conformal-Prediction-and-MC-Inference-for-Addressing-Uncertainty-in-Cervical-Cancer-Screening

      Public
      Application and comparison of conformal prediction and Monte Carlo inference for cervical cancer screening
      Python
      •0•0•0•0•Updated Aug 2, 2024Aug 2, 2024

    • qtim-lab.github.io

      Public
      A repository for the public-facing web page of the Quantiative Tumor Imaging Lab at the Martinos Center.
      HTML
      •
      MIT License
      •3•4•0•1•Updated Jul 5, 2024Jul 5, 2024

    • dinov2_imagenet1k_example

      Public
      To get DinoV2 running on a non-slurm environment on ImageNet 1K
      Python
      •2•4•1•0•Updated Jun 15, 2024Jun 15, 2024

    • RSNA-Pneumonia-Challenge-Models

      Public
      Python
      •0•0•0•1•Updated May 3, 2024May 3, 2024

    • dl-prediction-brca-tiph

      Public
      Implementation of the paper "Deep Learning-based Prediction of Breast Cancer Tumor and Immune Phenotypes from Histopathology" by Tiago Gonçalves, Dagoberto Pulido-Arias, Julian Willett, Katharina V. Hoebel, Mason Cleveland, Syed Rakin Ahmed, Elizabeth Gerstner, Jayashree Kalpathy-Cramer, Jaime S. Cardoso, Christopher P. Bridge and Albert E. Kim.
      Python
      •
      MIT License
      •1•4•0•0•Updated May 3, 2024May 3, 2024

    • hardwareProjects

      Public
      C
      •
      MIT License
      •0•0•0•0•Updated Apr 23, 2024Apr 23, 2024