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    51 repositories

    • SCEMILA

      Public
      Single cell based explainable multiple instance learning algorithm (SCEMILA) for genetic acute myeloid leukemia subtype classification.
      Python
      •
      MIT License
      •1•9•0•0•Updated Mar 24, 2026Mar 24, 2026

    • DinoBloom

      Public
      Blood Cell Foundation Model based on DINOv2
      Python
      •
      Apache License 2.0
      •11•69•3•0•Updated Jan 29, 2026Jan 29, 2026

    • HematoFatePrediction

      Public
      Code accompanying "Prospective identification of hematopoietic lineage choice by deep learning", Nature methods 2017, DOI:10.1038/nmeth.4182
      MATLAB
      •6•21•0•1•Updated Dec 18, 2025Dec 18, 2025

    • cAItomorph

      Public
      cAItomorph: Hematological Diagnostics from Peripheral Blood Cytomorphology
      Python
      •
      MIT License
      •0•5•0•0•Updated Oct 17, 2025Oct 17, 2025

    • causalspyne

      Public
      Python data generation tool with unobserved confounding as testbed for causal discovery and causal abstraction
      Python
      •0•3•8•1•Updated Oct 16, 2025Oct 16, 2025

    • aNCA

      Public
      Python
      •0•3•0•0•Updated Oct 6, 2025Oct 6, 2025

    • NCA-WSS

      Public
      Python
      •0•1•0•0•Updated Sep 23, 2025Sep 23, 2025

    • HistoGPT

      Public
      A vision language model for gigapixel whole slide images in histopathology
      Jupyter Notebook
      •
      Apache License 2.0
      •20•96•2•0•Updated Sep 4, 2025Sep 4, 2025

    • RedTell

      Public
      Python
      •5•10•1•0•Updated Jul 24, 2025Jul 24, 2025

    • CAR_T_TargetExpression

      Public
      Jupyter Notebook
      •
      MIT License
      •0•1•0•0•Updated May 12, 2025May 12, 2025

    • LVLM_cytomorphology_eval

      Public
      Evaluation of large vision language models on cytomorphology tasks
      0•0•0•0•Updated Apr 23, 2025Apr 23, 2025

    • BatchDetect

      Public
      BatchDetect: a python package for detect systematic batch effects in datasets
      Python
      •
      MIT License
      •0•3•0•0•Updated Mar 31, 2025Mar 31, 2025

    • hNCA

      Public
      Python
      •0•1•0•0•Updated Mar 22, 2025Mar 22, 2025

    • DomainLab

      Public
      modular domain generalization: https://pypi.org/project/domainlab/
      domain-generalization-causality-deep-learning
      domain-generalization-causality-deep-learning
      Python
      •
      MIT License
      •3•46•21•18•Updated Mar 18, 2025Mar 18, 2025

    • BaSiC

      Public
      A BaSiC Tool for Background and Shading Correction of Optical Microscopy Images
      MATLAB
      •17•67•10•0•Updated Mar 12, 2025Mar 12, 2025

    • ContMIL

      Public
      Python
      •0•0•0•0•Updated Feb 10, 2025Feb 10, 2025

    • MLL23

      Public
      Jupyter Notebook
      •0•1•1•0•Updated Jan 10, 2025Jan 10, 2025

    • WBC-NCA

      Public
      Jupyter Notebook
      •1•4•1•0•Updated Aug 20, 2024Aug 20, 2024

    • MILPLE

      Public
      Python
      •0•1•0•0•Updated Apr 8, 2024Apr 8, 2024

    • initial-data-point-selection

      Public
      Jupyter Notebook
      •
      MIT License
      •1•1•0•0•Updated Feb 20, 2024Feb 20, 2024

    • pxpermute

      Public
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Jan 12, 2024Jan 12, 2024

    • SHAPR_torch

      Public
      SHAPR: Code for "Capturing Shape Information with Multi-Scale Topological Loss Terms for 3D Reconstruction"
      deep-learningimage-reconstructionpytorch
      deep-learningimage-reconstructionpytorchsegmentationpersistent-homologytopological-data-analysistopological-machine-learningcubical-complexes
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •7•41•0•0•Updated Oct 28, 2023Oct 28, 2023

    • scifAI-notebooks

      Public
      Jupyter Notebook
      •
      MIT License
      •1•0•0•0•Updated Oct 11, 2023Oct 11, 2023

    • scifAI

      Public
      scifAI: An explainable AI python framework for the analysis of multi-channel imaging data
      Python
      •
      MIT License
      •0•9•0•0•Updated Oct 11, 2023Oct 11, 2023

    • AE-CFE

      Public
      Python
      •4•4•2•0•Updated Jul 10, 2023Jul 10, 2023

    • AE-CFE-1

      Public
      Python
      •4•0•0•0•Updated Jul 4, 2023Jul 4, 2023

    • DISPR

      Public
      A Diffusion Model Predicts 3D Shapes from 2D Microscopy Images
      Python
      •
      Apache License 2.0
      •6•39•4•0•Updated May 31, 2023May 31, 2023

    • SHAPR

      Public
      SHAPR - An AI approach to predict 3D cell shapes from 2D microscopic images
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •7•15•0•0•Updated May 31, 2023May 31, 2023

    • Bright2Nuc

      Public
      Preprint: https://www.biorxiv.org/content/10.1101/2022.08.30.505835v1.full.pdf
      Python
      •
      MIT License
      •1•1•0•0•Updated May 31, 2023May 31, 2023

    • InstantDL

      Public
      InstantDL: An easy and convenient deep learning pipeline for image segmentation and classification
      dockerdeep-learninggpu
      dockerdeep-learninggpuregressionclassificationimage-segmentationsemantic-segmentationinstance-segmentationpixel-wise-regression
      Python
      •
      MIT License
      •8•45•2•2•Updated Mar 24, 2023Mar 24, 2023
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