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    15 repositories

    • 2025_Kalinin_mAP

      Public
      A versatile information retrieval framework for evaluating profile strength and similarity (Nat Comms, 2025)
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•1•0•1•Updated Apr 30, 2026Apr 30, 2026

    • 2025_Haghighi_Mito

      Public
      Repository accompanied with the Mito paper
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •2•0•0•0•Updated Apr 21, 2026Apr 21, 2026

    • 2024_vanDijk_PLoS_CytoSummaryNet

      Public
      CytoSummaryNet learns an optimal way to aggregate single-cell features into population-level profiles
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •0•4•13•1•Updated Jan 26, 2026Jan 26, 2026

    • 2023_Haghighi_IJCAI

      Public
      Pseudo-Labeling Enhanced by Privileged Information and its application to In Situ Sequencing Images
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•2•Updated Jan 19, 2026Jan 19, 2026

    • 2024_Arevalo_NeurIPS_MotiVE

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •4•21•1•0•Updated Jan 13, 2026Jan 13, 2026

    • 2024_Iyer_Genemod

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•0•1•Updated Aug 11, 2025Aug 11, 2025

    • 2022_Rohban_CellSystems

      Public
      Virtual screening for small-molecule pathway regulators by image-profile matching
      HTML
      •
      BSD 3-Clause "New" or "Revised" License
      •0•2•0•1•Updated Aug 11, 2025Aug 11, 2025

    • 2023_Cimini_NatureProtocols

      Public
      Optimizing the Cell Painting assay for image-based profiling
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •2•21•7•1•Updated Aug 11, 2025Aug 11, 2025

    • 2023_Arevalo_NatComm_BatchCorrection

      Public
      Evaluating batch correction methods for image-based cell profiling
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •8•15•1•2•Updated Aug 11, 2025Aug 11, 2025

    • 2022_Haghighi_NatureMethods

      Public
      High-Dimensional Gene Expression and Morphology Profiles of Cells across 28,000 Genetic and Chemical Perturbations
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •7•55•9•2•Updated Aug 11, 2025Aug 11, 2025

    • InfoAlign

      Public
      The code for "Learning Molecular Representation in a Cell"
      Python
      •8•0•0•2•Updated Apr 18, 2025Apr 18, 2025

    • 2024_LacosteHaghighi_Cell_Mislocalization

      Public
      Cell-painting data analysis corresponding to the "Pervasive mislocalization of pathogenic coding variants underlying human diseases" paper
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•2•2•1•Updated Jan 3, 2025Jan 3, 2025

    • 2025_Seal_CellCount

      Public
      Cell Count Baselines
      Jupyter Notebook
      •2•0•0•0•Updated Dec 5, 2024Dec 5, 2024

    • 2024_Chandrasekaran_NatureMethods

      Public
      A benchmark dataset of three million of images of cells perturbed by chemical and genetic perturbations
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •13•0•0•0•Updated Mar 19, 2024Mar 19, 2024

    • .github

      Public
      0•0•0•0•Updated Apr 3, 2023Apr 3, 2023
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