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    • A versatile information retrieval framework for evaluating profile strength and similarity (Nat Comms, 2025)
      Python
      BSD 3-Clause "New" or "Revised" License
      1101Updated Apr 30, 2026Apr 30, 2026
    • Repository accompanied with the Mito paper
      Jupyter Notebook
      BSD 3-Clause "New" or "Revised" License
      2000Updated Apr 21, 2026Apr 21, 2026
    • CytoSummaryNet learns an optimal way to aggregate single-cell features into population-level profiles
      Jupyter Notebook
      BSD 3-Clause "New" or "Revised" License
      04131Updated Jan 26, 2026Jan 26, 2026
    • Pseudo-Labeling Enhanced by Privileged Information and its application to In Situ Sequencing Images
      Jupyter Notebook
      BSD 3-Clause "New" or "Revised" License
      0002Updated Jan 19, 2026Jan 19, 2026
    • Python
      BSD 3-Clause "New" or "Revised" License
      42110Updated Jan 13, 2026Jan 13, 2026
    • Python
      BSD 3-Clause "New" or "Revised" License
      1001Updated Aug 11, 2025Aug 11, 2025
    • Virtual screening for small-molecule pathway regulators by image-profile matching
      HTML
      BSD 3-Clause "New" or "Revised" License
      0201Updated Aug 11, 2025Aug 11, 2025
    • Optimizing the Cell Painting assay for image-based profiling
      Jupyter Notebook
      BSD 3-Clause "New" or "Revised" License
      22171Updated Aug 11, 2025Aug 11, 2025
    • Evaluating batch correction methods for image-based cell profiling
      Python
      BSD 3-Clause "New" or "Revised" License
      81512Updated Aug 11, 2025Aug 11, 2025
    • 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
      75592Updated Aug 11, 2025Aug 11, 2025
    • InfoAlign

      Public
      The code for "Learning Molecular Representation in a Cell"
      Python
      8002Updated Apr 18, 2025Apr 18, 2025
    • 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
      0221Updated Jan 3, 2025Jan 3, 2025
    • Cell Count Baselines
      Jupyter Notebook
      2000Updated Dec 5, 2024Dec 5, 2024
    • 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
      13000Updated Mar 19, 2024Mar 19, 2024
    • .github

      Public
      0000Updated Apr 3, 2023Apr 3, 2023
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