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    97 repositories

    • pediatric_cancer_atlas_analysis

      Public
      Image2Image Translation Model Optimization and Training to Predict Stains from Brightfield with Cell Painting Data
      HTML
      •
      BSD 3-Clause "New" or "Revised" License
      •2•0•0•1•Updated Apr 17, 2026Apr 17, 2026

    • ZedProfiler

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•1•0•Updated Apr 16, 2026Apr 16, 2026

    • iceberg-bioimage

      Public
      A format-agnostic framework for cataloging and querying bioimaging data (Zarr, OME-TIFF) with Apache Iceberg
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•1•0•1•Updated Apr 14, 2026Apr 14, 2026

    • napari-ome-arrow

      Public
      A Napari plugin for OME-Arrow and OME-Parquet bioimage data
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•1•1•2•Updated Apr 14, 2026Apr 14, 2026

    • ome-arrow

      Public
      Using OME specifications with Apache Arrow for fast, queryable, and language agnostic bioimage data.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•5•5•0•Updated Apr 14, 2026Apr 14, 2026

    • buscar

      Public
      Jupyter Notebook
      •1•3•18•2•Updated Apr 12, 2026Apr 12, 2026

    • targeted_fibrosis_drug_screen

      Public
      Image analysis and image-based profiling of a fibrosis drug screen to identify compound hits using a machine learning model.
      Jupyter Notebook
      •
      Creative Commons Zero v1.0 Universal
      •4•3•12•1•Updated Apr 10, 2026Apr 10, 2026

    • NF1_2D_organoid_profiling_pipeline

      Public
      Jupyter Notebook
      •
      Creative Commons Zero v1.0 Universal
      •2•0•2•0•Updated Apr 8, 2026Apr 8, 2026

    • pccma_repo1_screen_image_profiling

      Public
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•0•0•Updated Apr 6, 2026Apr 6, 2026

    • meerqat

      Public
      Validate bioimaging datasets by detecting missing files, metadata gaps, and structural inconsistencies early.
      BSD 3-Clause "New" or "Revised" License
      •1•0•0•1•Updated Mar 30, 2026Mar 30, 2026

    • nuclear_speckle_image_profiling

      Public
      Image analyis and image-based profiling of nuclear speckle dataset extracting intensity based features.
      Jupyter Notebook
      •
      Creative Commons Zero v1.0 Universal
      •1•0•0•0•Updated Mar 30, 2026Mar 30, 2026

    • ome-arrow-benchmarks

      Public
      Benchmarking OME Arrow through Parquet, Vortex, LanceDB, and more.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•5•2•Updated Mar 30, 2026Mar 30, 2026

    • duckdb_zarr

      Public
      A DuckDB extension for querying Zarr arrays with SQL through relational projection.
      C++
      •
      MIT License
      •1•1•0•0•Updated Mar 29, 2026Mar 29, 2026

    • NF1_organoid_profile_analysis

      Public
      This repo contains analysis code of profiles generated in multiple image-based profiling repos.
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •3•1•1•1•Updated Mar 29, 2026Mar 29, 2026

    • NF1_organoid_cell_segmentation

      Public
      Deep learning–based vision model for segmentation of cells within NF1 organoids.
      data-sciencemachine-learningdeep-learning
      data-sciencemachine-learningdeep-learningartificial-intelligencedata-wranglingcell-biology
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•2•0•0•Updated Mar 27, 2026Mar 27, 2026

    • JUMP-single-cell

      Public
      Single cell analysis of the JUMP Cell Painting consortium pilot data (cpg0000)
      pythonimage-processingcellprofiler
      pythonimage-processingcellprofilerimage-analysiscell-paintingpycytominer
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •5•4•2•0•Updated Mar 25, 2026Mar 25, 2026

    • NF1_3D_organoid_profiling_pipeline

      Public
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •3•4•11•0•Updated Mar 24, 2026Mar 24, 2026

    • nViz

      Public
      A tool for creating and visualizing n-dimensional microscopy images.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •5•3•26•6•Updated Mar 16, 2026Mar 16, 2026

    • pccma_atlas_image_profiling

      Public
      Image analysis and image-based profiling workflows to extract morphology profiles from the PCCMA Atlas dataset.
      BSD 3-Clause "New" or "Revised" License
      •1•0•0•0•Updated Mar 10, 2026Mar 10, 2026

    • demo-cellprofiler

      Public
      Demonstrating various CellProfiler development or implementations.
      Shell
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•1•0•Updated Mar 8, 2026Mar 8, 2026

    • pyroptosis_live-cell_timelapse

      Public
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•2•3•Updated Mar 6, 2026Mar 6, 2026

    • pediatric_cancer_atlas_profiling

      Public
      Image analysis and image-based profiling of pediatic cancer cell lines to extract morphological profiles.
      Jupyter Notebook
      •
      Creative Commons Zero v1.0 Universal
      •5•6•3•1•Updated Feb 10, 2026Feb 10, 2026

    • playbooks

      Public
      Playbooks relevant to the operations of the Way Lab and similar labs.
      Shell
      •
      Creative Commons Zero v1.0 Universal
      •2•0•8•1•Updated Feb 6, 2026Feb 6, 2026

    • virtual_stain_flow

      Public
      For developing virtual staining models
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•2•3•0•Updated Jan 12, 2026Jan 12, 2026

    • CPBS7601

      Public
      Course on computing skills in biomedical informatics
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •21•5•0•2•Updated Jan 8, 2026Jan 8, 2026

    • predicting_cardiac_fibrosis_etiologies

      Public
      Predicting cardiac fibrosis etiologies through machine learning using morphology profiles acquired from Cell Painting cardiac fibroblasts.
      Jupyter Notebook
      •
      Other
      •2•0•4•1•Updated Jan 6, 2026Jan 6, 2026

    • PRISM_Agent_LITL_experiments

      Public
      Exploring how to better utilize Lab In The Loop (LITL) data in agentic systems with DSPy. Built with DSPy, this repo provides modular agent tools and academic …
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •1•1•0•1•Updated Dec 12, 2025Dec 12, 2025

    • MIICE

      Public
      MIICE performs evaluation on microscopy images for issues with image quality (illumination and contrast).
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •2•3•5•0•Updated Dec 10, 2025Dec 10, 2025

    • serpula_rasa

      Public
      Blank snake implementation prototype for image-based single-cell profiling
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•1•1•Updated Nov 24, 2025Nov 24, 2025

    • gene-process-dependencies

      Public
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •5•4•2•0•Updated Nov 14, 2025Nov 14, 2025
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