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    Repositories list

    107 repositories

    • pccma_repo1_screen_analysis

      Public
      Analyzing the high-throughput drug screens across pediatric cancer cell lines from PCCMA
      1•0•0•0•Updated Sep 25, 2026Sep 25, 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•3•6•Updated Sep 25, 2026Sep 25, 2026

    • buscar

      Public
      Single cell hit calling for high-content screens
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •2•8•6•1•Updated Sep 25, 2026Sep 25, 2026

    • NF1_3D_organoid_profiling_pipeline

      Public
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •4•4•16•2•Updated Sep 24, 2026Sep 24, 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•7•3•2•Updated Sep 24, 2026Sep 24, 2026

    • pccma_repo1_screen_image_profiling

      Public
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •2•0•3•1•Updated Sep 23, 2026Sep 23, 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•8•7•0•Updated Sep 21, 2026Sep 21, 2026

    • virtual_stain_flow

      Public
      For developing virtual staining models
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•2•7•2•Updated Sep 18, 2026Sep 18, 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
      •5•3•13•1•Updated Sep 17, 2026Sep 17, 2026

    • playbooks

      Public
      Playbooks relevant to the operations of the Way Lab and similar labs.
      Shell
      •
      Creative Commons Zero v1.0 Universal
      •3•0•8•0•Updated Sep 16, 2026Sep 16, 2026

    • virtual_staining_metric_analysis

      Public
      Metrics analysis surrounding virtual staining model evaluation contexts.
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•1•2•Updated Sep 14, 2026Sep 14, 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•0•Updated Sep 14, 2026Sep 14, 2026

    • 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•2•Updated Sep 14, 2026Sep 14, 2026

    • gene-process-dependencies

      Public
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •7•4•2•1•Updated Sep 12, 2026Sep 12, 2026

    • meerqat

      Public
      Validate bioimaging datasets by detecting missing files, metadata gaps, and structural inconsistencies early.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•1•1•5•Updated Sep 9, 2026Sep 9, 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•0•Updated Sep 9, 2026Sep 9, 2026

    • CPBS7601

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

    • aberrant_nuclear_speckle_phenotype_treatment_analysis

      Public
      For detecting treatments causing aberrant nuclear speckle phenotypes.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Sep 8, 2026Sep 8, 2026

    • jump_image_data_downloader

      Public
      Allows JUMP users to download JUMP images by filtering JUMP image metadata.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•1•0•0•Updated Sep 8, 2026Sep 8, 2026

    • sandbox

      Public
      A place to mess around learning github
      MIT License
      •24•0•0•0•Updated Sep 8, 2026Sep 8, 2026

    • Benchmarking_NF1_data

      Public
      Benchmarking data processing strategies for Cell Painting data of NF1 Schwann cells. See analysis repository (https://github.com/WayScience/NF1_SchwannCell_data…
      machine-learningimage-analysiscell-painting
      machine-learningimage-analysiscell-paintingneurofibromatosis-type-1schwann-cells
      Jupyter Notebook
      •
      Creative Commons Zero v1.0 Universal
      •17•6•6•0•Updated Sep 8, 2026Sep 8, 2026

    • habomero

      Public
      Reproducible server-style OMERO deployment for Linux workstations using Docker Compose, Ansible, and uv.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•0•0•Updated Sep 2, 2026Sep 2, 2026

    • OME-IRIS

      Public
      Open Microscopy Environment (OME) Interoperable Reference Imaging Sets (IRIS) for reproducible benchmarking and validation of imaging data, analytical outputs, …
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•2•0•0•Updated Sep 1, 2026Sep 1, 2026

    • ZedProfiler

      Public
      Featurizing high-content 3D microscopy images
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •3•2•6•0•Updated Sep 1, 2026Sep 1, 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•0•Updated Sep 1, 2026Sep 1, 2026

    • iceberg-bioimage

      Public
      A format-agnostic framework for cataloging and querying bioimaging data (Parquet, OME-Zarr, OME-TIFF) with Apache Iceberg
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •2•3•2•0•Updated Sep 1, 2026Sep 1, 2026

    • formascute

      Public
      🐢 Exploring the structure of software workflow execution through small, reproducible experiments.
      Shell
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•0•0•Updated Aug 24, 2026Aug 24, 2026

    • tesserift

      Public
      Measure how bioimaging storage layouts shape performance, analysis, and biological discovery.
      BSD 3-Clause "New" or "Revised" License
      •1•0•0•1•Updated Aug 19, 2026Aug 19, 2026

    • nuclear_speckles_analysis

      Public
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •1•1•2•0•Updated Aug 18, 2026Aug 18, 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•1•Updated Aug 17, 2026Aug 17, 2026
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