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    114 repositories

    • iohub

      Public
      Pythonic and parallelizable I/O for N-dimensional imaging data with OME metadata
      pythonimage-metadatabioimagingndimensional-arraysome-zarrome-zarr-converter
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •12•48•40•8•Updated Feb 10, 2026Feb 10, 2026

    • grassp

      Public
      GRaph-based Analysis of Subcellular/Spatial Proteomics
      spatial-proteomicsscanpyanndataproteomics-data-analysissubcellular-localization
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•7•0•2•Updated Feb 10, 2026Feb 10, 2026

    • shrimPy

      Public
      shrimPy: Smart High-throughput Robust Imaging & Measurement in Python
      multi-modal-imaginglightsheethigh-throughput-data-analysislabelfreehigh-throughput-imaging
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •5•12•30•0•Updated Feb 8, 2026Feb 8, 2026

    • napari-iohub

      Public
      OME-Zarr viewer for napari with iohub as the I/O backend
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•3•8•2•Updated Feb 6, 2026Feb 6, 2026

    • biahub

      Public
      HUB for Bio Image Analysis
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •2•12•70•17•Updated Feb 2, 2026Feb 2, 2026

    • uxibxx-io-board

      Public
      Simple USB-interfaced I/O boards for lab automation
      Python
      •
      Other
      •1•1•0•0•Updated Feb 2, 2026Feb 2, 2026

    • compmicro-ndutils-env

      Public
      Shared ndutils environment for maintained by the CompMicro platform
      Dockerfile
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•2•1•Updated Jan 30, 2026Jan 30, 2026

    • python-fish-sorter

      Public
      Software suite for microscope control with image acquisition and processing tools
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•3•0•0•Updated Jan 23, 2026Jan 23, 2026

    • ulc-malaria-scope

      Public
      Instrument control software for the Remoscope project.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•1•0•6•Updated Jan 22, 2026Jan 22, 2026

    • 2024-accs-pub

      Public
      Main public repo for the 2024 Automated Cell Culture Splitter publication
      Python
      •0•3•0•0•Updated Jan 22, 2026Jan 22, 2026

    • accs-cell-counting-imager-pub

      Public
      Public repo for software that drives the ACCS Cell Counting Imager
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Jan 22, 2026Jan 22, 2026

    • comparison-RNAVelo

      Public
      Comparison of single-cell RNA Velocity methods in developmental contexts
      Jupyter Notebook
      •
      Other
      •0•2•1•0•Updated Jan 22, 2026Jan 22, 2026

    • matlab-organoid-printer

      Public
      Scripts to extend existing Cell Picker instrumentation for organoid printing
      MATLAB
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Jan 21, 2026Jan 21, 2026

    • zebrahub-multiome-analysis

      Public
      A repository for scripts and notebooks to process and analyze single-cell Multiome datasets from early zebrafish embryos (zebrahub)
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•4•0•0•Updated Jan 17, 2026Jan 17, 2026

    • lfm-data-utilities

      Public
      A collection of auxiliary data processing tools used in the Remoscope project.
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•0•2•Updated Jan 8, 2026Jan 8, 2026

    • tabula-sapiens

      Public
      Single Cell Transcriptomics of 25 Human Organs to Create a Tabula Sapiens
      transcriptomicssingle-cell-rna-seqsapienscell-atlascell-ontologieshuman-anatomy
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •9•44•6•2•Updated Dec 10, 2025Dec 10, 2025

    • create-sds-app

      Public template
      Repo template for npx create-sds-app
      TypeScript
      •
      MIT License
      •1•1•0•0•Updated Dec 4, 2025Dec 4, 2025

    • protdata

      Public
      Dataloader for common proteomics search engine outputs into AnnData format
      pythonproteomicsproteomics-datasetsanndata
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•14•0•0•Updated Nov 24, 2025Nov 24, 2025

    • protoSpaceJAM

      Public
      CRISPR knock-in design at scale
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •2•12•10•0•Updated Nov 18, 2025Nov 18, 2025

    • Rapid-QC-MS

      Public
      Realtime quality control for mass spectrometry data acquisition
      metabolomicsmass-spectrometryplotly-dash
      Python
      •
      Other
      •2•21•15•0•Updated Nov 17, 2025Nov 17, 2025

    • Organelle_IP_analyses_and_figures

      Public
      Jupyter notebooks for analysis and figures related to the native organelle IP paper
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •3•13•1•1•Updated Nov 13, 2025Nov 13, 2025

    • compmicro-biautils-env

      Public
      Dockerfile
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•4•1•Updated Aug 26, 2025Aug 26, 2025

    • CZB--Metadata-Standards

      Public
      Easily-accesible documentation site for CZB's metadata standards efforts
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Aug 12, 2025Aug 12, 2025

    • ulc-malaria-autofocus

      Public
      A single-shot autofocus CNN for the Remoscope project
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•0•0•Updated Jun 23, 2025Jun 23, 2025

    • coPylot

      Public
      coPylot - microscope control
      pythoninstrument-control
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •11•8•26•16•Updated Jun 12, 2025Jun 12, 2025

    • excellxgene

      Public
      JavaScript
      •
      MIT License
      •6•13•5•1•Updated Apr 17, 2025Apr 17, 2025

    • .github

      Public
      Organization-level readme and documentation
      0•0•0•0•Updated Apr 15, 2025Apr 15, 2025

    • remo-stats-utils

      Public
      This is a collection of statistics utilities used to support the Remoscope project at the Chan Zuckerberg Biohub San Francisco.
      machine-learningblooddiagnosticsmalariaedge-computinglow-costmalaria-detectionhematology
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•0•0•Updated Apr 5, 2025Apr 5, 2025

    • subcellular-proteomics-curation

      Public
      Code and documentation for the curation of proteinxlocation datasets
      Python
      •
      MIT License
      •29•0•0•0•Updated Mar 25, 2025Mar 25, 2025

    • reglo-icc-pump-control

      Public
      Python communication driver for Masterflex Ismatec Reglo ICC programmable peristaltic pumps
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•1•0•0•Updated Mar 6, 2025Mar 6, 2025