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    • iohub

      Public
      Pythonic and parallelizable I/O for N-dimensional imaging data with OME metadata
      Python
      1248408Updated Feb 10, 2026Feb 10, 2026
    • grassp

      Public
      GRaph-based Analysis of Subcellular/Spatial Proteomics
      Python
      0702Updated Feb 10, 2026Feb 10, 2026
    • shrimPy

      Public
      shrimPy: Smart High-throughput Robust Imaging & Measurement in Python
      Python
      512300Updated Feb 8, 2026Feb 8, 2026
    • napari-iohub

      Public
      OME-Zarr viewer for napari with iohub as the I/O backend
      Python
      0382Updated Feb 6, 2026Feb 6, 2026
    • biahub

      Public
      HUB for Bio Image Analysis
      Python
      2127017Updated Feb 2, 2026Feb 2, 2026
    • uxibxx-io-board

      Public
      Simple USB-interfaced I/O boards for lab automation
      Python
      1100Updated Feb 2, 2026Feb 2, 2026
    • compmicro-ndutils-env

      Public
      Shared ndutils environment for maintained by the CompMicro platform
      Dockerfile
      1021Updated Jan 30, 2026Jan 30, 2026
    • python-fish-sorter

      Public
      Software suite for microscope control with image acquisition and processing tools
      Python
      1300Updated Jan 23, 2026Jan 23, 2026
    • ulc-malaria-scope

      Public
      Instrument control software for the Remoscope project.
      Python
      1106Updated Jan 22, 2026Jan 22, 2026
    • 2024-accs-pub

      Public
      Main public repo for the 2024 Automated Cell Culture Splitter publication
      Python
      0300Updated Jan 22, 2026Jan 22, 2026
    • Public repo for software that drives the ACCS Cell Counting Imager
      Python
      0000Updated Jan 22, 2026Jan 22, 2026
    • Comparison of single-cell RNA Velocity methods in developmental contexts
      Jupyter Notebook
      0210Updated Jan 22, 2026Jan 22, 2026
    • Scripts to extend existing Cell Picker instrumentation for organoid printing
      MATLAB
      0000Updated Jan 21, 2026Jan 21, 2026
    • A repository for scripts and notebooks to process and analyze single-cell Multiome datasets from early zebrafish embryos (zebrahub)
      Python
      1400Updated Jan 17, 2026Jan 17, 2026
    • A collection of auxiliary data processing tools used in the Remoscope project.
      Jupyter Notebook
      1002Updated Jan 8, 2026Jan 8, 2026
    • Single Cell Transcriptomics of 25 Human Organs to Create a Tabula Sapiens
      Jupyter Notebook
      94462Updated Dec 10, 2025Dec 10, 2025
    • create-sds-app

      Public template
      Repo template for npx create-sds-app
      TypeScript
      1100Updated Dec 4, 2025Dec 4, 2025
    • protdata

      Public
      Dataloader for common proteomics search engine outputs into AnnData format
      Python
      01400Updated Nov 24, 2025Nov 24, 2025
    • CRISPR knock-in design at scale
      Python
      212100Updated Nov 18, 2025Nov 18, 2025
    • Realtime quality control for mass spectrometry data acquisition
      Python
      221150Updated Nov 17, 2025Nov 17, 2025
    • Jupyter notebooks for analysis and figures related to the native organelle IP paper
      Jupyter Notebook
      31311Updated Nov 13, 2025Nov 13, 2025
    • Dockerfile
      0041Updated Aug 26, 2025Aug 26, 2025
    • Easily-accesible documentation site for CZB's metadata standards efforts
      0000Updated Aug 12, 2025Aug 12, 2025
    • A single-shot autofocus CNN for the Remoscope project
      Python
      1000Updated Jun 23, 2025Jun 23, 2025
    • coPylot

      Public
      coPylot - microscope control
      Python
      1182616Updated Jun 12, 2025Jun 12, 2025
    • JavaScript
      61351Updated Apr 17, 2025Apr 17, 2025
    • .github

      Public
      Organization-level readme and documentation
      0000Updated Apr 15, 2025Apr 15, 2025
    • This is a collection of statistics utilities used to support the Remoscope project at the Chan Zuckerberg Biohub San Francisco.
      Python
      1000Updated Apr 5, 2025Apr 5, 2025
    • Code and documentation for the curation of proteinxlocation datasets
      Python
      29000Updated Mar 25, 2025Mar 25, 2025
    • Python communication driver for Masterflex Ismatec Reglo ICC programmable peristaltic pumps
      Python
      0100Updated Mar 6, 2025Mar 6, 2025