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    113 repositories

    • zebrahub-multiome-analysis

      Public
      A repository for scripts and notebooks to process and analyze single-cell Multiome datasets from early zebrafish embryos (zebrahub)
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •1•2•0•0•Updated Aug 11, 2025Aug 11, 2025

    • 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
      •10•39•34•4•Updated Aug 9, 2025Aug 9, 2025

    • biahub

      Public
      HUB for Bio Image Analysis
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •2•7•45•14•Updated Aug 9, 2025Aug 9, 2025

    • 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•42•6•2•Updated Aug 6, 2025Aug 6, 2025

    • create-sds-app

      Public template
      Repo template for npx create-sds-app
      TypeScript
      •
      MIT License
      •2•0•0•0•Updated Aug 6, 2025Aug 6, 2025

    • grassp

      Public
      GRaph-based Analysis of Subcellular/Spatial Proteomics
      spatial-proteomicsscanpyanndataproteomics-data-analysissubcellular-localization
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•2•0•2•Updated Aug 5, 2025Aug 5, 2025

    • compmicro-ndutils-env

      Public
      Shared ndutils environment for maintained by the CompMicro platform
      Dockerfile
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•1•1•Updated Aug 2, 2025Aug 2, 2025

    • 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•11•23•6•Updated Aug 1, 2025Aug 1, 2025

    • 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•1•Updated Jul 29, 2025Jul 29, 2025

    • ulc-malaria-scope

      Public
      Instrument control software for the Remoscope project.
      Python
      •1•1•1•3•Updated Jul 29, 2025Jul 29, 2025

    • uxibxx-io-board

      Public
      Simple USB-interfaced I/O boards for lab automation
      C
      •
      Other
      •1•1•0•0•Updated Jul 22, 2025Jul 22, 2025

    • protdata

      Public
      Dataloader for common proteomics search engine outputs into AnnData format
      pythonproteomicsproteomics-datasetsanndata
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•5•0•0•Updated Jul 17, 2025Jul 17, 2025

    • 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•7•2•Updated Jul 3, 2025Jul 3, 2025

    • proteinxlocation-cxg-fork-old

      Public archive
      🚨🚨 new and updated fork in pxl-explorer repo
      JavaScript
      •
      MIT License
      •140•0•0•0•Updated Jun 27, 2025Jun 27, 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

    • protoSpaceJAM

      Public
      CRISPR knock-in design at scale
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•11•10•0•Updated Jun 15, 2025Jun 15, 2025

    • coPylot

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

    • interns-2025-gitbasics

      Public
      Repo for summer 2025 interns to learn about git.
      12•0•0•5•Updated Jun 4, 2025Jun 4, 2025

    • CZB--Metadata-Standards

      Public
      Easily-accesible documentation site for CZB's metadata standards efforts
      MIT License
      •0•0•0•0•Updated Apr 23, 2025Apr 23, 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
      •28•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

    • WellLit

      Public
      Version of WellLit that supports well to well transfers
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Feb 27, 2025Feb 27, 2025

    • WellLit-TubeToWell

      Public
      Module needed to run Well-Lit in the "Tube to Well" configuration
      Python
      •
      Other
      •0•0•0•0•Updated Feb 14, 2025Feb 14, 2025

    • WellLit-WelltoWell

      Public
      WelltoWell implementation of the WellLit library
      Jupyter Notebook
      •
      Other
      •1•0•0•0•Updated Feb 14, 2025Feb 14, 2025

    • DeepGenotype

      Public
      Quality control of CRISPR edits using deep amplicon sequencing
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•1•0•0•Updated Jan 31, 2025Jan 31, 2025

    • czb-ui

      Public archive
      CZ Biohub's higher level components made with CZI's Science Design System Component Library.
      TypeScript
      •
      BSD 3-Clause "New" or "Revised" License
      •0•5•13•1•Updated Jan 28, 2025Jan 28, 2025

    • 2024-accs-pub

      Public
      Main public repo for the 2024 Automated Cell Culture Splitter publication
      Python
      •0•2•0•0•Updated Jan 27, 2025Jan 27, 2025