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    109 repositories

    • 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•9•1•Updated Mar 10, 2025Mar 10, 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
      •7•34•36•10•Updated Mar 8, 2025Mar 8, 2025

    • ulc-malaria-scope

      Public
      Instrument control software for the Remoscope project.
      Python
      •0•1•1•2•Updated Mar 8, 2025Mar 8, 2025

    • 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 Mar 7, 2025Mar 7, 2025

    • compmicro-ndutils-env

      Public
      Shared ndutils environment for maintained by the CompMicro platform
      Dockerfile
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•1•0•Updated Mar 7, 2025Mar 7, 2025

    • subcellular-proteomics-curation

      Public
      Code and documentation for the curation of proteinxlocation datasets
      Python
      •
      MIT License
      •26•0•0•0•Updated Mar 7, 2025Mar 7, 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

    • 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
      •2•8•30•2•Updated Mar 6, 2025Mar 6, 2025

    • proteinxlocation

      Public
      An interactive explorer for single-cell transcriptomics data
      JavaScript
      •
      MIT License
      •130•0•0•0•Updated Feb 28, 2025Feb 28, 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

    • coPylot

      Public
      coPylot - microscope control
      instrument-controlpython
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •10•8•26•16•Updated Feb 27, 2025Feb 27, 2025

    • protoSpaceJAM

      Public
      CRISPR knock-in design at scale
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•9•11•0•Updated Feb 18, 2025Feb 18, 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
      •0•0•0•0•Updated Feb 14, 2025Feb 14, 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
      •0•0•0•0•Updated Feb 13, 2025Feb 13, 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--Metadata-Standards

      Public
      Easily-accesible documentation site for CZB's metadata standards efforts
      MIT License
      •0•0•0•0•Updated Jan 30, 2025Jan 30, 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•0•0•0•Updated Jan 27, 2025Jan 27, 2025

    • accs-protocol-software-pub

      Public
      Public repo for the Automated Cell Culture Splitter protocol framework and tools
      C++
      •
      BSD 3-Clause "New" or "Revised" License
      •0•1•0•0•Updated Jan 13, 2025Jan 13, 2025

    • 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 Dec 20, 2024Dec 20, 2024

    • ulc-malaria-autofocus

      Public
      A single-shot autofocus CNN for the Remoscope project
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Dec 19, 2024Dec 19, 2024

    • 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
      •0•0•0•0•Updated Dec 18, 2024Dec 18, 2024

    • napari-plugins-docker

      Public
      Build a Napari image with common plugins
      Dockerfile
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Nov 26, 2024Nov 26, 2024

    • comparison-RNAVelo

      Public
      Comparison of single-cell RNA Velocity methods in developmental contexts
      Jupyter Notebook
      •
      Other
      •0•1•0•0•Updated Nov 19, 2024Nov 19, 2024

    • zebrahub_analysis

      Public
      Analysis of single-cell single-embryo RNA seq data from the zebrafish developmental atlas Zebrahub.
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •1•5•0•0•Updated Nov 16, 2024Nov 16, 2024

    • 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
      •2•6•1•0•Updated Oct 28, 2024Oct 28, 2024

    • Rapid-QC-MS

      Public
      Realtime quality control for mass spectrometry data acquisition
      metabolomicsmass-spectrometryplotly-dash
      Python
      •
      Other
      •2•15•15•0•Updated Oct 24, 2024Oct 24, 2024

    • uxibxx-io-board

      Public
      Simple USB-interfaced I/O boards for automation
      C
      •
      Other
      •0•1•0•0•Updated Oct 8, 2024Oct 8, 2024

    • 2021-opencell-figures

      Public
      Public read-only repo for code and data related to the 2021 OpenCell preprint
      Jupyter Notebook
      •
      Other
      •1•5•2•0•Updated Sep 10, 2024Sep 10, 2024