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@czbiohub-sf

Chan Zuckerberg Biohub San Francisco

CZ Biohub SF logo

The Chan Zuckerberg Biohub San Francisco is a nonprofit research institute focused on developing new technologies and tackling ambitious research projects, with the aim of understanding dynamic cell systems across scales in both health and disease. We also join forces with the Bay Area’s leading academic institutions (Stanford University; University of California, Berkeley; and University California, San Francisco) to support bold, visionary science that can’t be done elsewhere.

CZ Biohub San Francisco is part of the CZ Biohub Network, a group of nonprofit research institutes created and supported by the Chan Zuckerberg Initiative.

Affiliated GitHub organizations

The following GitHub organizations are also part of CZ Biohub San Francisco's GitHub presence:

Contact us!

We welcome comments, questions, and inquiries. Please use this form to contact us.

Interested in working with us? Search our job openings here.

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  1. noise2self noise2self Public

    A framework for blind denoising with self-supervision.

    Jupyter Notebook 355 77

  2. tabula-muris tabula-muris Public

    Code and annotations for the Tabula Muris single-cell transcriptomic dataset.

    HTML 192 95

  3. xicor xicor Public archive

    xi correlation method adapted for python

    Jupyter Notebook 149 17

  4. tabula-muris-senis tabula-muris-senis Public

    Tabula Muris Senis

    Jupyter Notebook 103 26

  5. tabula-sapiens tabula-sapiens Public

    Single Cell Transcriptomics of 25 Human Organs to Create a Tabula Sapiens

    Jupyter Notebook 42 9

  6. zebrahub_analysis zebrahub_analysis Public

    Analysis of single-cell single-embryo RNA seq data from the zebrafish developmental atlas Zebrahub.

    Jupyter Notebook 5 1

Repositories

Showing 10 of 111 repositories
  • lfm-data-utilities Public

    A collection of auxiliary data processing tools used in the Remoscope project.

    czbiohub-sf/lfm-data-utilities’s past year of commit activity
    Jupyter Notebook 0 BSD-3-Clause 1 0 1 Updated Jul 9, 2025
  • biahub Public

    HUB for Bio Image Analysis

    czbiohub-sf/biahub’s past year of commit activity
    Python 5 BSD-3-Clause 2 32 15 Updated Jul 8, 2025
  • ulc-malaria-scope Public

    Instrument control software for the Remoscope project.

    czbiohub-sf/ulc-malaria-scope’s past year of commit activity
    Python 1 1 1 3 Updated Jul 8, 2025
  • iohub Public

    Pythonic and parallelizable I/O for N-dimensional imaging data with OME metadata

    czbiohub-sf/iohub’s past year of commit activity
    Python 38 BSD-3-Clause 10 35 (1 issue needs help) 3 Updated Jul 7, 2025
  • napari-iohub Public

    OME-Zarr viewer for napari with iohub as the I/O backend

    czbiohub-sf/napari-iohub’s past year of commit activity
    Python 3 BSD-3-Clause 0 7 2 Updated Jul 3, 2025
  • shrimPy Public

    shrimPy: Smart High-throughput Robust Imaging & Measurement in Python

    czbiohub-sf/shrimPy’s past year of commit activity
    Python 11 BSD-3-Clause 4 22 7 Updated Jul 3, 2025
  • zebrahub-multiome-analysis Public

    A repository for scripts and notebooks to process and analyze single-cell Multiome datasets from early zebrafish embryos (zebrahub)

    czbiohub-sf/zebrahub-multiome-analysis’s past year of commit activity
    Jupyter Notebook 2 BSD-3-Clause 1 0 0 Updated Jul 3, 2025
  • proteinxlocation-cxg-fork-old Public archive Forked from chanzuckerberg/cellxgene

    🚨🚨 new and updated fork in pxl-explorer repo

    czbiohub-sf/proteinxlocation-cxg-fork-old’s past year of commit activity
    JavaScript 0 MIT 136 0 0 Updated Jun 27, 2025
  • ulc-malaria-autofocus Public

    A single-shot autofocus CNN for the Remoscope project

    czbiohub-sf/ulc-malaria-autofocus’s past year of commit activity
    Python 0 BSD-3-Clause 1 0 0 Updated Jun 23, 2025
  • compmicro-ndutils-env Public

    Shared ndutils environment for maintained by the CompMicro platform

    czbiohub-sf/compmicro-ndutils-env’s past year of commit activity
    Dockerfile 0 BSD-3-Clause 1 1 2 Updated Jun 16, 2025
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