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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 378 81

  2. tabula-muris tabula-muris Public

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

    HTML 202 94

  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 110 26

  5. tabula-sapiens tabula-sapiens Public

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

    Jupyter Notebook 51 11

  6. zebrahub_analysis zebrahub_analysis Public

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

    Jupyter Notebook 11 1

Repositories

Showing 10 of 130 repositories
  • 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 56 BSD-3-Clause 13 47 (1 issue needs help) 12 Updated Sep 9, 2026
  • biahub Public

    HUB for Bio Image Analysis

    czbiohub-sf/biahub's past year of commit activity
    Python 13 BSD-3-Clause 2 90 32 Updated Sep 9, 2026
  • grassp Public

    GRaph-based Analysis of Subcellular/Spatial Proteomics

    czbiohub-sf/grassp's past year of commit activity
    Python 10 BSD-3-Clause 0 0 2 Updated Sep 9, 2026
  • inTRACKtive Public Forked from royerlab/inTRACKtive

    Interactive visualization and sharing of cell tracking data in the browser

    czbiohub-sf/inTRACKtive's past year of commit activity
    TypeScript 0 MIT 9 0 5 Updated Sep 9, 2026
  • shrimPy Public

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

    czbiohub-sf/shrimPy's past year of commit activity
    Python 17 BSD-3-Clause 5 30 5 Updated Sep 9, 2026
  • subcellular-proteomics-curation Public Forked from mffrank/subcellular-proteomics-curation

    Code and documentation for the curation of proteinxlocation datasets

    czbiohub-sf/subcellular-proteomics-curation's past year of commit activity
    Python 0 MIT 31 0 0 Updated Aug 26, 2026
  • nd-embedding-atlas Public

    An interactive browser-based dashboard linking AI embeddings to source nD image data for rapid exploration and annotation.

    czbiohub-sf/nd-embedding-atlas's past year of commit activity
    TypeScript 3 MIT 0 9 2 Updated Aug 25, 2026
  • protoSpaceJAM Public

    CRISPR knock-in design at scale

    czbiohub-sf/protoSpaceJAM's past year of commit activity
    Python 13 BSD-3-Clause 3 10 0 Updated Aug 22, 2026
  • cyclops-monorepo Public

    Mono-repo for the cyclOPS Optical Pooled Screening image-processing, modeling, and analysis pipelines

    czbiohub-sf/cyclops-monorepo's past year of commit activity
    Shell 0 BSD-3-Clause 0 0 0 Updated Aug 17, 2026
  • cyclops-model Public

    Deep-learning models for Optical Pooled Screening (OPS) image analysis (Leonetti group, Biohub SF)

    czbiohub-sf/cyclops-model's past year of commit activity
    Python 0 BSD-3-Clause 0 0 0 Updated Aug 17, 2026

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