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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 understanding the underlying mechanisms of disease and on developing new technologies that will lead to actionable diagnostics and effective therapies. We are a regional research endeavor with international reach, where the San Francisco Bay Area’s leading academic institutions (Stanford University; University of California, Berkeley; and University California, San Francisco) join forces with CZ Biohub’s innovative internal team to catalyze impact, spurring partnerships that benefit people around the world. The tools and technologies we create will always be freely available to scientists everywhere.

Affiliated GitHub organizations

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

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  1. noise2self Public

    A framework for blind denoising with self-supervision.

    Jupyter Notebook 344 76

  2. tabula-muris Public

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

    HTML 190 95

  3. xicor Public archive

    xi correlation method adapted for python

    Jupyter Notebook 149 17

  4. tabula-muris-senis Public

    Tabula Muris Senis

    Jupyter Notebook 100 26

  5. tabula-sapiens Public

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

    Jupyter Notebook 41 9

  6. 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 109 repositories
  • CZB--Metadata-Standards Public

    Easily-accesible documentation site for CZB's metadata standards efforts

    0 MIT 0 0 0 Updated Apr 15, 2025
  • shrimPy Public

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

    Python 9 BSD-3-Clause 3 17 3 Updated Apr 14, 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 2 BSD-3-Clause 1 0 0 Updated Apr 14, 2025
  • biahub Public

    HUB for Bio Image Analysis

    Python 1 BSD-3-Clause 0 31 10 Updated Apr 14, 2025
  • ulc-malaria-scope Public

    Instrument control software for the Remoscope project.

    Python 1 0 1 0 Updated Apr 10, 2025
  • lfm-data-utilities Public

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

    Jupyter Notebook 0 BSD-3-Clause 0 0 0 Updated Apr 8, 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.

    Python 0 BSD-3-Clause 0 0 0 Updated Apr 5, 2025
  • iohub Public

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

    Python 34 BSD-3-Clause 8 30 (1 issue needs help) 3 Updated Apr 4, 2025
  • compmicro-ndutils-env Public

    Shared ndutils environment for maintained by the CompMicro platform

    Dockerfile 0 BSD-3-Clause 0 2 0 Updated Mar 31, 2025
  • coPylot Public

    coPylot - microscope control

    Python 8 BSD-3-Clause 10 26 (4 issues need help) 16 Updated Mar 26, 2025