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@mehta-lab

Computational Microscopy Platform (Mehta Lab), CZ Biohub

Computational Microscopy, CZ Biohub SF

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.

This GitHub organization is home to the computational imaging and computer vision projects of the Computational Microscopy Platform at the CZ Biohub SF. We also maintain forks of related open-source projects and the code for reproducing our published work on this organization. Our projects on high throughput microscopy and next generation file format are maintained on the main CZ Biohub org.

Contact Us!

The organization is maintained by Shalin Mehta, who leads the Computational Microscopy Platform. Please contact Shalin or other members of the team with your questions. If you have a bug report or question about one of our projects, please open an issue on that project.

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

Pinned

  1. recOrder recOrder Public

    3D quantitative label-free imaging with phase and polarization

    Python 10 3

  2. waveorder waveorder Public

    A generalist library of wave optical models and inverse algorithms for label-free imaging of density & orientation.

    Python 10 3

  3. dynamorph dynamorph Public archive

    Learn morphological states of dynamic cells

    Jupyter Notebook 13 1

  4. dynacontrast dynacontrast Public archive

    Image-based phenotyping of single cells using self-supervised contrastive learning

    Python 5 1

  5. multiSero multiSero Public

    serological measurements from multiplexed ELISA assays

    Jupyter Notebook 5 3

  6. VisCy VisCy Public

    computer vision models for single-cell phenotyping

    Python 16 2

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