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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.

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  1. recOrder recOrder Public

    3D quantitative label-free imaging with phase and polarization

    Python 14 4

  2. waveorder waveorder Public

    Wave optical models and inverse algorithms for label-agnostic imaging of density & orientation.

    Python 21 4

  3. dynamorph dynamorph Public archive

    Learn morphological states of dynamic cells

    Jupyter Notebook 12 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 6 4

  6. VisCy VisCy Public

    computer vision models for single-cell phenotyping

    Python 40 3

Repositories

Showing 10 of 26 repositories
  • recOrder Public

    3D quantitative label-free imaging with phase and polarization

    mehta-lab/recOrder’s past year of commit activity
    Python 14 BSD-3-Clause 4 43 13 Updated Dec 28, 2024
  • VisCy Public

    computer vision models for single-cell phenotyping

    mehta-lab/VisCy’s past year of commit activity
    Python 40 BSD-3-Clause 3 23 12 Updated Dec 23, 2024
  • waveorder Public

    Wave optical models and inverse algorithms for label-agnostic imaging of density & orientation.

    mehta-lab/waveorder’s past year of commit activity
    Python 21 BSD-3-Clause 4 16 1 Updated Dec 22, 2024
  • dynacontrast Public archive

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

    mehta-lab/dynacontrast’s past year of commit activity
    Python 5 BSD-3-Clause 1 2 0 Updated Sep 3, 2024
  • pycro-manager Public Forked from micro-manager/pycro-manager

    Python control of micro-manager for customized data acquisition

    mehta-lab/pycro-manager’s past year of commit activity
    Jupyter Notebook 0 BSD-3-Clause 53 0 1 Updated Apr 19, 2024
  • NDViewer Public Forked from micro-manager/NDViewer

    N-D multichannel multiresolution image viewer for Micro-Manager

    mehta-lab/NDViewer’s past year of commit activity
    Java 0 5 0 0 Updated Apr 19, 2024
  • NDTiffStorage Public Forked from micro-manager/NDStorage

    N-dimensional, multiresolution file format for Micro-Manager

    mehta-lab/NDTiffStorage’s past year of commit activity
    Java 0 BSD-3-Clause 10 0 0 Updated Apr 19, 2024
  • AcqEngJ Public Forked from micro-manager/AcqEngJ

    Java-based acquisition engine for Micro-manager

    mehta-lab/AcqEngJ’s past year of commit activity
    Java 0 BSD-3-Clause 6 0 0 Updated Apr 19, 2024
  • mmCoreAndDevices Public Forked from micro-manager/mmCoreAndDevices

    Micro-Manager's device control layer, written in C++

    mehta-lab/mmCoreAndDevices’s past year of commit activity
    C++ 0 112 6 0 Updated Apr 10, 2024
  • TriggerScopeMM Public Forked from micro-manager/TriggerScopeMM

    Micro-Manager-specific firmware for the TriggerScope

    mehta-lab/TriggerScopeMM’s past year of commit activity
    C++ 0 4 0 0 Updated Apr 5, 2024

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