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@baradlab

baradlab

Barad Lab at OHSU

Welcome to the GitHub organization for software tools developed in the Barad Lab at Oregon Health & Science University

Mission

Our goal is to develop tools to enable integrative structural and cellular biology using Cryo-ET and other technologies, and to share them freely to help the community better study biology across scales.

Software Principles

  1. Unless it is not possible because of dependencies, software will be licensed permissively
  2. We are biologists first, and cannot let the perfect be the enemy of the good. We hope that all of our software will eventually be polished, flexible, and easy to use, but we will not wait for those things to be true before sharing our tools as is!
  3. While this organization will host Barad lab specific tools, we encourage contribution to larger shared organizations, such as teamtomo when the scope of the project is appropriate

Contributors

The Barad lab organization welcomes contributions from outside of the lab. We expect contributors to respect our lab's collaboratively developed compact

Popular repositories Loading

  1. surface_morphometrics surface_morphometrics Public

    Morphometrics for Membrane Surfaces Segmented from Cryo-ET or other volumetric imaging.

    Python 36 13

  2. Geopickr Geopickr Public

    Geometry-supported particle picking for Cryo-ET in ChimeraX

    Python 6

  3. surface-morphometrics-gui surface-morphometrics-gui Public

    GUI for Surface Morphometrics Pipeline

    Python 4 2

  4. morphometricsx morphometricsx Public

    ChimeraX bundle to load and color quantified .vtp morphometrics surfaces (curvature, thickness, distances, ...) from surface_morphometrics / pycurv.

    Python 2

  5. baradlab.github.io baradlab.github.io Public

    Barad Lab Website

    HTML 1 1

  6. michigan_tutorial michigan_tutorial Public

    Segmentation Tutorial for U Michigan

    1

Repositories

Showing 9 of 9 repositories
  • surface_morphometrics Public

    Morphometrics for Membrane Surfaces Segmented from Cryo-ET or other volumetric imaging.

    baradlab/surface_morphometrics's past year of commit activity
    Python 36 GPL-3.0 13 5 2 Updated Nov 12, 2026
  • baradlab.github.io Public

    Barad Lab Website

    baradlab/baradlab.github.io's past year of commit activity
    HTML 1 BSD-3-Clause 1 1 1 Updated Sep 30, 2026
  • filament_morphometrics Public

    Filament addon to the surface morphometrics pipeline

    baradlab/filament_morphometrics's past year of commit activity
    Python 0 MIT 0 0 0 Updated Sep 3, 2026
  • morphometricsx Public

    ChimeraX bundle to load and color quantified .vtp morphometrics surfaces (curvature, thickness, distances, ...) from surface_morphometrics / pycurv.

    baradlab/morphometricsx's past year of commit activity
    Python 2 GPL-3.0 0 0 0 Updated Jul 31, 2026
  • Geopickr Public

    Geometry-supported particle picking for Cryo-ET in ChimeraX

    baradlab/Geopickr's past year of commit activity
    Python 6 GPL-3.0 0 2 0 Updated Jul 21, 2026
  • surface-morphometrics-gui Public

    GUI for Surface Morphometrics Pipeline

    baradlab/surface-morphometrics-gui's past year of commit activity
    Python 4 MIT 2 7 0 Updated Jul 9, 2026
  • morphometrics_2hr Public

    Condensed 2-hour Surface Morphometrics tutorial (EMPIAR-12534 IMM/OMM)

    baradlab/morphometrics_2hr's past year of commit activity
    Shell 0 BSD-3-Clause 0 0 0 Updated Jul 9, 2026
  • michigan_tutorial Public

    Segmentation Tutorial for U Michigan

    baradlab/michigan_tutorial's past year of commit activity
    1 BSD-3-Clause 0 0 0 Updated Jun 11, 2026
  • .github Public
    baradlab/.github's past year of commit activity
    0 0 0 0 Updated Mar 4, 2024

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