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Surface Morphometrics Pipeline

  • Description

    a pipeline of tools to generate robust open mesh surfaces from voxel segmentations of biological membranes using the Screened Poisson algorithm and calculate morphological features including curvature and membrane-membrane distance using pycurv's vector voting framework with tools to convert these morphological quantities into morphometric insights.

  • Usage

    To list all executables provided by Surface Morphometrics Pipeline, run: $ sbgrid-list surface-morphometrics Copy to clipboard

  • Usage Notes

    Aliases have been created for each of the python scripts so that in place of running python SCRIPT.py users can just run SCRIPT.py. Please note that version 1.1 works only in RHEL9 or newer.

  • Installation

    Use the following command to install this title with the CLI client: $ sbgrid-cli install surface-morphometrics Copy to clipboard Available operating systems: Linux 64

  • Primary Citation*

    B. A. Barad, M. Medina, D. Fuentes, R. L. Wiseman, and D. A. Grotjahn. 2022. A surface morphometrics toolkit to quantify organellar membrane ultrastructure using cryo-electron tomography. bioRxiv 2022.01.23.477440.


    • *Full citation information available through

  • Keywords

    Electron Microscopy, Tomography

  • Default Versions

    Linux 64:  1.1 (3.1 GB)

  • Other Versions

      Linux 64:

      0.2 (3.1 GB)

  • Developers

    Benjamin A Barad

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