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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.

  • 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

  • Citation Note

    Please visit the website for additional citation guidance.

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