Computational protocol: MorphoTester: An Open Source Application for Morphological Topographic Analysis

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Protocol publication

[…] Visualization and mathematical functions of MorphoTester are supported by pre-existing open source Python packages. These include the Numpy and Scipy stack [], which provides data structures and functions for the large-format multidimensional arrays and matrices that are used to store polygonal mesh data. Mesh visualization is supported by the package Mayavi [], and this package is integrated with PyQt4 [] and the non-Python open source library Qt4 (www.qt.io) to implement the graphical user interface. Matplotlib [] is used for data plotting tasks. A full list of package dependencies can be found in . All of these backend packages have full documentation and so can be leveraged to modify MorphoTester code in a straightforward fashion for future needs.In addition to being supported by third-party Python packages, this software incorporates and is supplied with Python packages and scripts to provide useful functions for working with triangulated polygon mesh data. Principal among these is plython, a package integrated with MorphoTester that provides functions for inputting, manipulating, and saving triangulated polygon mesh data within Python. Four other command line scripts are provided as well: meshrotate, which rotates individual PLY-format meshes in XYZ coordinate space; meshrotate-batch, which extends meshrotate to process multiple files; PLYtoOFF, which converts PLY-format mesh data to OFF-format; and BINtoASC, which converts PLY-format mesh from binary encoding to ASCII encoding. BINtoASC is useful as MorphoTester specifically interprets ASCII encoded PLY-format meshes, while some applications for modifying 3D meshes such as Geomagic only allow saving PLY-format meshes with binary encoding.The code structure of MorphoTester is split between a single module containing support for visualization, the user interface, and integration of topographic shape metrics (Morpho.py), and three individual modules providing support for topographic shape metrics. Of the topographic algorithms, support for the calculation of DNE, RFI, and OPCR are provided by the modules DNE.py, RFI.py, and OPC.py respectively. Description of the calculation of these metrics follows. […]

Pipeline specifications

Software tools Numpy, matplotlib
Application Miscellaneous
Organisms Homo sapiens