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Biomat

  1. 1.
    0522714 - FGÚ 2020 RIV CZ eng L4 - Software
    Janáček, Jiří
    Biomat.
    Internal code: BM_2020_1.0.1 ; 2019
    Technical parameters: Pluginy v Biomat jsou nástroje pro detekci a analýzu kapilárního řečiště a převodního systému v srdci
    Economic parameters: Jedná se o volně dostupný software
    R&D Projects: GA MŠk(CZ) LTC17023
    Institutional support: RVO:67985823
    Keywords : tensor images * ImageJ * fiber networks * Lipschitz envelope * heat equation * Crank-Nicolson method
    OECD category: Anatomy and morphology (plant science to be 1.6)
    https://imagej.net/Biomat

    Biomat is collection of ImageJ plugins distributed in FiJi.
    1) Plugins for 3D image preprocessing.
    Stack Linear Contrast - multiplies images in stack by coefficient obtained by linear interpolation of the “first” and “last” coefficient. A simple tool for compensation of contrast decreasing with depth within thick sample.
    Lipschitz 3D Filter - top hat - subtracts slowly varying background calculated as lower Lipschitz envelope from the image.
    2) Plugins for detection of fibres in 3D image.
    Tensor Line 3D Filter - enhances white fibers of uniform width sparsely distributed on dark background.
    Vector Line 3D Filter - enhances white fibers of varying thickness. Crossection of the fibers need not be circular.
    3) Plugins for evaluation of 2D images using heat equation.
    2D Tensor Color Coding - standard color coding of 2D tensor image. Symmetric tensor is coded as channels of 32 bit image stacks.
    2D Heat Kernel Tensor - second order moments of heat kernel calculated from 8 bit binary image by Crank-Nicolson method.
    2D Tensor Statistics - summary of tensor image (in ROI). “Value” is average trace of the tensor, “shape” is the ratio of its eigenvalues and “angle” of the first eigenvector is measured counterclockwise from the horizontal axis.

    Permanent Link: http://hdl.handle.net/11104/0307162

     
     
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