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Shape Filter

    Name

    Shape Filter Plugin

    Software

    ImageJ/Fiji

    Author

    Thorsten Wagner

    Maintainer

    Thorsten Wagner

    Source

    Github [2 ]

    Status

    active

    General Description

    The ImageJ Shape Filter Plugin use the [ij-blob] library to characterize and filter objects in binary scenes by its shape. Therefore, several features are calculated as shown below. Shape_Filter_GUI.png

    If you like to cite the Shape Filter plugin in a scientific publication, please cite:

    Wagner, T and Lipinski, H 2013. IJBlob: An ImageJ Library for Connected Component Analysis and Shape Analysis. Journal of Open Research Software 1(1):e6, DOI: http://dx.doi.org/10.5334/jors.ae

    Shape Features

    • Area (\(A\)): The area enclosed by the outer contour of an object.
    • Area Convex Hull (\(C\)): The area enclosed by the convex hull of the outer contour of an object.
    • Perimeter (\(P\)): The perimeter of the outer contour of an object.
    • Perimeter Convex Hull (\(H\)): The perimeter of the convex hull of the particle.
    • Feret Diameter: The maximum distance between the two parallel tangents touching the particle outline in all directions.
    • Min. Feret Diameter: the minimum distance between the two parallel tangents touching the particle outline in all directions.
    • Max. Inscr. Circle Diameter: The diameter of the maximum inscribed circle.
    • Area eq. circle diameter: Equivalent circle diameter \(2\sqrt{\frac{A}{\pi}}\)
    • Long Side Minimum Bounding Rectangle (\(L\)): The larger side of the minimum bounding rectangle.
    • Short Side Minimum Bounding Rectangle (\(S\)): The smaller side of the minimum bounding rectangle.
    • Aspect Ratio: Defined as \(L/S\)
    • Area to Perimeter Ratio: Defined as \(A/P\)
    • Circularity: Defined as \(P^{2}/A\)
    • Elongation: Defined as \(1 - S/L\)
    • Convexity: Defined as \(H/P\)
    • Solidity: Defined as \(A/C\)
    • Number of Holes: The number of holes inside an object.
    • Thinnes Ratio: Inverse proportional to the circularity. Furthermore it normed. It is defined as \(4\pi A/P^{2}\)
    • Contour Temperatur: It has a strong relationship to the fractal dimension, defined as \(\left(log_{2}\left(\frac{2P}{P-H}\right)\right)^{-1}\)
    • Orientation: The orientation of the major axis from in grad (measured counter clockwise from the positive x axis).
    • Fractal Box Dimension: Estimated fractal dimension by the box count algorithm. The default box-sizes are “2,3,4,6,8,12,16,32,64”.

    Installation

    You could simply use our update site “Biomedgroup “ to install the shape filter plugin.