Difference between revisions of "Shape Filter"

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== General Description ==
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= General Description =
  
 
The ImageJ Shape Filter Plugin uses the [https://github.com/thorstenwagner/ij-blob [ij-blob]] library to characterize and filter objects in binary scenes by its shape. Therefore, several features are calculated as shown below.
 
The ImageJ Shape Filter Plugin uses the [https://github.com/thorstenwagner/ij-blob [ij-blob]] library to characterize and filter objects in binary scenes by its shape. Therefore, several features are calculated as shown below.
 
[[File:Shape Filter GUI.png|200px|thumb]]
 
[[File:Shape Filter GUI.png|200px|thumb]]
= Shape Features =
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== Shape Features ==
  
 
* '''Area''' (<math>A</math>): The area enclosed by the outer contour of an object.
 
* '''Area''' (<math>A</math>): The area enclosed by the outer contour of an object.
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* '''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”.
 
* '''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”.
  
=Examples=
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==Examples==
  
 
=Installation=
 
=Installation=

Revision as of 09:59, 15 July 2015

Shape Filter Plugin (ImageJ/Fiji)
Author Thorsten Wagner
Maintainer Thorsten Wagner (wagner@biomedical-imaging.de)
File shape_filter_x.y.z.jar [1]
Source Github [2]
Latest version v1.2.1 (16 Jul 2015)
Development status active


General Description

The ImageJ Shape Filter Plugin uses 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

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.
  • Long Side Minimum Bounding Rectangle: The larger side of the minimum bounding rectangle.
  • Short Side Minimum Bounding Rectangle: 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}
  • 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”.

Examples

Installation