Difference between revisions of "Shape Filter"

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| filename              = shape_filter_x.y.z.jar [https://github.com/thorstenwagner/ij-shape-filter/releases/latest [1]]
 
| filename              = shape_filter_x.y.z.jar [https://github.com/thorstenwagner/ij-shape-filter/releases/latest [1]]
 
| source                = Github [https://github.com/thorstenwagner/ij-shape-filter [2]]
 
| source                = Github [https://github.com/thorstenwagner/ij-shape-filter [2]]
| latest version        = v1.3.0 (16 Jul 2015)
+
| latest version        = v1.4.0 (21 Sep 2015)
 
| status                = active  
 
| status                = active  
  
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* '''Feret Diameter''': The maximum distance between the two parallel tangents touching the particle outline in all directions.
 
* '''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.
 
* '''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.
 
* '''Long Side Minimum Bounding Rectangle''': The larger side of the minimum bounding rectangle.
 
* '''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.
 
* '''Short Side Minimum Bounding Rectangle''': The smaller side of the minimum bounding rectangle.
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* '''Thinnes Ratio''': Inverse proportional to the circularity. Furthermore it normed. It is defined as <math>4\pi A/P^{2}</math>
 
* '''Thinnes Ratio''': Inverse proportional to the circularity. Furthermore it normed. It is defined as <math>4\pi A/P^{2}</math>
 
* '''Contour Temperatur''': It has a strong relationship to the fractal dimension, defined as <math>\left(log_{2}\left(\frac{2P}{P-H}\right)\right)^{-1}</math>
 
* '''Contour Temperatur''': It has a strong relationship to the fractal dimension, defined as <math>\left(log_{2}\left(\frac{2P}{P-H}\right)\right)^{-1}</math>
 +
* '''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”.
 
* '''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=
 
=Installation=
 
You could simply use our update site "[http://fiji.sc/List_of_update_sites biomedgroup]" to install the shape filter plugin.
 
You could simply use our update site "[http://fiji.sc/List_of_update_sites biomedgroup]" to install the shape filter plugin.

Revision as of 03:33, 21 September 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 v1.4.0 (21 Sep 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.
  • Max. Inscr. Circle Diameter: The diameter of the maximum inscribed circle.
  • 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}
  • 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.