Difference between revisions of "Shape Filter"
Line 6: | Line 6: | ||
| 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. | + | | latest version = v1.4.0 (21 Sep 2015) |
| status = active | | status = active | ||
Line 23: | Line 23: | ||
* '''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. | ||
Line 34: | Line 35: | ||
* '''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 04:33, 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 Features
- Area (): The area enclosed by the outer contour of an object.
- Area Convex Hull (): The area enclosed by the convex hull of the outer contour of an object.
- Perimeter (): The perimeter of the outer contour of an object.
- Perimeter Convex Hull (): 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
- Area to Perimeter Ratio: Defined as
- Circularity: Defined as
- Elongation: Defined as
- Convexity: Defined as
- Solidity: Defined as
- Number of Holes: The number of holes inside an object.
- Thinnes Ratio: Inverse proportional to the circularity. Furthermore it normed. It is defined as
- Contour Temperatur: It has a strong relationship to the fractal dimension, defined as
- 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.