Difference between revisions of "Shape Filter"
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| software = ImageJ/Fiji | | software = ImageJ/Fiji | ||
| name = Shape Filter Plugin | | name = Shape Filter Plugin | ||
− | | author = | + | | author = {{Person|Twagner}} |
− | | maintainer = | + | | maintainer = {{Person|Twagner}} |
− | | filename = | + | | 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 = v1.2 | + | | latest version = v1.4.2 (14 July 2016) |
| status = active | | status = active | ||
}} | }} | ||
− | + | = General Description = | |
− | The ImageJ Shape Filter Plugin | + | The ImageJ Shape Filter Plugin use 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]] | ||
− | + | If you like to cite the Shape Filter plugin in a scientific publication, please cite: | |
− | * Area (<math>A</math>): The area enclosed by the outer contour of an object. | + | 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 |
− | * Area Convex Hull (<math>C</math>): The area enclosed by the convex hull of the outer contour of an object. | + | |
− | * Perimeter (<math>P</math>): The perimeter of the outer contour of an object. | + | |
− | * Perimeter Convex Hull (<math>H</math>): The perimeter of the convex hull of the particle. | + | == Shape Features == |
− | * 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. | + | * '''Area''' (<math>A</math>): The area enclosed by the outer contour of an object. |
− | * Long Side Minimum Bounding Rectangle: The larger side of the minimum bounding rectangle. | + | * '''Area Convex Hull''' (<math>C</math>): The area enclosed by the convex hull of the outer contour of an object. |
− | * Short Side Minimum Bounding Rectangle: The smaller side of the minimum bounding rectangle. | + | * '''Perimeter''' (<math>P</math>): The perimeter of the outer contour of an object. |
− | * Aspect Ratio: Defined as <math>L/S</math> | + | * '''Perimeter Convex Hull''' (<math>H</math>): The perimeter of the convex hull of the particle. |
− | * Area to Perimeter Ratio: Defined as <math>A/P</math> | + | * '''Feret Diameter''': The maximum distance between the two parallel tangents touching the particle outline in all directions. |
− | * Circularity: Defined as <math>P^{2}/A</math> | + | * '''Min. Feret Diameter''': the minimum distance between the two parallel tangents touching the particle outline in all directions. |
− | * Elongation: Defined as <math>1 - S/L</math> | + | * '''Max. Inscr. Circle Diameter''': The diameter of the maximum inscribed circle. |
− | * Convexity: Defined as <math>H/P</math> | + | * '''Area eq. circle diameter''': Equivalent circle diameter <math>2\sqrt{\frac{A}{\pi}}</math> |
− | * Solidity: Defined as <math>A/C</math> | + | * '''Long Side Minimum Bounding Rectangle''' (<math>L</math>): The larger side of the minimum bounding rectangle. |
− | * Number of Holes: The number of holes inside an object. | + | * '''Short Side Minimum Bounding Rectangle''' (<math>S</math>): The smaller side of the minimum bounding rectangle. |
− | * Thinnes Ratio: Inverse proportional to the circularity. Furthermore it normed. It is defined as <math>4\pi A/P^{2}</math> | + | * '''Aspect Ratio''': Defined as <math>L/S</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> | + | * '''Area to Perimeter Ratio''': Defined as <math>A/P</math> |
− | * 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”. | + | * '''Circularity''': Defined as <math>P^{2}/A</math> |
+ | * '''Elongation''': Defined as <math>1 - S/L</math> | ||
+ | * '''Convexity''': Defined as <math>H/P</math> | ||
+ | * '''Solidity''': Defined as <math>A/C</math> | ||
+ | * '''Number of Holes''': The number of holes inside an object. | ||
+ | * '''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> | ||
+ | * '''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 "{{ListOfUpdateSites|Biomedgroup}}" to install the shape filter plugin. |
Latest revision as of 18:26, 13 December 2018
Shape Filter Plugin (ImageJ/Fiji) | |
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Author | Thorsten Wagner |
Maintainer | Thorsten Wagner |
File | shape_filter_x.y.z.jar [1] |
Source | Github [2] |
Latest version | v1.4.2 (14 July 2016) |
Development 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.
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 (): 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.
- Area eq. circle diameter: Equivalent circle diameter
- 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.