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BioVoxxel Toolbox

541 bytes added, 11:29, 14 March 2017
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Future: will be implemented for 32-bit images as well. The upper intensity limit will be made individually adjustable. Suggestions welcome!
 
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=Adaptive Filter=
(separate plugin under {{bc | Plugins | BioVoxxel}})
 
Purpose/How to: This filter allows the choice between two basic filter modes (''median'' and ''mean''). The filter ''Radius'' defines the size of a square kernel (so actually not really a radius but to keep the entries intuitively similar to other filters in Fiji this label was chosen).
The ''Shape'' option enables a basic pre-selection of pixels from the kernel neighborhood to be taken into account for filtering. After pressing 'Ok', a checkbox grid will be displayed from which the user can adjust the selected pixels for the final filter according to the filtering needs (e.g. to remove power lines in a photograph).
 
''Tolerance'' sets a threshold which will change intensity values after filtering only for those pixels where the difference to the original intensity is at least as high as the tolerance (0.2 = 20%). This enables to remove extreme outliers from the image while preserving the original pixel values in image areas without such outliers (at least for shot noise).
 
In the image below the upper pannels show the original photograph and a version with artificial shot noise added. The lower pannels depict the noisy image after a median filter (radius=2) or after the Adaptive Filter (radius = 2 and tolerance set to 0.2) using a circle-like kernel.
 
[[File:AdaptiveFilter.png]]
 
Output: The filter will be applied directly on the input image. It is undoable (by pressing [z]).
 
Limitation: So far, the filter is only applicable on 8-bit and 16-bit single images.
 
Installation: Part of the BioVoxxel update site in Fiji and can be found under {{bc | Plugins | BioVoxxel}}
 
Form: plugin, recording still not fully functional!!!
 
Status: maintenance active
 
Future: Will be adjusted für 32-bit float-type images as well as RGB images and stacks. Suggestions are welcome!
 
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=Recursive Filters=
 
Purpose: The recursive filters plugin allows to repetitively apply one of the three basic image filters (Gaussian Blur, Mean, Median) with small radii (max = 3) by adjusting the iteration. The previously filtered image will then be taken as basis for the next image filtering
 
The maximum iteration can be set by the user up to 500 times but will be stopped if two consecutive filtered images do not show any further difference.
 
[[File:RecursiveFilters01.png]]
 
Form: recordable plugin
 
Status: maintenance active
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Form: plugin, recordable
 
Status: maintenance active
 
Future: Will be adjusted für 32-bit float-type images as well as RGB images and stacks. Suggestions are welcome!
 
----
 
=Adaptive Filter=
(separate plugin under {{bc | Plugins | BioVoxxel}})
 
Purpose/How to: This filter allows the choice between two basic filter modes (''median'' and ''mean''). The filter ''Radius'' defines the size of a square kernel (so actually not really a radius but to keep the entries intuitively similar to other filters in Fiji this label was chosen).
The ''Shape'' option enables a basic pre-selection of pixels from the kernel neighborhood to be taken into account for filtering. After pressing 'Ok', a checkbox grid will be displayed from which the user can adjust the selected pixels for the final filter according to the filtering needs (e.g. to remove power lines in a photograph).
 
''Tolerance'' sets a threshold which will change intensity values after filtering only for those pixels where the difference to the original intensity is at least as high as the tolerance (0.2 = 20%). This enables to remove extreme outliers from the image while preserving the original pixel values in image areas without such outliers (at least for shot noise).
 
In the image below the upper pannels show the original photograph and a version with artificial shot noise added. The lower pannels depict the noisy image after a median filter (radius=2) or after the Adaptive Filter (radius = 2 and tolerance set to 0.2) using a circle-like kernel.
 
[[File:AdaptiveFilter.png]]
 
Output: The filter will be applied directly on the input image. It is undoable (by pressing [z]).
 
Limitation: So far, the filter is only applicable on 8-bit and 16-bit single images.
 
Installation: Part of the BioVoxxel update site in Fiji and can be found under {{bc | Plugins | BioVoxxel}}
 
Form: plugin, recording still not fully functional!!!
Status: maintenance active
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