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BioVoxxel Toolbox

90 bytes added, 19:36, 21 August 2015
Use arrow template for menu commands
=Extended Particle Analyzer=
Purpose: The "Extended Particle Analyzer" is based on the ImageJ "Analyze Particles..." command. It enables the user to further restrict the analysis on particles according to many more parameter spezifications of shape descriptors and angle orientations. Thus, setting minimal and maximal exclusion ranges of different parameters enables to extract particles from a binary image. The output types are the same as for the >Analyze >{{arrow}} Analyze Particles.
Example: If you want to extract/analyze only particles with a certain Feret's Angle or exclude elongated structures using the aspect ratio (AR) or circilarity you can specify so in the initial dialog box.
How to: You need either choose the two images in the "Flat-field" version or specify a gaussian blurring radius for the "Pseudo flat-field correction" in a way to eliminate specific feature appearance but to keep the difference in shading/lighting. Therefore, rather big radii (sigma) are needed (potentially between 40-150, but this depends on image and feature size).
Remark: The pseudo flat field correction menu command links to the plugin with the same name under >Plugins >{{arrow}} BioVoxxel (necessary to additionally download from the BioVoxxel update site together with the Toolbox).
Advantage of the Pseudo flat field correction: This is now recordable and works with stacks. Thus, time-lapse movies e.g. from a brightfield microscope can be completely corrected for unequal lighting according to the individual differences in each frame. The blurring is visualized on the currently active frame to be able to sufficiently eliminate structural information.
=Scaled Intensity Plot=
Purpose: The tool creates a intensity plot along any kind of lines as well as from rectangular selections (as does >Analyze >{{arrow}} Plot Profile) but with the initial possibility to influence the displayed intensity scale. This enables to create plots which can be overlayed by choosing "add to existing plot". In the case of a rectangular selection it can be chosen if the plotting direction should be horizontal or vertical. The intensities along the other direction are then averaged. Additionally, the color and look of the plot line can be chosen.
This should enable to better compare intensity plots from different images or selections which is only possible if they have the same scaling. The latter is done in unscaled units (pixels).
If a new plot line is added to an existing plot the choice "Draw grid lines" is either ignored or forced depending on how the destination plot was created using the same tool.
=Gaussian weighted Median filter=
(separate plugin under >Plugins >{{arrow}} BioVoxxel)
Purpose/How to: This filter is basically a normal median filter (as in ImageJ/Fiji) but with a weighted filter matrix. The radius is given in pixels. The weight is determined automatically by a 2D gaussian function (approximated to integer values) over the size of the filter grid. Thus, pixel closer to the filter center get a higher weight compared to more distant ones. This reduces the intensity homogenizing effect from a normal median filter but increases the edge-perservation of features.
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 >Plugins >{{arrow}} BioVoxxel
Form: plugin, recordable
=Adaptive Filter=
(separate plugin under >Plugins >{{arrow}} BioVoxxel)
Purpose/How to: This filter allows the choise 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).
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 >Plugins >{{arrow}} BioVoxxel
Form: plugin, recording still not fully functional!!!
=Enhance True Color Contrast=
(separate plugin under >Plugins >{{arrow}} BioVoxxel)
Purpose: This image filter enhances the contrast of true color images similar to the method Enhance Contrast in Fiji. If the latter would be applied to true color images this leads to a change in color values and saturation. This unwanted effects are eliminated by the recordable "Enhance True Color Contrast" plugin. It preserves color tone and saturation while enhancing the contrast in the brightness channel of the HSB color space. This is done using high precision float value calculation and not by a simple conversion o fthe image to HSB color space as available in ImageJ/Fiji. The latter would lead to a loss in quality since due to conversion and back-conversion to RGB.
=Mode and Differential Limited Mean Binarization=
(separate plugin under >Plugins >{{arrow}} BioVoxxel)
Purpose: The mode-limited mean (MoLiM) and the differential-limited mean (DiLiM) are two binarization algorithms which initially limit the image histogram according to its mode value (MoLiM) or its mode, an initial mean or the median (DiLiM). A more detailed description can be found under:
The limitation step eliminates all intensity information in the histogram up to the limit (mode, mean or median) and calculates a new mean value which is taken as final threshold. "Force to smaller partition" anables to extract the pixels which occupy rather the smaller histogram partition besides the limit.
Download: Part of the BioVoxxel update site in Fiji and can be found under >Plugins >{{arrow}} BioVoxxel
Form: plugin, recordable
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