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The BioVoxxel Toolbox is a suite which contains plugins and some macros dealing with image filtering, image segmentation and binary image processing and analysis. The following plugins are hosted here:

• Extended Particle Analyzer
• Binary Feature Extractor
• Speckle Inspector
• Watershed Irregular Features
• EDM Binary Operations
• Filter Check
• Pseudo flat-field correction
• Convoluted Background Subtraction
• 2D Particle Distribution (Distribution_Analysis)
• Cluster Indicator
• SSIDC Cluster Indicator
• Gaussian weighted Median filter
• Adaptive Filter
• Enhance True Color Contrast
• Mode and Differential Limited Mean Binarization
• Basic Recursive Filter

A content-adaptive representation of fluorescence microscopy images called Adaptive Particle Representation (APR), which replaces the regular grid of pixels with particles positioned according to image content. This overcomes storage bottlenecks, as data compression does, but additionally overcomes memory and processing bottlenecks, since the APR can directly be used in processing without going back to pixels.

Software for computing single molecule localization accuracies and resolution measures

The FandPLimitTool is a GUI based software module that allows users to calculate the limits to the accuracy with which parameters can be estimated from single molecule imaging data. The software supports calculation of limits for the 2D/3D location estimation problem and the 2D/3D distance-estimation/resolution problem. The location estimation problem is concerned with the task of determining the position of a single molecule and the distance-estimation/resolution problem is concerned with the task of determining the distance of separation between two single molecules. The user can calculate limits for a variety of imaging scenarios.

Non linear registration intensity based for MRI brain exams. To be applied after FLIRT

FLIRT (FMRIB's Linear Image Registration Tool) is a fully automated robust and accurate tool for linear (affine) intra- and inter-modal brain image registration.

FLIRT comes with a main GUI as well as three supporting guis:

• ApplyXFM - for applying saved transformations and changing FOVs
• InvertXFM - for inverting saved transformations
• ConcatXFM - for concatenating saved transformations