Automated

This plugin provides a painter to visualize 2D flows. 2D Flows are couples of two sequences, one for the horizontal displacements, the other for the vertical displacements. This plugin provides a painter that draws flow arrows on top of another sequence.

This plugin facilitates the assembly of a mosaic of overlapping individual images, or tiles. It provides a semi-automated solution where the initial rough positioning of the tiles must be performed by the user, and where the final delicate adjustments are performed by the plugin.

The MosaicJ plugin requires that a second plugin, named TurboReg, is installed. 

This plugin allows to analyze the local direction and frequency of sinusoidal waves, for example muscle repetitive stripy pattern.

The output are optionally smoothed lambda (inversely proportional to the frequency) and phi (direction in degrees).

This plugin performs Strahler analysis on topographic skeletons (2D/3D). Strahler numbering is a numerical procedure that summarizes the branching complexity of mathematical trees.

Drop Shape Analysis is a collection of two methods (DropSnake and LBADSA) for high-accuracy measure of contact angles for drop measurement.

Retinex filtering is based on Land's theory of image perception, proposed to explain the perceived colour constancy of objects under varying illumination conditions. Several approaches exist to implement the retinex principles, among these the multiscale retinex with colour restoration algorithm (MSRCR) combines colour constancy with local contrast enhancement so images are rendered similarly to how human vision is believed to operate.

Three different methods for correcting fluorescence bleaching. 1. Simple (framewise ratio based) 2. Exponential (curve fitting with exponential decay model) 3. Histogram matching (register histogram shape. with 16 bit, it takes long time... it should be improved).

This plugin automatically threshold an image using the Mixture Modeling algorithm. It is an histogram-based technique that assumes that the histogram distribution is represented by two Gaussian curves.

View your multi-channel data as a montage with one image per channel plus a merged, color channel (useful to create figures for communication). 

This viewer plugin will split all N channels of the active sequence into a montage of N+1 images, with one image for each channel, plus an additionnal color (merge) rendering.

Anisotropic filter implements the classical Coherence Enhancing Diffusion Filter [Weickert]. The plugins works on the first band of a 2D, 3D and 4D sequence. 2D and 3D algorithms are proposed. For the 3D case 2 options are available: CED 1D option is the classical filter that acts mainly on the most homogeneous structure direction; CED 2D option acts on the tangential plane of the structure.

Image segmentation by representative colors selection. Two versions are available :

• thresholding
• positive and negative colors selection and SVM learning

Released in 2007, there is a newer "remastered" version "DeconvolutionLab2" (2017)

A complete parametric framework and set of MATLAB tools for computing steerable wavelet frames in 2-D.

TrackProcessor for the TrackManager plugin that allows importing/exporting tracks. Input and output files are in the .xml format used for the ISBI'2012 Particle Tracking Challenge. Tracks are loaded/exported in/from the TrackManager plugin