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Manually selecting line ROIs and align two images. 

This plugin provides an extended depth of field algorithm to obtain in focus microscopic images of 3D objects and organisms using different algorithms: Sobel, variance, real and complex wavelets.

This plugin calculates the optic flow for each pair of images made with the given stack.

Outline The incessant development of improved microscopy imaging techniques, as well as the advent of highly selective fluorescent dyes has made possible the precise identification of tagged molecules in almost any biological specimen. Of particular interest are the visualization and the study of living cells, which induce tight constraints on the imaging process. To avoid the alteration of the sample and to achieve a high temporal resolution, low fluorophore concentrations, low-power illumination and short exposure time need to be used in practice.

Mice Profiler uses geometrical primitives to model and track two mice without requiring any specific tagging. The program monitors a comprehensive repertoire of behavioral states and their temporal evolution, allowing the identification of key elements that trigger social contact.

Mice Profiler Label Analyser performs temporal analysis of data from Mice Profiler.

Mice Profiler tracks multiple mice from a top view video.

Manual angle measurements. 

No javadoc accessible, but can be downloaded from the webpage. 

Layer for the 3D Viewer, allowing the user to move the camera in a more intuitive way.

This plugin allows the creation of custom animations for 3D viewing. It will generate a new sequence that can be edited in Icy, and saved.

The animation is based on key framing, as in most of 3D rendering software projects.

Wavelet-based method to merge a stack of micrographs taken at different focal positions (aligned along the optical axis) into a single, entirely focused composite image.

MonogenicJ performs multiresolution monogenic analyses of 2D images. It extracts wavelet-domain features that characterize the local orientation, the phase and the dominant frequency of an image patch at various levels of resolution.

A canvas plugin using JFreeChart to show intensity profile of a specific row or column. Initially used in a 1-row image of 1D signal representation. Can also used with Micro-Manager for Icy Plugin to show 1D signal from hardware like data acquisition device as waveform. Common 2D+ sequence is also supported. Using it by select the plugin icon in the canvas type combobox of the sequence window, a JFreeChart line chart will show up.