plugin

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

Saves a RGB image (typically a screenshot) into a CMYK TIFF (required by publishers for high-fidelity color printing).

Wavelet Spot Detector for Blocks, to integrate in Icy protocols.

Ads a magnifier on top of the default 2D viewer to zoom in and inspect individual pixel values

The track manager enables the use of DSP-like trackProcessors. This can affect the display of tracks, selection in time or by ROIs, and also compute some views like the overlaid and animated local flow graph, polar graph.

IdentifySecondaryObjects identifies objects (e.g., cells) using objects identified by another module (e.g., nuclei) as a starting point.

DisplayScatterPlot plots the values for two measurements.

CorrectIlluminationCalculate calculates an illumination function that is used to correct uneven illumination/lighting/shading or to reduce uneven background in images.

The swiss army knife of plugin developers. Automatically generates elegant graphical interfaces with rich and intuitive user interaction based on your algorithm’s parameters.

Automatic detection of the variance (i.e. standard deviation, power) of the noise that affects a sequence, assuming that it is a white additive Gaussian noise.

Fills holes below a given threshold. 3D data is currently processed slice per slice.

Translate the tracks so that first detection is at 0,0,0 location.

Track Processor to color tracks in the Track Manager

Crop crops or masks an image.

This module crops images into a rectangle, ellipse, an arbitrary shape provided by you, the shape of object(s) identified by an Identify module, or a shape created using a previous Crop module in the pipeline.

3D reslicing and threshold-enabled 3D visualization.

Fills the holes in all the ROI of the active sequence (also works in Protocols).

OverlayOutlines is a module from CellProfiler to place outlines of objects over a desired image.

The grayscale watershed segmentation is useful to segment particles in contact when the model of shape is unknown a priori.

This plugin copies the pixel size from the calibration of one image or stack to a second image or stack. This allows one to copy the spatial calibration from one stack to another.

A second dialog allows to enter the scale factors.

This plugin extracts groups of connected pixels in 2D and 3D based on their intensity and that of the background. Works on both binary and gray-scale data. Output can be pushed to the swimming pool for other plug-ins to further exploit the extracted objects.

A Java package for running ImageJ and Fiji within Matlab.

A TrackProcessor that allows the user to monitor, visualize, and export, the intensity profile of tracks in time lapse sequences of 2D images.

This display the Instant Speed of tracks for the Icy Track Manager.

GrayToColor takes grayscale images as input and assigns them to colors in a red, green, blue (RGB) image or a cyan, magenta, yellow, black (CMYK) image. Each color’s brightness can be adjusted independently by using relative weights.

Quantize a color image in any given number of colors.

Calculate Statistics calculates measures of assay quality (V and Z' factors) and dose response data (EC50) for all measured features made from images.

This plugin explores the algorithms for reconstructing scientific images as a combination of other scientific images drawing from a large database of scientific imagery.