Plugin List
Current number of plugins: 187
3
3D Active Mesh plug-in for cell segmentation and tracking in 3D images and sequences.
(1)Takes the active 3D VTK viewer and records a 360-degree rotation of the data into a video ...
(1)a
This plug-in implements fast active contours for image segmentation. Their representation ...
(4)This plug-in implements fast active surfaces for 3D image segmentation. Their representati...
(1)This is an icy package that encapsulates tools to design and implement parametric active c...
(1)Fast multiple coupled active contours using edge and region information for segmentation a...
(1)The adaptive histogram equalization implements the Contrast-Limited Adaptive Histogram Equ...
(1)Anisotropic filter implements the classical Coherence Enhancing Diffusion Filter [Weickert...
(1)Simple tool for annotations / notes on your sequences. (This plugin requires Icy v. 1.2.0....
(1)Plugin Library used to provide autocompletion to JTextComponents, such as JTextArea or JTe...
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b
Choose the best auto thresholding technique for your data. Ported from Auto Threshold plug...
(1)c
Creates a linear montage that shows each channel separately plus a final merged channel (u...
(1)Creates a colocalization scatter plot based on 2 channels. This plugin can take 1 ROI as i...
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Image segmentation by representative colors selection. Two versions are available :
- thr...
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This plugin permit to measure the signal spread of a molecule with respect to the cell are...
(2)This plugin provides some useful functions to work with complex-valued sequences.
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This plugin extracts groups of connected pixels in 2D and 3D based on their intensity and ...
(2)Exports connected components data in XLS. Exports All, by T or by ROI
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The right click on sequences and ROIs will open a menu with various features, such as imag...
(2)d
This plugins debleaches your sequence by either reversing exponential decrease of fluoresc...
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This tutorial explain how to use a deviation renderer JFreeChart chart in ICY.
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e
The swiss army knife of plugin developers. Automatically generates elegant graphical inter...
(3)Tutorial showing EzPlug\'s features in action. Check out the documentation to have a direc...
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f
Fast MultiThreaded 3D Filtering, use ellipsoidal neighbourhood, works for 5D images.
(1)The Icy Feature Detector plug-in implements a series of optimized contour and ridge detect...
(2)Fills holes below a given threshold. 3D data is currently processed slice per slice
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Provides a selection of spatial, separable and customizable filters in 1D and 2D, with Ope...
(1)This plugin provides a painter to visualize 2D flows.
2D Flows are couples of two seque...
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Layer for the 3D Viewer, allowing the user to move the camera in a more intuitive way.
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g
Automatic detection of the variance (i.e. standard deviation, power) of the noise that aff...
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This plugin generates a bug in a thread, to show the capabilities of the automatic bug rep...
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This tutorial details how to generate images of all differents types. (byte, int, short, u...
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h
Compute and display the histogram of a sequence, with a more accurate control on the histo...
(1)Enhances the global contrast by equalizing the histogram.
This plugin transforms pixel...
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This segmentation method performs a N-class thresholding based on a K-Means classification...
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i
Performs tests and write a diagnose file that can be used to understand user problem and t...
(1)Plots an intensity profile of a given ROI.
Can plot mean over T or/and Z too.
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Multi-threaded intensity projection along Z or T with multiple algorithms (mean, max, medi...
(1)This plugin monitors your internet connection.
The result image is updated every 5 second...
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TrackProcessor for the TrackManager plugin that allows importing/exporting tracks. Input a...
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Dedicated to score tracking dataset from the ISBI tracking challenge
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j
A tool to parse the javadoc of a file.
Mostly used now by the Script Editor.
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This plugin enables Python scripts that are run inside Icy to communicate with other Pytho...
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Supplementary material for the Jython scripting engine (Lib, jline, jni).
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k
This tool provides the means to outline moving cells over time, and to generate the kymogr...
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l
2D canvas allowing to view the log-data of an image. Useful to observe high dynamic range ...
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m
Extension of the default 2D viewer with an extra magnifier widget to zoom in on a specific...
(2)This plugin is designed to manipulate binary masks over images. It contains all the basic ...
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Execute some simple math operations on sequences, such as addition, product, absolute valu...
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Execute complex math operations on sequences, such as '3*sequence1 + log(sequence2)/sequen...
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Low-level functions for interactive communication between Icy and Matlab.
To use this p...
(1)Low-level library for reading and writing Matlab .mat files. This library also provides to...
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Use Icy as an image viewer from Matlab.
This plugin provides an improved imshow functio...
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The median filter remove the salt and pepper noise.
The plugins works on 2D, 3D and 4...
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Cell membranes appear as structures of co-dimension 2, and suffer from discontinuities in ...
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Computes RCC8D relationship in MereoTopology. Inputs should be labelled images in unsigned...
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Mice Profiler Video Label Maker processes tracking data to label a sequence thanks to a re...
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Micro-Manager plugin for Icy. Use your microscope and microscopic devices in Icy! Now comp...
(1)* Removed from the lib folder of Icy
* Groups all 3 needed Micro-Manager JAR files.
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(Beta) Allows one to use various Micro Managers for Icy features inside Blocks plugin.
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This plugin can display a 2D flow as a color-coded sequence, following the Middlebury colo...
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Morphomath operators: erosion, dilation, opening, closing, top-hat, gradient, distance map...
(3)Unleash the power of your fingers and drag, rotate & zoom in your image using two-finger g...
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Multi-touch provider allowing developers to let their plug-in receive rich multi-touch int...
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n
A patched version of the Jama library.
Internal structures accessors and package name a...
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Add some noise with customizable characteristics (Gaussian noise, salt & pepper, etc.) to ...
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Non-linear filter implements the classical Perona-Malik PDE filter and the regularized ver...
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This plugin calculates the Nyquist sampling, in the radial and axial direction for your Mi...
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o
Optical Flow plugin
This plugin computes a displacement map from a sequence of at least...
(1)p
Creates an overlay on which you can draw. This can also be used to generate specific data ...
(1)Provides easy-to-use yet powerful tools to automatically create realistic synthetic image ...
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Simple particles animation.
Up to 100 000 particles following the mouse cursor movement.
...
(2)Shock Filter for image enhancement
works on 2D, 3D or 4D sequence.
implements the clas...
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Multiple particle tracking methods for 2D and 3D microscopy images. Particles exhibiting b...
(2)This tutorial focus on tools ICY provides to easialy process image data without having to ...
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This tutorial details how to create a mask with several ROIs, and then process those areas...
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Projects data over Z-Stack or over Time, using max, min, mean, sum saturated, and sum unsa...
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Visual programming environment, letting you develop image processing protocols graphically...
(4)This tool cuts existing ROIs by an angle using the graphical protractor tool.
This plugin...
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r
This plugin provides tools for finite elements modeling on rectangular 2D grids.
It pro...
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This library is used for JavaScript in the Scripting Editor. It is integrated in Java 6 & ...
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Creates ROI rings from existing ROI
Each ROI are substracted by the first ROI of smaller ...
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Compute and display the intensity evolution for regions of interests (ROIs) through time. ...
(1)This tutorial explain how to create an intensity profile over an ROI.
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This tool compute measures on the ROIs of the chosen sequence, updates the measures live w...
(1)Displays a live tool tip on the current focused ROI in an image.
The tooltip displays t...
(1)s
Displays a scale bar overlay on the sequence. Be advised, this plugin needs correct Metada...
(1)Create powerful scripts to implement what's missing with plugins. Syntax Color and Autocom...
(4)This plugin allows one to use various basic sequence operations within Blocks.
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This plugin is intended for plugin developers. It provides some tools to dynamically gener...
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This plugin provides a convenient interface to measure and compare the differences between...
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add, difference, etc between 2 sequences
absolute value, inversion, etc. for 1 sequence
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A slightly different painter than Simple painter 1, focusing on viewer parameters instead ...
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A set of classes and functions which can be used by plugins performing spot detection and...
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Spot detector detects and counts spots.
- Detects spots in noisy images 2D/3D.
- Depen...
(6)The SSIM is an index measuring the structural similarity between two images. It is valued ...
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Rotate the 3D stack from Front view to Right view or from Front view to Top view.
...
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The plugin rotates each 2D image of the stack with a preset angle.
The angle can be set f...
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To analyze statistically the spatial colocalization of objects (fluorescent spots...) afte...
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This is an icy plug-in that implements a stereo vision system. Renders 3D stacks simulatin...
(2)This tutorial focus on how to send any type of data in the swimming pool.
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This tutorial focus on how to watch the swimming pool and get callback when an object is d...
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This plugin provides a color highlighting on text. Based on RSyntaxTextArea library of Fif...
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t
It is a toy plugin to test semi-supervised texture segmentation using the new SLBPriu text...
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For each ROI, computes the number of pixel over a threshold. This plugin also provides the...
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The track manager enables the use of DSP-like trackProcessors. This can affect the display...
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display the flows generated by a set of tracks in the Track Manager plugin
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A TrackProcessor that allows the user to monitor, visualize, and export, the intensity pro...
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Track processor measuring various speed statistics, including total displacement (absolute...
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Clip depth processor forTrack Manager plugin
Show only the Detections in the range of c...
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TrackProcessor for the TrackManager plugin that allows computing several measures of trac...
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u
Reconstruct an image up to a desired scale, and do not add resulting residual.
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v
Record what you are doing on a sequence as a .avi file, fully compatible with Icy.
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This plugin shows how to display different type of 3D painter in the VTK canvas 3D.
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w
Wavelet Spot Detector for Blocks, to integrate in protocols.
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This plugin generates the point-spread function (PSF) for a Widefield Fluorescence Microsc...
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Toolbox to create and manipulate result tables with plug-ins and protocols, and export the...
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Edit the workspaces with a simple drag'n drop system (Requires Icy 1.2 at least).
(4)x
Tutorial on how to access single images in a video file. (Requires Icy 1.2.3)
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Protocol List
Current number of protocols: 10
bComplete detection protocol with 3 outputs: excel, binary, and detection screenshot
c
Display detections performed in 2 channels and colocalized detection.
This protocol duplicates the input sequence as well as the ROI that are selected by the user
This protocol crops the input sequence to the bounding box of each ROI (thus producing a list of cropped seque...
e
Extract channels from a sequence to display or process them individually
g
This protocol performs a smooth on the image.
m
Perform a median filter on the active sequence using the ImageJ rank filter plugin, and convert the result bac...
o
This protocol computes the optical flow of a 2D+T sequence.
The results are displayed with flow arrows pain...
s
This is the first protocol with spot detection for test purposes.
t
Tracks a cell in a 2D video using active contours, and produces a list of ROI where intensity is measured and ...