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Icy: an open community platform for bioimage informatics

Icy provides the software resources to visualize, annotate and quantify bioimaging data.

  • Rate and comment plugins
  • Graphical programming with protocols
  • Write scripts in javascript or python
  • Reactive forum and support
  • Native ImageJ integration
  • Native Micro-Manager integration
  • Share your plugins and protocols online
  • Search and install features directly from Icy
  • Intuitive user interface
  • Get the keyboard layout
  • Connect Icy to Matlab
  • Interactive widgets
  • Build your graphical interface with EzPlug
  • Use the power of your graphic card with OpenCL
  • Watch sequences in polarized stereo
  • Watch 3D data in ray-casting with VTK
  • Access images in MPEG video with Xuggler
  • Watch Matlab image in Icy with Matlab X-server
  • Customize your workspace
  • From left to right: Thierry Pécot (IRISA), Christian Rouvière (BioDev), Perrine Paul-Gilotteaux (Curie), Jérome Mutterer (IBMP), Stéphane Dallongeville (Pasteur), Daniel Sage (EPFL), Virgine Ulhmann (EPFL), Nicolas Chenouard (NYU), Fabrice de Chaumont (Pasteur) - more info
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    25 Nov 14H - Location: King's College London - New Hunts House G.10
    Level 1: Introduction to Icy
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    26 Nov 09H - Location: King's College London - New Hunts House G.10
    Level 2: Protocols & Scripts
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    New plugins: How to install a plugin
    not rated yet
    Alexandre Dufour
    Tag: 3-D
    SDK for 3D ROI creation and manipulation using polygonal (surface) and polyhedral (volume) meshes.
    (1)
    Thomas Boudier
    Tag: 3-D
    This plugin implements the seeded watershed algorithm. It can be used for spots segmentation where spots centres are very bright, or in conjunction with distance map to separate to...
    (1)
    Stephane Dallongeville
    Tag: video
    This plugin allows Icy to open many different video file format using the Xuggler library.
    Most popular plugins:
    (6)
    Alexandre Dufour
    Visual programming environment, letting you develop image processing protocols graphically. No programming skills required !!
    (5)
    Alexandre Dufour
    Tag: ezplug
    Intensity projection along depth or time with multiple algorithms: mean, max, median, variance, standard deviation, saturated sum. Projection can be restricted to ROI.
    (8)
    Fabrice de Chaumont
    Spot detector detects and counts spots. - Detects spots in noisy images 2D/3D. - Depending on objective, spots can be nuclei, nucleus or cell - Versatile input: sequence or ba...
    (4)
    Biomedical Imaging Group
    This plug-in implements fast active contours for image segmentation. Their representation in terms of spline curves allows for a natural and intiutive manipulation of the active co...
    (5)
    Nicolas Chenouard
    This plugin ships automated methods for extracting trajectories of multiples objects in a sequence of 2D or 3D images. Up to version 2 it was known as the 'Probabilistic particle t...
    (5)
    Nicolas Hervé
    Tag: gui
    Browse files in directories with thumbnails view
    (4)
    Thomas Provoost
    Tag: script
    Create powerful scripts to implement what's missing with plugins. Syntax Color and Autocomplete features implemented (still need testing). Should be used with Icy-Master on gith...
    (4)
    Alexandre Dufour
    View your multi-channel data as a montage with one image per channel plus a merged, color channel (useful to create figures for communication)
    (3)
    Alexandre Dufour
    Tag: library
    The swiss army knife of plugin developers. Automatically generates elegant graphical interfaces with rich and intuitive user interaction based on your algorithm's parameters.
    (4)
    Nicolas Chenouard
    Compute and display the intensity evolution for regions of interests (ROIs) through time. Results can be refreshed automatically as ROIs are changed. Multiple channels are handl...
    (3)
    Alexandre Dufour
    Track manager plug-in measuring motion statistics in 2D/3D, including min/max/avg/total displacement (absolute & relative to origin), and displacement profiles along all spatial ax...
    (3)
    Alexandre Dufour
    Tag: gui
    Ads a magnifier on top of the default 2D viewer to zoom in and inspect individual pixel values
    (4)
    Thomas Provoost
    Displays a scale bar overlay on the sequence. Be advised, this plugin needs correct Metadata on the sequence to be effective or it will display wrong values.
    (2)
    Alexandre Dufour
    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 ...
    (2)
    Alexandre Dufour
    Extract image features based on one or more intensity thresholds, and output the result as a labeled image or as a region of interest.
    (2)
    Daniel Sage
    This plugins reloads all the plugins without restarting Icy. It is specially useful when changes are happening in the code of the plugins, typically during the development phase. T...
    (2)
    Nicolas Chenouard
    This plugin allows the extraction of the kymograph representation of pixel intensity evolution through time and along a defined spatial path. Different utilities are embedded to de...
    (2)
    Thomas Provoost
    Tag: camera
    Layer for the 3D Viewer, allowing the user to move the camera in a more intuitive way.
    (2)
    Alexandre Dufour
    Tag: library
    Software Development Kit for the 'Protocols' programming environment
    (2)
    Yoann Le Montagner
    Tag: Matlab
    Low-level functions for interactive communication between Icy and Matlab. To use this plugin, you have to configure your Matlab application in a specific way: please have a look...
    (2)
    Biomedical Imaging Group
    Tag: 3-D
    This plug-in implements fast active surfaces for 3D image segmentation. Their representation in terms of spline surfaces allows for a natural and intiutive manipulation of the surf...
    (2)
    Biomedical Imaging Group
    Icy Feature Detector plug-in implements a series of optimized contour and ridge detectors. The filters are steerable and are based on the optimization of a Canny-like criterion. Th...
    (2)
    Ricard Delgado-Gonzalo
    This is an icy plug-in that implements a stereo vision system. Renders 3D stacks simulating a dual view camera. Each 3D view is rendered in fullscreen in a different monitor.
    (3)
    Alexandre Dufour
    Tag: 3-D
    View a single channel of a 2D image as a 3D elevation map (X,Y,Intensity).
    (4)
    Fabrice de Chaumont
    Mice Profiler tracks multiple mice from a top view video.
    (3)
    Alexandre Dufour
    Tag: roi
    This tool compute measures on the ROIs of the chosen sequence, updates the measures live when ROIs are changed and allows to copy/paste the measures to 3rd-party sheet edition soft...
    (4)
    Alexandre Dufour
    Tag: 3-D
    Takes the active 3D VTK viewer and records a 360-degree rotation of the data into a video sequence.
    (2)
    Nicolas Hervé
    Tag: flickr
    Grab random images from Flickr :
    • in recent uploads
    • in interestingness stream
    • from tags search
    (2)
    Christian rouviere
    Tag: canvas
    Manually explore 4D sequences to find the best z of interest, and construct the result sequence. Note that right arrow will automatically select the current z without pressing the...
    (2)
    Alexandre Dufour
    Tag: ezplug
    Multiple cell tracking in 2D/3D video-microscopy. Just draw ROI around cells in the first image, and the cells are automatically tracked over time.
    (2)
    Alexandre Dufour
    Like to do things old-school? Track your objects manually, the Icy way!
    (2)
    Wei Ouyang
    Tag: chart
    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-Manage...
    (2)
    Yoann Le Montagner
    Compute and display the histogram of a sequence, with a more accurate control on the histogram parameters (such as the number of bins) than the built-in Icy widget. In particular, ...
    (3)
    Thomas Provoost
    Tag: daemon
    The right click on sequences and ROIs will open a menu with various features, such as image and ROI copy, data conversion and extraction. See documentation for more information.
    (1)
    Alexandre Dufour
    Track Manager plugin that displays available tracks on the selected sequence, in both 2D and 3D viewers, with various visualisation options. Tracks never looked so good!
    (1)
    Biomedical Imaging Group
    Tag: toolbox
    This is an icy package that encapsulates tools to design and implement parametric active contours. The package provides fast 2D and 3D filters for image preprocessing, and a framew...
    (1)
    Timothée Lecomte
    Tag: script
    Python engine for Icy, based on Jython
    (1)
    Alexandre Dufour
    Select a portion of a sequence in all 5 dimensions (XYZCT)
    (1)
    Thomas Provoost
    Micro-Manager plugin for Icy. Use your microscope and microscopic devices in Icy ! Compatible with MM 1.4.16 or above.
    (1)
    Alexandre Dufour
    This segmentation method performs a N-class thresholding based on a K-Means classification of the image histogram, then extracts objects in a bottom-up manner using user-defined mi...
    (1)
    Stephane Dallongeville
    Tag: video
    This plugin allows Icy to open many different video file format using the Xuggler library.
    (1)
    Timothée Lecomte
    Tag: jython
    Enables Python scripts that are run inside Icy to communicate with other Python instances outside Icy. This allows the access to CPython-only libraries such as Numpy.
    (1)
    Wei Ouyang
    A machine learning plugin uses RapidMiner, a powerful data mining software, to learn image data.Both supervised and unsupervised learning are supported. Note:RapidMiner libraries s...
    (1)
    Jerome Mutterer
    Helps with measuring hue values from arabidopsis plantlets on dishes. This provides a neutral tool for chlorosis scoring. Co authors : Gaëtan Pochon, Dominique Gagliardi, IBMP-CN...
    (1)
    Nicolas Chenouard
    Isotropic wavelets transform for 2D images. The plugin provides a multiscale representation of 2D images without directional bias. The transform defines a 'tight frame' so that ...
    (1)
    Thibault Lagache
    This plugin uses the Ripley's K function to analyze robustly the spatial organization of molecules.
    (1)
    Yoann Le Montagner
    Add some noise with customizable characteristics (Gaussian noise, Poisson noise, salt & pepper, etc.) to a sequence. This plugin is useful to test and validate the denoising and re...
    (2)
    Thibault Lagache
    This plugin permit to measure the signal spread of a molecule with respect to the cell area.
    (2)
    Fabrice de Chaumont
    Display the track number on the viewer.
    (2)
    Alexandre Dufour
    View 3D data in three orientations simultaneously (XY, YZ, XZ)
    (2)
    Alexandre Dufour
    Tag: roi
    Rescale one or more ROI in a sequence about their center of mass
    (2)
    Thomas Provoost
    Tag: camera
    Generate nice dataset animations with interpolated camera points.
    (2)
    Thibault Lagache
    To analyze statistically the spatial colocalization of objects (fluorescent spots...) after detection in a given(s) region(s) of interest (ROI(s)).
    (1)
    Yoann Le Montagner
    Tag: toolbox
    Import Matlab *.mat files as sequences in Icy.
    (1)
    Thomas Provoost
    Simple tool for annotations / notes on your sequences. (This plugin requires Icy v. 1.2.0.0)
    (1)
    Thomas Provoost
    Move your XY Stage and Focus Device with your mouse.
    (1)
    Alexandre Dufour
    Tag: ezplug
    Provides a selection of spatial, separable and customizable filters in 1D and 2D, with OpenCL implementation if supported.
    (1)
    Nicolas Hervé
    Tag: mask
    This plugin is designed to manipulate binary masks over images. It contains all the basic tools to manage such objects.
    (1)
    Nicolas Hervé
    Quantize a color image in any given number of colors.
    (1)
    Thomas Provoost
    Creates an overlay on which you can draw. This can also be used to generate specific data (for tests).
    (1)
    Thomas Boudier
    Tag: 3-D
    This plugin implements the seeded watershed algorithm. It can be used for spots segmentation where spots centres are very bright, or in conjunction with distance map to separate to...
    (1)
    Yoann Le Montagner
    Tag: Matlab
    Use Icy as an image viewer from Matlab. This plugin provides an improved imshow function, called icy_imshow, to replace the default Matlab viewer by Icy. It also provides some t...
    (1)
    Timothée Lecomte
    Tag: flow
    This plugin computes a displacement map from a sequence of at least two consecutive images.
    (1)
    Thomas Boudier
    Tag: 3-D
    Fast MultiThreaded 3D Filtering, use ellipsoidal neighbourhood, works for 5D images.
    (1)
    Thomas Provoost
    Tag: video
    This plugin should import any kind of video.
    (1)
    Thibault Lagache
    This plugin computes the Manders coefficients between ROIs in 2 sequences (Intensity and surface coefficients). A p value (probability of signal colocalization) is also computed wi...
    (1)
    Yoann Le Montagner
    Tag: toolbox
    Export sequences from Icy to Matlab *.mat files.
    (1)
    No author name provided
    Edge detection by Deriche's method.
    (2)
    Fabrice de Chaumont
    Plots an intensity profile of a given ROI. Can plot mean over T or/and Z too.
    (2)
    Stephane Dallongeville
    Simple particles animation. Up to 100 000 particles following the mouse cursor movement.
    (1)
    Fabrice de Chaumont
    Interactive counter. Click on the sequence to add detection, see number of detection in ROIs directly over the sequence.
    (1)
    Praveen Pankajakshan
    Tag: FFT
    Fast Fourier Transform (FFT) for 2D/3D images
    (1)
    Wei Ouyang
    Tag: chart
    An useful and cool painter plugin which displays the intensity profile of a roi within a resizable rectangle ROI.
    (1)
    Stephane Dallongeville
    Tag: roi
    Displays a live tool tip on the current focused ROI in an image. The tooltip displays the following informations about the ROI: - position and size. - number of interior point...
    (1)
    Thomas Provoost
    Tag: tools
    Simple chronometer for Icy.
    not rated yet
    Alexandre Dufour
    Tag: roi
    Creates convex versions of regions of interests in 2D or 3D using the QuickHull library.
    not rated yet
    Alexandre Dufour
    Tag: roi
    Extracts labeled objects from a binary or labeled image into ROI using connected component analysis
    not rated yet
    Thomas Boudier
    Tag: 3-D
    3D geometrical and shape measurements of 3D Area Rois (3D objects).
    not rated yet
    Yrvann EMZIVAT
    Tag: vtk
    Two-phase spherical parameterization algorithm for closed zero genus meshes.
    not rated yet
    Nicolas Chenouard
    Tag: toolbox
    A open-source utility library for linear programming in Java with the simplex algorithm. Problems are of the type: min/max c*x st. Ax <= b x >= 0 The primal problem is solve...
    not rated yet
    Stephane Dallongeville
    This plugin allows you to create a private repository to distribute your plugins and workspaces from your own server.
    not rated yet
    Thibault Lagache
    This plugin measures the percentage of elongated spots in a sequence.
    not rated yet
    Alexandre Dufour
    Tag: roi
    Fills the holes in all the ROI of the active sequence (also works in Protocols).
    not rated yet
    Stephane Dallongeville
    Tag: roi
    Block (Protocols) to convert ROI(s) into a binary image / sequence.
    not rated yet
    Alexandre Dufour
    Tag: ImageJ
    Import ROI from a zip file produced with ImageJ's ROI manager. Works as a standalone plugin and as a block for Protocols
    not rated yet
    Alexandre Dufour
    Tag: ezplug
    Saves a RGB image (typically a screenshot) into a CMYK TIFF (required by publishers for high-fidelity color printing)
    not rated yet
    Biomedical Imaging Group
    This plug-in implements a user-friendly way to design shape-priors for the Active Cells plug-in.
    not rated yet
    Wei Ouyang
    A simple DICOM/DICONDE receiver used to recieve, store and open dcm images. This plugin is a part of EVA project, http://oeway.github.io/EVA/.
    not rated yet
    Thibault Lagache
    This plugin contains most of existing colocalization methods in fluorescence microscopy: Pearson and Manders coefficients, Intensity Correlation Quotient (ICQ), Image Cross Correla...
    not rated yet
    worm
    convert a 2D Image to workbook
    not rated yet
    worm
    *get the information of 1D singal in frequence domain ,also works in protocols
    not rated yet
    worm
    Save the data sequence as a series of CSV files,also works in protocols
    not rated yet
    Timothée Lecomte
    Supplementary material for the Jython engine (Lib, jline, jni, etc.).
    not rated yet
    Alexandre Dufour
    Tag: 3-D
    SDK for 3D ROI creation and manipulation using polygonal (surface) and polyhedral (volume) meshes.
    not rated yet
    Thibault Lagache
    Create two synthetic sequences with given numbers of spots and colocalization properties (percentage, distance mean and standard deviation)
    not rated yet
    worm
    Draw the Envelope Line based on the Hilbert transform.Also works in protocols. The icon pic from http://wikipedia.org/wiki/Group_velocity
    not rated yet
    worm
    Using DB wavelet to filter the signal noise,also works in portocols
    not rated yet
    Alexandre Dufour
    Computes fast quasi-exact euclidean distance transforms in 2D/3D from a set of regions of interest.
    not rated yet
    Nicolas Chenouard
    This software smooth and denoise images while preserving sharp edges. The method relies on the Total Variation criterion for image regularization and exploits the FISTA based metho...
    not rated yet
    Daniel Sage
    Tag: PSF
    PSF Generator is a software package that allows one to generate and visualize various 3D models of a microscope PSF. The current version has more than fifteen different models incl...
    not rated yet
    Daniel Sage
    Tag: tools
    PermuteAxis5D is a collection of tools to permute the axis of a 5D sequence. The plugin PermuteAxis has a GUI allowing to customize. The other plugins Permute XT, Permute XZ, Permu...
    not rated yet
    Daniel Sage
    Tag: library
    The Apache Commons Mathematics Library. "Commons Math is a library of lightweight, self-contained mathematics and statistics components addressing the most common problems not av...
    not rated yet
    Peter Saxon
    Takes rectangles, ellipses and polygons and generates a series of gradually smaller/larger concentric shapes. Useful for looking at intensities etc. as a function of distance fr...
    not rated yet
    Fabrice de Chaumont
    Mice Profiler Video Label Maker processes tracking data to label a sequence thanks to a repertoire.
    not rated yet
    Thomas Provoost
    Live video plugin for Micro-Manager for Icy.
    not rated yet
    Alexandre Dufour
    Tag: gui
    Multi-touch provider allowing developers to let their plug-in receive rich multi-touch interaction. Currently supports Mac OS X, and generates raw finger events as well as pre-proc...
    not rated yet
    Thomas Provoost
    Snap complex images easily.
    not rated yet
    Thomas Provoost
    Advanced Acquisition plugin for microscope.
    not rated yet
    Alexandre Dufour
    Unleash the power of your fingers and drag, rotate & zoom in your image using two-finger gestures (in 2D and 3D)
    not rated yet
    Fabrice de Chaumont
    A protractor to measure angles on images
    not rated yet
    Fabrice de Chaumont
    Tag: gui
    Widget to measure distances over images considering current image scale.
    not rated yet
    Alexandre Dufour
    Tag: ezplug
    Tutorial showing EzPlug\'s features in action. Check out the documentation to have a direct view of the code
    not rated yet
    Nicolas Hervé
    Image segmentation by representative colors selection. Two versions are available : - thresholding - positive and negative colors selection and SVM learning
    not rated yet
    Alexandre Dufour
    Test plugin which performs computations on the GPU using the JavaCL library.
    not rated yet
    Nicolas Hervé
    It is a toy plugin to test semi-supervised texture segmentation using the new SLBPriu texture descriptor.
    not rated yet
    Timothée Lecomte
    Enhances the global contrast by equalizing the histogram. This plugin transforms pixel intensities so that they are uniformly distributed over the gray-scale range. It operates...
    not rated yet
    Yoann Le Montagner
    This plugin provides a convenient interface to measure and compare the differences between a reference sequence and several tested sequences. The user can chose among several the d...
    not rated yet
    Yoann Le Montagner
    The SSIM is an index measuring the structural similarity between two images. It is valued between -1 and 1. When two images are nearly identical, their SSIM is close to 1. SSIM ...
    not rated yet
    Fabrice de Chaumont
    Tag: roi
    Creates ROI rings from existing ROI Each ROI are substracted by the first ROI of smaller surface.
    not rated yet
    Timothée Lecomte
    Tag: contour
    Draws a contour plot on top of a sequence.
    not rated yet
    Fabrice de Chaumont
    Tag: widget
    This tool cuts existing ROIs by an angle using the graphical protractor tool. This plugin also enable pie cut or ROI.
    not rated yet
    Thibault Lagache
    This plugins allows debleaching of time sequences of fluorescence images.
    not rated yet
    Alexandre Dufour
    Toolbox to create and manipulate result tables with plug-ins and protocols, and export as text file or to your favorite spreadsheet software
    not rated yet
    Yoann Le Montagner
    Execute complex math operations on sequences, such as '3*sequence1 + log(sequence2)/sequence3', in a single step. All the operations are executed pointwise.
    not rated yet
    Yoann Le Montagner
    Execute some simple math operations on sequences, such as addition, product, absolute value extraction, rounding to the closest integer, etc. All the operations are executed pointw...
    not rated yet
    Fabrice de Chaumont
    Mice profiler temporal analysis of data
    not rated yet
    Alexandre Dufour
    Tag: gui
    Displays 3D data as 2D montages of all slices.
    not rated yet
    Yoann Le Montagner
    This plugin provides some useful functions to work with complex-valued sequences.
    not rated yet
    Yoann Le Montagner
    Tag: library
    Low-level library for reading and writing Matlab .mat files. This library also provides tools to convert the 5D Icy sequences into the Matlab data structure, which is basically a n...
    not rated yet
    Yoann Le Montagner
    Tag: Matlab
    Import and export Icy sequences into Matlab .mat files within protocols.
    not rated yet
    Thomas Boudier
    Computes RCC8D relationship in MereoTopology. Inputs should be labelled images in unsigned byte of short format.
    Plugin are displayed on this page if their imageTooltip is defined. Sort is based on ( ranking + alpha * log ( 1 + number of notation ) ) with alpha=2.