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 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
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Alexandre Dufour
Creates a linear montage that shows each channel separately plus a final merged channel (useful to create figures for communication)
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Biomedical Imaging Group
Tag: detector
The 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...
not rated yet
Yoann Le Montagner
Tag: denoising
Add some noise with customizable characteristics (Gaussian noise, salt & pepper, etc.) to a sequence. This plugin is useful to test and validate the denoising and restoration algor...
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Biomedical Imaging Group
Tag: segmentation
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...
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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.
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Fabrice de Chaumont
Tag: spot count
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...
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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...
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Alexandre Dufour
Tag: comptage
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 ...
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Ricard Delgado-Gonzalo
Tag: visualization
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.
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Biomedical Imaging Group
Tag: detector
The 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...
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Nicolas Hervé
Tag: flickr
Grab random images from Flickr :
- in recent uploads
- in interestingness stream
- from tags search
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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...
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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...
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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...
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Thomas Provoost
Tag: microscopy
Micro-Manager plugin for Icy. Use your microscope and microscopic devices in Icy! Now compatible with MM 1.4.14.
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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...
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Alexandre Dufour
Tag: segmentation
Binarizes the input sequence based on manual or automatically computed thresholds
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Stephane Dallongeville
Simple particles animation.
Up to 100 000 particles following the mouse cursor movement.
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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.
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Alexandre Dufour
View a single channel of a 2D image as a 3D elevation map (X,Y,Intensity).
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Alexandre Dufour
Creates a linear montage that shows each channel separately plus a final merged channel (useful to create figures for communication)
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Alexandre Dufour
Tag: 3-D
Takes the active 3D VTK viewer and records a 360-degree rotation of the data into a video sequence.
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Thomas Boudier
Tag: 3-D
Fast MultiThreaded 3D Filtering, use ellipsoidal neighbourhood, works for 5D images.
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Alexandre Dufour
Tag: ezplug
Fast multiple coupled active contours using edge and region information for segmentation and tracking
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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...
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Alexandre Dufour
Tag: ezplug
Provides a selection of spatial, separable and customizable filters in 1D and 2D, with OpenCL implementation if supported.
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Thomas Provoost
Tag: annotation
Simple tool for annotations / notes on your sequences. (This plugin requires Icy v. 1.2.0.0)
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Timothée Lecomte
Tag: flow
Optical Flow plugin
This plugin computes a displacement map from a sequence of at least two consecutive images. It implements a 2D variational optical flow method.
The proble...
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Thomas Provoost
Tag: annotation
Creates an overlay on which you can draw. This can also be used to generate specific data (for tests).
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Thibault Lagache
Tag: spread
This plugin permit to measure the signal spread of a molecule with respect to the cell area.
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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.
- perimeter and surface.
...
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not rated yet
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...
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Yoann Le Montagner
Tag: Matlab
Import and export Icy sequences into Matlab .mat files within protocols.
not rated yet
Yoann Le Montagner
Tag: low-level features
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...
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Yoann Le Montagner
Tag: low-level features
This plugin provides some useful functions to work with complex-valued sequences.
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Fabrice de Chaumont
Tag: tracking
Mice Profiler Video Label Maker processes tracking data to label a sequence thanks to a repertoire.
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Yoann Le Montagner
Tag: low-level features
Execute complex math operations on sequences, such as '3*sequence1 + log(sequence2)/sequence3', in a single step. All the operations are executed pointwise.
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Fabrice de Chaumont
Creates ROI rings from existing ROI
Each ROI are substracted by the first ROI of smaller surface.
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Timothée Lecomte
Supplementary material for the Jython scripting engine (Lib, jline, jni).
not rated yet
Timothée Lecomte
Tag: jython
This plugin 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.
not rated yet
Yoann Le Montagner
Tag: denoising
Add some noise with customizable characteristics (Gaussian noise, salt & pepper, etc.) to a sequence. This plugin is useful to test and validate the denoising and restoration algor...
not rated yet
Thomas Boudier
Computes RCC8D relationship in MereoTopology. Inputs should be labelled images in unsigned byte of short format.
not rated yet
Alexandre Dufour
Tag: results management
Toolbox to create and manipulate result tables with plug-ins and protocols, and export them into workbooks (compatible with OpenOffice and MS Office)
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Fabrice de Chaumont
This tool cuts existing ROIs by an angle using the graphical protractor tool.
This plugin also enable pie cut or ROI.
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Biomedical Imaging Group
Tag: segmentation
This tool provides the means to outline moving cells over time, and to generate the kymograph built as the temporal evolution of the profile intensity.
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Yoann Le Montagner
Tag: low-level features
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 ...
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Alexandre Dufour
Tag: segmentation
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...
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Timothée Lecomte
Tag: histogram
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...
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Nicolas Hervé
Tag: segmentation
It is a toy plugin to test semi-supervised texture segmentation using the new SLBPriu texture descriptor.
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Alexandre Dufour
Tag: tutorial
Test plugin which performs computations on the GPU using the JavaCL library.
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Nicolas Hervé
Tag: mask
This plugin is designed to manipulate binary masks over images. It contains all the basic tools to manage such objects.
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Nicolas Hervé
Tag: segmentation
Image segmentation by representative colors selection. Two versions are available :
- thresholding
- positive and negative colors selection and SVM learning
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Alexandre Dufour
Tag: ezplug
Tutorial showing EzPlug\'s features in action. Check out the documentation to have a direct view of the code
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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...
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Alexandre Dufour
Tag: visualization
Unleash the power of your fingers and drag, rotate & zoom in your image using two-finger gestures (in 2D and 3D)
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Yoann Le Montagner
Tag: protocol
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...
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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.