Alexandre Dufour

Yes, it is finally here. A user-friendly interface to Docker, letting you run containers within your plug-ins in no time.

Interface for the protocol used to analyse the datasets from the 2015 Cel Tracking Challenge

Well plate support for Icy, with an interactive well plate viewer and batch processing capabilities within Protocols

Protocol block that measures pairwise distances between 2 sets of ROI up to a given distance

Similary to classical OrthoViewer from Alexandre Dufour from which this Canvas is an extension, you can browse your data [..]

Library that detects the connection of USB drives (works on Mac, Linux and Windows)

Measures velocities, pressure and forces inside the cell using 2D or 3D video microscopy data

Calculates the number of objects (e.g. spots, bacteria etc.) inside larger objects (e.g. nuclei, cells etc.), as well as [..]

The Apache POI library. POI is a library dedicated to reading/writing Microsoft Office and compatible documents (Word, E [..]

Import data from the Opera high-content screening system straight into Icy

JMathPlot: interactive 2D and 3D plots. Library written by Yann Richet

JMathIO: easy to use read/write classes for double arrays. Written by Yann Richet.

Splits regions of interest into smaller sub-regions based on size. This is useful to separate clustered objects.

JMatIO is a library to open Matlab files. More info at https://github.com/gradusnikov/jmatio

Track Manager module that calculates the time and duration of interactions between tracked objects based on a given distance threshold.

This plug-in activates keyboard shortcuts on the current viewer, allowing to move and copy regions of interest (ROI) in [..]

Reconstructs an isosurface from volumetric image data, and converts the surface into a 3D region of interest.

A simple tool to correct chromatic shifts as well as temporal drift (including translations and rotations), based on spectral correlation.

OpenCV (Open Computer Vision) library for Icy. see more at http://opencv.org

SDK for 3D ROI creation and manipulation using polygonal (surface) and polyhedral (volume) meshes.

Track Manager plugin that displays available tracks on the selected sequence, in both 2D and 3D viewers, with various vi [..]

Plug-in for the Track Manager that loads (and saves) tracks from (to) the sequence metadata. Your tracking data will never be lost again!

Computes fast quasi-exact euclidean distance transforms in 2D/3D from a set of regions of interest.

Two-phase spherical parameterization algorithm for closed zero genus meshes.

Like to do things old-school? Track your objects manually, the Icy way!

Creates convex versions of regions of interests in 2D or 3D using the QuickHull library.

QuickHull library for Icy. Computes convex envelopes of random point sets in 2D or 3D.

Extracts labeled objects from a binary or labeled image into ROI using connected component analysis

This plugin is a test case for the automatic bug reporting feature in Icy. It generates an error in a bundle of plugins. [..]

Track Processor plugin that computes the relative distance between detections and their evolution over time, with possib [..]

Extrudes ROI along time, depth and/or channels to simplify manual segmentation and tracking

This plugin allows to create an Icy plugin from a Python script, and produce a jar that can distributed to other Icy use [..]

Extracts Python files stored in plugins so that they can be used in Icy.

Rescale one or more ROI in a sequence about their center of mass

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

Automatically assign a colour to each ROI of the sequence based on their perimeter

Import ROI from a zip file produced with ImageJ's ROI manager. Works as a standalone plugin and as a block for Protocols

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

View your multi-channel data as a montage with one image per channel plus a merged, color channel (useful to create figures for communication)

Displays a customizable time stamp over a 2D sequence. This book chapter proposes a video tutorial on the TimeStamp Ove [..]

Enables Python scripts that are run inside Icy to communicate with other Python instances outside Icy. This allows the a [..]

Supplementary material for the Jython engine (Lib, jline, jni, etc.).

Python engine for Icy, based on Jython

Toolbox to create and manipulate result tables with plug-ins and protocols, and export as text file or to your favorite spreadsheet software

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

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

Draws a contour plot on top of a sequence.

This plugin can display a 2D flow as a color-coded sequence, following the Middlebury color code. See http://vision.m [..]

Extract local extrema (maxima, minima or both) from a sequence.

Execute complex math operations on sequences, such as ‘3*sequence1 + log(sequence2)/sequence3’, in a single [..]

View a single channel of a 2D image as a 3D elevation map (X,Y,Intensity).

View 3D data in three orientations simultaneously (XY, YZ, XZ)

Track manager plug-in measuring motion statistics in 2D/3D, including min/max/avg/total displacement (absolute & rel [..]

Additional operations for cell segmentation protocol

Cell membranes appear as structures of co-dimension 2, and suffer from discontinuities in intensity and orientation. Ani [..]

Takes the active 3D VTK viewer and records a 360-degree rotation of the data into a video sequence.

3D Active Mesh plug-in for cell segmentation and tracking in 3D images and sequences.

Execute some simple math operations on sequences, such as addition, product, absolute value extraction, rounding to the [..]

Software Development Kit for the ‘Protocols’ programming environment. This plugin has been merged into ̵ [..]

Displays a scale bar overlay on the sequence. Warning: this plugin needs correct sequence metadata to be effective. Othe [..]

This plugin computes a displacement map from a sequence of at least two consecutive images.

This plugin provides a painter to visualize 2D flows. 2D Flows are couples of two sequences, one for the horizontal d [..]

This plugin provides tools for finite elements modeling on rectangular 2D grids. It provides formulations for bilinea [..]

Choose the best auto thresholding technique for your data. Ported from Auto Threshold plugin in ImageJ by G. Landini (pl [..]

Select a portion of a sequence in all 5 dimensions (XYZCT)

The adaptive histogram equalization implements the Contrast-Limited Adaptive Histogram Equalization (CLAHE) for 2D, 3D o [..]

Clip depth processor forTrack Manager plugin Show only the Detections in the range of current Z slice +-Value. Value [..]

2D viewer allowing to view image data in logarithmic scale. Useful to observe high dynamic range images, e.g. Fourier spectra or 16-bits images.

Displays 3D data as 2D montages of all slices.

Unleash the power of your fingers and drag, rotate & zoom in your image using two-finger gestures (in 2D and 3D)

Multi-touch provider allowing developers to let their plug-in receive rich multi-touch interaction. Currently supports M [..]

computes ROI measurements. Measures include geometric (bounding box) and intensity information updates measurements liv [..]

Intensity projection along each of the 5 sequence axes (X, Y, C, Z, T), with multiple algorithms: mean, max, median, var [..]

Enhances the global contrast by equalizing the histogram. This plugin transforms pixel intensities so that they are [..]

This segmentation method performs a N-class thresholding based on a K-Means classification of the image histogram, then [..]

add, difference, etc between 2 sequences absolute value, inversion, etc. for 1 sequence

The plugin rotates each 2D image of the stack with a preset angle. The angle can be set for each 2D plane: XY, XZ,YZ. [..]

Rotate the 3D stack from Front view to Right view or from Front view to Top view.

Extract image features based on one or more intensity thresholds, and output the result as a labeled image or as a region of interest.

Test plugin which performs computations on the GPU using the JavaCL library.

The median filter remove the salt and pepper noise. The plugins works on 2D, 3D and 4D gray and color sequence. It imple [..]

Anisotropic filter implements the classical Coherence Enhancing Diffusion Filter [Weickert]. The plugins works on the [..]

Non-linear filter implements the classical Perona-Malik PDE filter and the regularized version [Catte et al.]. The pl [..]

Shock Filter for image enhancement works on 2D, 3D or 4D sequence. implements the classical, regularized and Gilboa et al. versions.

Some functions for PDE filtering

Tutorial showing EzPlug's features in action. Check out the documentation to have a direct view of the code

Provides a selection of spatial, separable and customizable filters in 1D and 2D, with OpenCL implementation if supported.

Image segmentation by representative colors selection. Two versions are available : – thresholding – positiv [..]

Automatically segment the boundary of a nucleus or cell starting from an approximate ROI. It supports 2D and 3D processi [..]

This plugin extracts groups of connected pixels in 2D and 3D based on their intensity and that of the background. Works [..]

The swiss army knife of plugin developers. Automatically generates elegant graphical interfaces with rich and intuitive [..]