Icy: an open community platform for bioimage informatics
Icy provides the software resources to visualize, annotate and quantify bioimaging data.
The Icy 2nd Coding Party (May 2015) - With Daniel Sage (EPFL Lausanne) , Perrine Paul-Gilloteaux (Curie/Strand), Fabrice Cordelières (BIC Bordeaux), Hugo Rositi (Créatis Lyon), Zsuzsanna Püspöki (EPFL Lausanne), Ihor Smal (ERASMUS MC), Jerome Mutterer (IBMP Strasbourg), Johnathan Léger (Observatory of Lyon), Daniel Schmitter (EPFL Lausanne), Thierry Pécot (SERPICO, INRIA Rennes), Jean-Yves Tinevez (Institut Pasteur), Piotr Kupczyk (ETH Zurich/OpenBIS), Juan Fuentes (ETH Zurich/OpenBIS), Raphaël Marée (Institut Pasteur/Université de Liège/Cytomine), Thibault Lagache (Institut Pasteur), Virgine Uhlmann (EPFL Lausanne), Anaïs Badoual (EPFL Lausanne)and people from the Icy Team: Stephane Dallongeville, Alexandre Dufour, Fabrice de Chaumont.
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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...
Select a portion of a sequence in all 5 dimensions (XYZCT)
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...
Displays and processes live webcam image using protocols. The processing protocol should start and end with an 'Image Passing Block'. This plugin was created during the 2nd I...
Fabrice de Chaumont
Interactive counter. Click on the sequence to add detection, see number of detection in ROIs directly over the sequence.
Fabrice de Chaumont
Display the track number on the viewer.
Simple particles animation. Up to 100 000 particles following the mouse cursor movement.
Computes fast quasi-exact euclidean distance transforms in 2D/3D from a set of regions of interest.
Draw the Envelope Line based on the Hilbert transform.Also works in protocols. The icon pic from http://wikipedia.org/wiki/Group_velocity
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...
This plugin allows fitting ellipses manually on an image. It can be used for generating gold standard segmentation results or to manually segment populations of cells/nuclei/ellips...
This plugin allows visualizing the output of the structure tensor in 3D. A field of ellipsoids are displayed on a regular grid. This function can be used to analyze the geometrical...
OpenCV (Open Computer Vision) library for Icy. see more at http://opencv.org
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/.
Biomedical Imaging Group
This plug-in implements a user-friendly way to design shape-priors for the Active Cells plug-in.
Supplementary material for the Jython engine (Lib, jline, jni, etc.).
Computes RCC8D relationship in MereoTopology. Inputs should be labelled images in unsigned byte of short format.
This plugin allows you to create a private repository to distribute your plugins and workspaces from your own server.
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.