Stephane Dallongeville

Nashorn Script Engine for Icy

The Apache HTTP client Library. https://commons.apache.org/proper/commons-lang/ Distributed on the Apache License, Versi [..]

EHCache 3 cache engine for Icy

MsgPack Core library for Icy. https://msgpack.org/ [..]

The Java Native Access (JNA) library for Icy https://github.com/java-native-access/jna [..]

The Oshi core library (JDK6) for Icy https://github.com/oshi/oshi [..]

The Bytedeco JavaCPP library for Icy https://github.com/bytedeco/javacpp [..]

The Google FlatBuffersLibrary for Icy. https://github.com/google/flatbuffers Distributed on the Apache License, Version [..]

Deeplearning4J library for Icy.

The Google Gson Library for Icy. https://github.com/google/gson Distributed on the Apache License, Version 2.0 [..]

The Apache Commons Lang Library. https://commons.apache.org/proper/commons-lang/ Distributed on the Apache License, Vers [..]

The Apache Commons CSV library Commons CSV is a library dedicated to reading/writing files in variations of the Comma Se [..]

JogAmp JOAL library for Icy

JogAmp JOCL library for Icy

Xuggler library for Icy.

JavaCL / JNA library for Icy

Full Parallel Colt library for Icy. It also embed JTransforms, CSparseJ, Optimization, JPlasma, Netlib-java, Arpack-comb [..]

Phys2D library for Icy

JFree Chart library for Icy.

JFree Common library for Icy.

EJML (Efficient Java Matrix Library) for Icy.

Jama Matrix Package library for Icy.

Java 3D library for Icy.
Note that it doesn’t contain Vecmath which is separated in a specific library plugin.

Vecmath library for Icy.
Vecmath is part of the Java 3D library.

Flanagan scientific library for Icy.

Flanagan library has been developed by Michael Thomas Flanagan.

JMF (JavaMedia Framework) Library for Icy. This is a very old library and it shouldn’t be used anymore. It’s [..]

The Apache XMLBeans Library. XMLBeans is a technology for accessing XML by binding it to Java types. https://xmlbeans.ap [..]

The Apache Commons Logging Library. https://commons.apache.org/proper/commons-logging/ Distributed on the Apache License [..]

The Apache Commons Collections Library. The Java Collections Framework was a major addition in JDK 1.2. It added many po [..]

The Apache Commons Codec Library. Apache Commons Codec (TM) software provides implementations of common encoders and dec [..]

Cytomine Client This plugins are compatible with Cytomine version 1 servers , NOT version 2 servers. Available plugins: [..]

Image denoising based on fusing multiple Compressed Sensing (CS) reconstructions, taking advantage of the robustness of [..]

This plugin will compute the intensity profile of ROI contour along Z (3D) and T (timelaps) dimension. It generates a wo [..]

This project contains plugins necessary to read and write large 2D images. The plugins available for this library are: L [..]

Importer to read hdf5 images in ICY using h5-BigDataViewer format.

To run this plugin you should have java-8 installed on your system.

BigDataViewer plugin library.

This plugin allows you to calculate the central moments. It was based in version written by R.Castaneda. See “2D e [..]

Angle descriptor for ROI (Region of Interest). It computes the angle (in degree) for PolyLine type ROI (only 3 points Po [..]

This plugin add blocks (Protocols) for the Spot Tracking plugin. These following blocks can be used : – estimate p [..]

This plugin / block allow to convert a DetectionResult object containing a set of Detection into a set of ROI.

This plugin / block allow to convert a set of ROI into a DetectionResult object containing a set of Detection.

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

Allows to use Micro-Manager for Icy features inside Protocols.

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

Display the colormap over the image using an overlay. Some settings are available as position, scale and labels…

Simple usage example for the Webcam Capture library.

Webcam Capture library for Icy. This library allow easy access to webcam from Icy. You can see an example with the Webca [..]

BridJ library for Icy.
https://code.google.com/p/bridj/

Set of block (for graphical programming with Protocols) to perform different operations on ROI (Region Of Interest).

This plugin allows Icy to open many different video file format using the Xuggler library. Here is an incomplete list of [..]

Stereo vision support added to the 3D VTK canvas.

Block (Protocols) to convert ROI(s) into a binary image / sequence.

This plugin allows you to create a private repository to distribute your plugins and workspaces from your own server.

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

Shows how to listen active sequence / viewer events.

Deprecated: Use the Xuggler Video Importer plugin instead !

This plugin should import any kind of video.

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

Used to be the micro manager libraries but now that is an empty plugin (provided for backward compatibility).

Library used by Micro-Manager for fast acquisition.

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

A tool to parse the javadoc of a file.
Mostly used now by the Script Editor.

This library is used for JavaScript in the Scripting Editor. It is integrated in Java 6 & 7 by default, but for a be [..]

This plugin provides a color highlighting on text. Based on RSyntaxTextArea library of Fifesoft.

Plugin Library used to provide autocompletion to JTextComponents, such as JTextArea or JTextField.

Create powerful scripts to implement what’s missing with plugins. Syntax Color and Autocomplete features implement [..]

Deprecated ! Use the new Micro-Manager blocks plugin.

This plugin allows one to use various basic sequence operations within Blocks.

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

Display your data in real time 3D (depending on your hardware).

Creates an overlay on which you can draw. This can also be used to generate specific data (for tests).

Record what you are doing on a sequence as a .avi file, fully compatible with Icy.

Displays a live tool tip on the current focused ROI in an image. The tooltip displays the following informations about t [..]

The right click on sequences and ROIs will open a menu with various features, such as image and ROI copy, data conversio [..]

Fast Fourier Transform (FFT) for 2D/3D images

Simple tool to add annotations on your images.

Edit the workspaces with a simple drag’n drop system.

Requires Icy 1.2 at least.

Calibrator for Pixel Size.

Manage all calibrators for your microscope.

Advanced Acquisition plugin for microscope.

Snap complex images easily.

Move your XY Stage and Focus Device with your mouse.

Live video plugin for Micro-Manager for Icy.

Micro-Manager plugin for Icy. Use your microscope and microscopic devices in Icy ! Compatible with Micro-Manager 1.4.19 [..]

Track Processor computing the MSD (Mean Square Displacement).

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

Simple particles animation.
Up to 100 000 particles following the mouse cursor movement.

The track manager enables the use of DSP-like trackProcessors. This can affect the display of tracks, selection in time [..]

This plugin generates a bug in a thread, to show the capabilities of the automatic bug report.

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

This plugin shows how to display different type of 3D overlay in the VTK canvas 3D.

A slightly different painter than Overlay tutorial 1, focusing on canvas parameters instead of image parameters.

An example of a very simple overlay.

This tutorial details how to process an image area defined by ROI.

Details how to listen and use events provided by the main interface.

Creating in a few lines a plugin with an action button.

Details how to create a custom GUI

This tutorial focus on how to watch the swimming pool and get callback when an object is dropped in.

This tutorial focus on how to send any type of data in the swimming pool.

This tutorial focus on tools that Icy provides to easily process image data without having to bother about image data type.

This tutorial explain how to retrieve informations about installed plugins.

This tutorial explain how to use a deviation renderer JFreeChart chart in Icy.

This tutorial explain how to create a simple Area ROI.

This tutorial explain how to create an intensity profile over an ROI.

This tutorial explain how to create an animated overlay.

The first hello world tutorial

Tutorial explaining how to display a JFreeChart graph in Icy.

This tutorial details how to generate images of all differents types. (byte, int, short, ushort, float, double). And how [..]

Spot detector detects and counts spots. – Detects spots in noisy images 2D/3D. – Depending on objective, spo [..]

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 [..]