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3-D3D3D coordinatesalignmentbasicsbatch processingCalciumcell trackingCLEMcolocalizationcomptageconfocalconnected componentscontributionconvolutioncorrelationdeconvolutiondeformable registrationdenoisingdetectiondetectordeveloperdisplacementsdistance mapexportezplugfeature detectionfeature matchingfilteringfluorescenceguiheadlesshelperHSV visualisationimage processImageJintensitymaskmavenmeasurementMHTmicroscopymonitoringmorphologymultiple hypothesis trackingnon rigid registrationoperatoroptimizationotsupluginpoint-spread functionprojectionprotocolPSFpythonregistrationreleaseRipley's K functionroiscriptscriptingsegmentationsequencesmoothingspatial distributionspotspot countstatisticssurfacesyntheticthresholdtoolboxtoolstrack processortrackingtutorialwarpingwavelet transformwaveletswidefieldworkbookXLS output
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  • Plugin Script Protocol FAQ Forum Topic Article
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Dynamics Classifier (TrackProcessor)
EHCache 3 for Icy
var total_items = 11;

JEP – Java Embedded Python

plugin
Amandine Tournay

Jep embeds CPython in Java through JNI.

Code on Python through Java !

Creating an Icy plugin with EzPlug

post
Amandine Tournay

The EzPlug library is meant to help developers write plug-ins fast and efficiently, i.e. focusing on the major aspect of the work (“the main code”) and leaving aside tedious aspects such as GUI design for parameter input and threading issues. Here, we will guide you through the use of EzPlug to develop your own Icy […]

Creating blocks for Icy protocols

post
Amandine Tournay

The plugin Protocols provide a graphical environment that enables anyone to create graphically and without any prior knowledge in programming a bioimage analysis workflow, and automate it on many images (batch processing). Protocols can also contain blocks with custom scripts and be run from the command line, which makes it a very powerful tool in […]

Migrate your old Icy plugin to maven

post
Stephane Dallongeville
Amandine Tournay
Stephane Dallongeville
Amandine Tournay

This tutorial explains how to migrate your old Icy plugin project (Eclipse) to a Maven project using our template. It will guide you using a concrete example (converting the Intensity Projection plugin) through the followings steps: Pre-requisites Converting Eclipse project to Maven project Setup POM file Building the project Testing Pre-requisites As we use Maven […]

Using image cursors on Icy

post
Daniel Felipe González Obando

This post explains the concept of image cursors, a new way of accessing image data without the struggle of handling image data types, developed by the Icy team. When developing plugins for Icy, we repeatedly struggle with handling images of different data types (int, short, long, float, double, etc.) The development team of Icy developed […]

Icy 2.1 – Importants changes for developers

post
Stephane Dallongeville
Marion Louveaux
Stephane Dallongeville
Marion Louveaux

There is two majors changes concerning Icy development project in Icy 2.1: Icy repository project is now hosted on GitLab: https://gitlab.pasteur.fr/bia/icy We chose to move on GitLab as it helps us to improve the project management processes. It also offers more control compared to GitHub, as everything is hosted internally while still being accessible from […]

Setting Icy development environment

post
Stephane Dallongeville
Marion Louveaux
Daniel Felipe González Obando
Stephane Dallongeville
Marion Louveaux
Daniel Felipe González Obando

You will find here the download links and instructions (when needed) to install required programs to start developing with Icy. Java 8 or later Icy is developed in Java. You need Java 8 or more. For your convenience, we directly provide the installation packages for all systems below. You can select OpenJDK or Oracle JDK […]

How to create a new Icy plugin

post
Stephane Dallongeville
Daniel Felipe González Obando
Marion Louveaux
Stephane Dallongeville
Daniel Felipe González Obando
Marion Louveaux

This tutorial explains how to set up your development environment and create a new Icy plugin using Maven. It will guide you through the following steps: Setting up your development environment Importing the plugin template from GitLab Modifying the pom.xml file to fit your plugin description / requirements Building the project Testing Examples and documentation […]

Introduction to Maven

post
Stephane Dallongeville
Amandine Tournay
Marion Louveaux
Daniel Felipe González Obando
Stephane Dallongeville
Amandine Tournay
Marion Louveaux
Daniel Felipe González Obando

In this article, we explain what is Maven and how Maven projects are structured. We recommend to use Maven projects to create new plugins for Icy. Maven is a project management tool. Here’s what we can read from the official What is Maven Apache web site : <<Its primary goal is to allow a developer […]

Contributing to Icy development

post
Daniel Felipe González Obando
Marion Louveaux
Stephane Dallongeville
Daniel Felipe González Obando
Marion Louveaux
Stephane Dallongeville

This article aims to guide you on how to contribute to Icy development, whether you are part of the Icy developers team or an external contributor. Although this article focus on contribution for Icy Kernel project as an example but it also fully applies to contribution to an existing plugin from our repository. If you […]

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