Frequently Asked Questions

Can i disable VTK warning messages (developer) ?

Yes, you can disable them by adding this line of code before using VTK functions :
canvas3D.getRenderer().SetGlobalWarningDisplay(0);

Can I run an ImageJ plugin in Icy ?

Yes, ImageJ is integrated in Icy. Just click on the ImageJ tab and convert your Icy image in ImageJ image, this way you can use ImageJ with almost 100% plugin compatibility.

Even when Icy is idle the CPU usage keep a high level, why ?

First, be sure you do not have any plugin running in background. If you are sure that is not the case, check the JVM (Java Virtual Machine) you are using. The OpenJDK JVM (on linux) is known to have issues like important CPU usage. Use the Sun/Oracle JVM instead.

How can I cite Icy in a publication ?

de Chaumont, F. et al. (2012) Icy: an open bioimage informatics platform for extended reproducible research, Nature Methods, 9, pp. 690-696 - http://icy.bioimageanalysis.org

How can I contact the dev team ?

Best practice is to use the support page.

How can I have more than 1.5Gb of memory available in Icy ?

If you use a 32bits Operating System, the Jave Virtual Machine (JVM) limits you to 1.5Gb. You should go for a 64bits OS (you need a 64bits computer) and you explicitly need to install a 64bits JVM. You can now fully use the available memory ! Memory settings are automaticaly set up at the first run of Icy, depending on your system and the memory available, you can change it afterwards in the preferences panel.

How can I publish a plugin ?

You need to register ( top of the page ). Once logged in, my plugins > Submit a new plugin.

How can I report a bug ?

If the bug happened in a plugin, use the automatic bug report window prompt in Icy.

If the bug is in the kernel of Icy, and a bug is displayed in the output window, use the report button.

You can also use the bug tracker of the project directly on GitHub issues tracker.
This way you can follow the issue and be notified when it is resolved.

How do I learn how to develop a plugin for Icy ?

You can watch this tutorial which explains how to create your first plugin in a few minutes. A number of tutorials are available online, you can directly check the commented source code on the online documentation, which is a good starting guide.

How to fix the -Cannot load VTK library- or -VTK unsatisfied link- error ?

You can fix the problem by adding the bin directory of your JRE in the PATH environment variable. Also on unix /linux system you have to install at least the VTK 5.8.0 library then add the installation path (ex : /usr/local/lib/vtk-5.8.0) to the LD_LIBRARY_PATH variable. For mac users, VTK is supported only on OSX 10.6 or above (it may work on 10.5 but we cannot guarantee it as native library support is not compatible with higher version).

How to use Icy under opensuse 11.4 linux ?

Running Icy in opensuse 11.4 linux (64 bit).

Install Java JDK system-wide.

Add the -science- repository in YaST: http://download.opensuse.org/repositories/science/openSUSE_11.4/

Add the following 3 packages using YaST:
vtk
vtk-devel
vtk-java

In addition, Yast will add a number of dependencies.

Unpack Icy, change directory to where Icy is installed and use this command line to run Icy: java -Xmx2g -jar icy.jar
Instructions courtesy of Gabriel Landini and Albert Cardona

I want to request a plugin !

Get to the forum section, post images and ideas to seduce a developer !

I want to submit a plugin, but without source code: is it possible ?

Yes and no: ICY is dedicated to an open community where knowledge is shared. If you want to publish a plugin on this website, its code has to be GPL.
More generally we strongly encourage people to distribute source code in theirs plugins.
You can still use private repositories to distribute your plugins (with or without source code) to a closed group of people.

Icy cannot connect to the internet, why ?

Make sure the proxy settings are correct (Preferences > Network).

Icy does not start on OSX 10.5, is Leopard supported ?

Yes, Icy also runs on Mac OS X 10.5.x a.k.a. Leopard. Yet, there is a small adjustment to perform in the system settings. In the Applications > Utilities folder, launch the _Java Preferences_ application. A list displays all version of Java installed on your system, by order of priority. Since Icy requires Java 1.6 or greater, simply drag the _Java SE 6_ machine(s) to the top of the list (make sure the latest version is on top). You can now use Icy on your favorite Leopard ! Note that you may experience incompatibility with the VTK library.

Icy does not start with OSX 10.8 or above ?

First, check you have java installed on your system. Java is not anymore bundled with OSX and you have to install it manually : http://www.oracle.com/technetwork/java/javase/downloads/index.html Then be sure you downloaded Icy from the website : http://icy.bioimageanalysis.org/download If you get Icy from an external drive (as a USB key) the system will prevent you from executing it (or you need to allow it by modifying your system security preferences).

Is Linux/Unix supported ?

Icy code is multi-platform, but it is up to the linux user to install VTK and all others current and future JNI third party libraries at his/her own delight.

The chat does not connect, why ?

Be sure your system network properties are correctly set and you have access to internet. If you use a proxy, verify you correctly defined the SOCKS proxy parameters (sometime removing them fix the problem).

VTK rendering is wrong, all i get is a blank canvas, how fix it ?

VTK use heavyweight component for rendering, sometime it can mix up with java Swing lightweight components. Sometime you have to disable special effects ou your Operating System, for instance on Unix / Linux you can fix blank rendering problem by disabling Compositing within KDEs desktop effects.

What is the minimum Java version needed ?

Java 1.6

What Java Runtime Environment should I download ?

Mac : The JRE is already installed on your computer. Make sure Java SE 6 is the system default

Windows: The java website provides a 32bits version by default, regardless if you are running a 32 or a 64bits OS. We strongly recommend a 64bits OS and JRE. You can download it here

Which Microsoft-Windows versions are supported ?

All versions which are compliant with Java 1.6+. ICY is tested on Windows XP/32/64 and Windows 7/64.