What Java Runtime Environment should I install to get Icy working ?

Current version of Icy requires Java 7 at least to work (if your system is limited to Java 6 then you can use Icy 1.8.6.0 which is the last version supporting Java 6) but we recommend to install Java 8 which is the most robust / stable version:

  • OSX: Install JDK8 (not JRE 8) that you can get from here, note that depending your OSX version you may also need to install this patch.
  • Windows: Be careful to install the proper 64 bit Java on 64 bit OS as some website provides a 32 bit Java for Windows by default. We strongly recommend a 64 bit OS and JRE 8 that you can download from here.
  • Linux: Avoid OpenJDK if possible (many issues / bugs), and prefer Oracle JDK 8 or Oracle JRE 8 that you can download from here.

I installed Icy on my mac but it doesn’t work. How to fix it ?

First, you need to have java installed on your system (refer to the first FAQ entry to get the instructions), then be sure that Icy is installed in the Applications folder.
The first time you try to launch the application it may not work because of the default Security preferences.
You can force its execution by doing right click on the application icon (or Ctrl+click) and use the Open command, then confirm / validate the operation. You should now be able to use Icy normally 🙂

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

Sometime you just need to add the bin directory of your JRE (Java Runtime Environment) in the PATH environment variable but it still doesn’t work, you may try the following solutions:

  • Unix / Linux: You may need to install VTK 6.3 library (with the java wrapper) by yourself depending your system distribution then add the installation path (ex : /usr/local/lib/vtk-6.3.0) to the LD_LIBRARY_PATH variable.
  • Windows 64: Sometime VTK 64 bit library is not loading correctly (work with java 32 bit), in this case you need to install the VC++ 2013 redistributable to fix it.
  • OSX: VTK is supported only for OSX > 10.7

How can I have more than 1 GB of memory available in Icy ?

A 32 bit Java Virtual Machine (JVM) limits you to 1 GB of memory maximum. To bypass this limit you should have a 64 bits OS and you explicitly need to install a 64 bits JVM. You can now fully use the available memory ! Memory settings are automatically 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 report a bug or contact the dev team ?

For bug report, you have the following possibilities:

  • If the bug happened in a plugin, use the automatic bug report window prompt in Icy (the author will receive it automatically)
  • 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.

You can also contact us for any question and/or support directly from the support page.

General update and plugins update fails, what is the problem?

Be sure the application have write permissions in the folder where Icy is installed.

  • Windows users: It is strongly discouraged to install it in the Program Files folder as it may not have write permissions in this folder, prefer something as C:\\Applications\\Icy or just C:\\Icy
  • OSX users: It is strongly encouraged to install Icy in the Applications folder (unlike on Windows)

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
https://icy.bioimageanalysis.org

How can I publish a plugin ?

You need to register (top of the page). Once logged in, you can go to Plugins > Add New.

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 work on my old Mac with OSX 10.5, is Leopard system supported ?

Only Icy 1.8.6.0 or older 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 won’t have access to the VTK 3D display.

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

VTK use heavyweight component for rendering, sometime it can mess 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.

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 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