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Frequently Asked Questions


A security warning message appears when i try to launch Icy on my mac.
Can i disable VTK warning messages (developer) ?
Can I run an ImageJ plugin in Icy ?
Even when Icy is idle the CPU usage keep a high level, why ?
General update and plugins update fails, what is the problem ?
How can I cite Icy in a publication ?
How can I contact the dev team ?
How can I have more than 1 GB of memory available in Icy ?
How can I publish a plugin ?
How can I report a bug ?
How can i revert to Java 6 on Mac OSX ?
How do I learn how to develop a plugin for Icy ?
How to fix the -Cannot load VTK library- or -VTK unsatisfied link- error ?
How to install or update to java 8 on Mac OSX ?
How to use Icy under opensuse 11.4 linux ?
I want to request a plugin !
I want to submit a plugin, but without source code: is it possible ?
Icy cannot connect to the internet, why ?
Icy does not start with OSX 10.8 or above, looking for Java 6. How to fix it ?
Icy does not work on my old Mac with OSX 10.5, is Leopard system supported ?
Icy is very slow when i zoom in the image on my Mac ! How to fix it ?
Is Linux/Unix supported ?
The chat does not connect, why ?
VTK rendering is wrong, all i get is a blank canvas, how fix it ?
What is the minimum Java version needed ?
What Java Runtime Environment should I download ?
Which Microsoft-Windows versions are supported ?


A security warning message appears when i try to launch Icy on my mac.

This is due to the security system of the OS which require signed application.
You can resolve the problem by going to :
System --> Preferences --> Security --> Privacy then change Allow applications downloaded from to Anywhere
Or you can select to authorize Icy application specifically.


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.


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

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


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 GB of memory available in Icy ?

A 32 bits 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 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 can i revert to Java 6 on Mac OSX ?

    Note: You do not need to revert to Java 6 anymore with Icy 1.8.0.0 or newer, just use the latest java version available and it should work perfectly.

    Java 7 and Java 8 introduced some problems on Apple system and sometime the only solution is to revert to the previous version so here is the procedure to revert to Java 6:
    Start by downloading this update.
    After you installed it you need to remove java 7 and/or java 8 from your system by typing these commands :
    sudo rm -fr /Library/Internet Plug-ins/JavaAppletPlugin.plugin
    sudo rm -r /Library/Java/JavaVirtualMachines/jdk1.7.0_25.jdk
    sudo rm -r /Library/Java/JavaVirtualMachines/jdk1.8.0_05.jdk
    Depending the installed version(s) on your system you may need to change the command to match the correct version.
    You can find here the related issue on github bug tracker.


    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 may need to install VTK 6.3 library then add the installation path (ex : /usr/local/lib/vtk-6.1.0) to the LD_LIBRARY_PATH variable. For mac users, VTK is supported only on OSX 10.7 or above.


    How to install or update to java 8 on Mac OSX ?

    You need to install the JDK 8 (and not the JRE) for Mac OSX from here then you may need to install this patch. It allows the Icy.app launcher to correctly find Java on newer OSX systems.


    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 with OSX 10.8 or above, looking for Java 6. How to fix it ?

    First, you need to install the last version of Java, sometime java is installed but just for web applications (JRE) so you need to install the JDK 8 for Mac OSX, you can see the procedure here.
    Also be sure you have authorized the application in the security preferences


    Icy does not work on my old Mac with OSX 10.5, is Leopard system 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 won\'t have access to the VTK features.


    Icy is very slow when i zoom in the image on my Mac ! How to fix it ?

    Hardware acceleration does not always properly work when using earlier java 8 or java 7 on OSX systems.
    Just update to last java 8 version to fix the issue !


    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 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.


    What is the minimum Java version needed ?

    Icy requires Java 6 (1.6) at least to work (that minimum requirement will change to Java 7 soon) but we recommend to use the last available Java version.


    What Java Runtime Environment should I download ?

  • Mac : JDK8 for OSX >= 10.7, you may also need to install this patch
  • 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 8. You can download it here


  • Which Microsoft-Windows versions are supported ?

    All versions which are compliant with Java 1.6+. ICY has been tested on Windows XP, 7, 8 / 8.1 and Windows 10.