Open Microscopy Environment

Dear all,

I'm writing to ask if there are any plans to provide the ImageJ plugin for OMERO as a Fiji-update-site? Recently, this process has been simplified quite a bit by the Fiji devs in providing a very simple and convenient way to have the update site hosted on the sites.imagej.net server. Bio-Formats already uses this to distribute daily builds (see [1] for more details about how to set it up).

Of course this would only help people that are actually using Fiji, but on the other hand having a convenient way to install (and update!) the OMERO plugin would be one more argument to tell the crowd to switch to Fiji

Alas, there is one thing that needs to be solved: currently the only way (at least that I'm aware of) to distribute different versions is to have multiple update sites. Which is not a big deal, imho. Probably Curtis or Johannes have more information and/or ideas about this anyway.

I'm just asking as I'm considering setting up another such "personal" site to facilitate the distribution of the plugin at our facility here, but I want to avoid re-inventing the wheel or doubling mine (or someone elses) work...

Cheers
~Niko

[1] http://fiji.sc/Personal_Update_Sites

Hi Niko

We certainly discussed distributing the Plugin using the update-site but we did not have the chance to do.
It almost needs to rework it to fix some problems related to old Bioformat version already installed.
If you have some bandwidth to do it, that will be very helpful. Happy to discuss

Thanks

Jmarie

Hi Jmarie,

what parts would need to be reworked for the update-site? If the plugin requires more recent Bioformats than shipped with default Fiji, they are available via the same channel (as mentioned in my inital post).

I could setup a test site so we can play a bit if you like?

Cheers
Niko

Hi Niko

I need to rework the section when old Bioformats jars are present, the plugin hangs but that's more for ImageJ.
The Bioformarts jars shipped are the released one e.g. 4.4.9 for the latest release.
That will be great if you could set up a test site.

Thanks

Jmarie

I agree that a Fiji update site would be a big help to reach a lot of potential Insight users. Currently OMERO.insight-ij crashes on my mac with Fiji:-

first attempt to run OMERO->Connect to OMERO gives:-
---
(Fiji Is Just) ImageJ 1.48o; Java 1.6.0_65 [64-bit]; Mac OS X 10.7.5; 32MB of 6127MB (<1%)

java.lang.NoSuchFieldError: IS_OS_WINDOWS_7
at org.openmicroscopy.shoola.util.ui.UIUtilities.isWindowsOS(UIUtilities.java:2026)
at org.openmicroscopy.shoola.util.ui.login.ScreenLogin.buildLogin(ScreenLogin.java:677)
at org.openmicroscopy.shoola.util.ui.login.ScreenLogin.buildGUI(ScreenLogin.java:772)
at org.openmicroscopy.shoola.util.ui.login.ScreenLogin.<init>(ScreenLogin.java:1047)
at org.openmicroscopy.shoola.env.ui.SplashScreenManager.initializedView(SplashScreenManager.java:177)
at org.openmicroscopy.shoola.env.ui.SplashScreenManager.<init>(SplashScreenManager.java:242)
at org.openmicroscopy.shoola.env.ui.SplashScreenProxy.<init>(SplashScreenProxy.java:123)
at org.openmicroscopy.shoola.env.ui.UIFactory.makeSplashScreen(UIFactory.java:59)
at org.openmicroscopy.shoola.env.init.SplashScreenInit.execute(SplashScreenInit.java:99)
at org.openmicroscopy.shoola.env.init.Initializer.doInit(Initializer.java:276)
at org.openmicroscopy.shoola.env.Container.startupInPluginMode(Container.java:478)
at org.openmicroscopy.shoola.env.Container.startupInPluginMode(Container.java:421)
at org.openmicroscopy.shoola.MainIJPlugin.run(MainIJPlugin.java:247)
at ij.IJ.runUserPlugIn(IJ.java:196)
at ij.IJ.runPlugIn(IJ.java:160)
at ij.Executer.runCommand(Executer.java:131)
at ij.Executer.run(Executer.java:64)
at java.lang.Thread.run(Thread.java:695)
---

second & subsequent attempts give:-
---
(Fiji Is Just) ImageJ 1.48o; Java 1.6.0_65 [64-bit]; Mac OS X 10.7.5; 20MB of 6127MB (<1%)

java.lang.NullPointerException
at org.openmicroscopy.shoola.env.Container.startupInPluginMode(Container.java:454)
at org.openmicroscopy.shoola.env.Container.startupInPluginMode(Container.java:421)
at org.openmicroscopy.shoola.MainIJPlugin.run(MainIJPlugin.java:247)
at ij.IJ.runUserPlugIn(IJ.java:196)
at ij.IJ.runPlugIn(IJ.java:160)
at ij.Executer.runCommand(Executer.java:131)
at ij.Executer.run(Executer.java:64)
at java.lang.Thread.run(Thread.java:695)
---

The "NoSuchFieldError" was reported in this post viewtopic.php?f=4&t=7379&p=13251 and fixed by updating Fiji to BF-5.