[ome-users] ImageJ-Omero problem

[Petr Walczysko (Staff)]

Hi Chris

Thank you for the feedback.
I could not repeat your problem. My workflow was:
  - have 5.1.1 Bio-formats and 5.1.2 plugin in Fiji, open the image (multi-z and multi-t, a .dv) and crop and save back to OMERO -> worked fine
  - upgrade to 5.1.2 Bio-formats and 5.1.2 plugin in Fiji, and repeat the workflow -> worked fine

So I wonder, what version of Bio-formats do you have in your Fiji please ? (Help > About Plugins > Bio-format plugins….)
I would suggest to upgrade to 5.1.2 Bio-formats (Help > Update Fiji) and to 5.1.2 plugin http://downloads.openmicroscopy.org/omero/5.1.2/artifacts/OMERO.insight-ij-5.1.2-ice35-b45.zip.
In case this does not solve the problem, would you please upload your file using http://qa.openmicroscopy.org.uk/qa/upload/  ?

Hope this helps
All the best
Petr

OME Team



On 11 Jun 2015, at 17:16, "Wood, Christopher" <CJW at stowers.org<mailto:CJW at stowers.org>> wrote:

Hi Jean-Marie,

Yes, I am using Fiji.

I also get this (below) when I open an image (z-stack, time series) with the plugin, crop it, and then try to save it back. If I save the cropped image to disk, then open it and save to omero, it works fine.

Chris

Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
at org.openmicroscopy.shoola.agents.fsimporter.chooser.FileSelectionTable.allowAddToQueue(FileSelectionTable.java:405)
at org.openmicroscopy.shoola.agents.fsimporter.chooser.FileSelectionTable.addFiles(FileSelectionTable.java:579)
at org.openmicroscopy.shoola.agents.fsimporter.chooser.ImportDialog.addImageJFiles(ImportDialog.java:1608)
at org.openmicroscopy.shoola.agents.fsimporter.chooser.ImportDialog.propertyChange(ImportDialog.java:1671)
at java.beans.PropertyChangeSupport.firePropertyChange(PropertyChangeSupport.java:339)
at java.beans.PropertyChangeSupport.firePropertyChange(PropertyChangeSupport.java:276)
at java.awt.Component.firePropertyChange(Component.java:8287)
at org.openmicroscopy.shoola.agents.fsimporter.chooser.LocationDialog.actionPerformed(LocationDialog.java:950)
at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2028)
at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2351)
at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:387)
at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:242)
at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonListener.java:236)
at java.awt.AWTEventMulticaster.mouseReleased(AWTEventMulticaster.java:272)
at java.awt.Component.processMouseEvent(Component.java:6414)
at javax.swing.JComponent.processMouseEvent(JComponent.java:3275)
at java.awt.Component.processEvent(Component.java:6179)
at java.awt.Container.processEvent(Container.java:2084)
at java.awt.Component.dispatchEventImpl(Component.java:4776)
at java.awt.Container.dispatchEventImpl(Container.java:2142)
at java.awt.Component.dispatchEvent(Component.java:4604)
at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4618)
at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4279)
at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4209)
at java.awt.Container.dispatchEventImpl(Container.java:2128)
at java.awt.Window.dispatchEventImpl(Window.java:2492)
at java.awt.Component.dispatchEvent(Component.java:4604)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:717)
at java.awt.EventQueue.access$400(EventQueue.java:82)
at java.awt.EventQueue$2.run(EventQueue.java:676)
at java.awt.EventQueue$2.run(EventQueue.java:674)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:86)
at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:97)
at java.awt.EventQueue$3.run(EventQueue.java:690)
at java.awt.EventQueue$3.run(EventQueue.java:688)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:86)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:687)
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:296)
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:211)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:201)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:196)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:188)
at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)

From: ome-users on behalf of jburel
Reply-To: "ome-users at lists.openmicroscopy.org.uk<mailto:ome-users at lists.openmicroscopy.org.uk>"
Date: Thursday, June 11, 2015 at 12:34 AM
To: "ome-users at lists.openmicroscopy.org.uk<mailto:ome-users at lists.openmicroscopy.org.uk>"
Subject: Re: [ome-users] ImageJ-Omero problem

Hi Chris

I assume you are using Fiji
The problem is due to a version conflict of the drawing library shipped with the plugin and the one available in fiji. Fiji comes with a most recent version of the library.
It is not platform specific.
Thanks for reporting the problem

Cheers

Jmarie


The University of Dundee is a registered Scottish Charity, No: SC015096
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