[ome-users] Retrieving original images from the server
Paulo Almeida
palmeida at igc.gulbenkian.pt
Thu Nov 29 12:52:20 GMT 2007
Hi Jason and Curtis, thanks for your replies.
> > We have plans to update the "Upload to OME" plugin to work with OMERO,
> > but have not yet had time to do so. It is definitely something we will
> > add in the future, though.
>
> We'd appreciate feedback on this point-- is this a major priority for
> the community? We know ImageJ is in heavy use, and therefore are
> considering devoting resources to this. Does the ImageJ community
> want this?
ImageJ/OMERO integration is important for our community, because we want to
minimize the number of applications people need in order to use OMERO. My
idea is to have OMERO.importer installed in the microscope computers and a
client (Insight and/or ImageJ) on the researcher's computers. Since they are
already using ImageJ to further process their images, it would be good if
they could just import them from the database within ImageJ.
Ideally, OMERO.importer could have basic annotation capabilities, because
people have been saying they have limited time on the microscopes, so they
will end up writing something on their notebook instead of using
OMERO.insight while they are acquiring images. Sometimes acquisition takes up
to a minute and that is the time they use to annotate, and of course the
image is still not available in Insight. Actually, it is not available in
Importer too, at that stage, so they would probably write something in
Notepad and paste it to Insight afterwards, but if they could paste it to
Importer instead, they would just need to use one program. What do you think?
> >> I have imported some .lif pictures into Omero and I am worried that
> >> information (such as laser power, filters, etc) may be lost in the
> >> process.
> >> Is there a way to easily retrieve (ie through the client) the
> >> original image
> >> from the server? I have been looking around and couldn't find a
> >> way to do it.
> >> (I saw the download icon when visualizing the image, but I
> >> couldn't get it to
> >> work).
> >
> > I am not sure; one of the OMERO developers will have to comment on
> > that. But that functionality is very important to my lab, so if it is
> > not already there we will find a way to do it at some point.
>
> When you import the file, you will see a check box at the bottom of
> the dialog where you specify the Project and Dataset for the incoming
> image, asking if you want to archive the original image. If you
> click this, the original file will be uploaded as well, and will be
> available for download inside the OMERO.insight DataManager. See the
> OMERO.importer movie at http://openmicroscopy.org/howto/ for more
> info on importing data.
Actually, I was checking that box in Importer, but I had the wrong permissions
in the /OMERO directory (File and Pixels belonged to root). However, even
after altering the permissions, I can see the original images are uploaded to
the server but I still can't download them from Insight. I am attaching the
error message I get when I try. I tried with a jpeg. Also, the names of the
pictures in the server are sequential numbers, which I'm not sure is the
correct behavior.
Regards,
Paulo
>
> Note that we have a known bug-- the Download button in OMERO.insight
> does not go gray when there is no original file uploaded. This
> requires some server-side updates that we need to do...
>
> As always, thanks for your feedback and support.
>
> Cheers,
>
> Jason
>
> > On Nov 28, 2007 6:29 AM, Paulo Almeida <palmeida at igc.gulbenkian.pt>
> >
> > wrote:
> >> Hi,
> >>
> >> Is there a way to import the images in an Omero server with
> >> ImageJ? If not,
> >> are there plans to implement that, as in Ome (I tried the Loci
> >> plugin, which
> >> gives me the option to import from Ome, but it did not work with
> >> the Omero
> >> server). Or do you think the development of the Omero client will
> >> make that
> >> unnecessary?
> >>
> >> I have imported some .lif pictures into Omero and I am worried that
> >> information (such as laser power, filters, etc) may be lost in the
> >> process.
> >> Is there a way to easily retrieve (ie through the client) the
> >> original image
> >> from the server? I have been looking around and couldn't find a
> >> way to do it.
> >> (I saw the download icon when visualizing the image, but I
> >> couldn't get it to
> >> work).
> >>
> >>
> >> Thank you,
> >> - Paulo Almeida
> >> _______________________________________________
> >> ome-users mailing list
> >> ome-users at lists.openmicroscopy.org.uk
> >> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
> >
> > _______________________________________________
> > ome-users mailing list
> > ome-users at lists.openmicroscopy.org.uk
> > http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>
> **************************
> Wellcome Trust Centre for Gene Regulation & Expression
> College of Life Sciences
> MSI/WTB/JBC Complex
> University of Dundee
> Dow Street
> Dundee DD1 5EH
> United Kingdom
>
> phone (01382) 385819
> Intl phone: 44 1382 385819
> FAX (01382) 388072
> email: jason at lifesci.dundee.ac.uk
>
> Lab Page: http://www.dundee.ac.uk/lifesciences/swedlow/
> Open Microscopy Environment: http://openmicroscopy.org
> **************************
-------------- next part --------------
java.lang.Exception: Cannot create the file
at org.openmicroscopy.shoola.env.ui.UserNotifierImpl.showErrorDialog(UserNotifierImpl.java:129)
at org.openmicroscopy.shoola.env.ui.UserNotifierImpl.notifyError(UserNotifierImpl.java:180)
at org.openmicroscopy.shoola.env.ui.UserNotifierImpl.notifyError(UserNotifierImpl.java:169)
at org.openmicroscopy.shoola.agents.util.archived.DownloaderLoader.handleException(DownloaderLoader.java:108)
at org.openmicroscopy.shoola.env.data.events.DSCallAdapter.eventFired(DSCallAdapter.java:84)
at org.openmicroscopy.shoola.env.data.views.BatchCallMonitor$1.run(BatchCallMonitor.java:124)
at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:209)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:597)
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:273)
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:183)
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:177)
at java.awt.Dialog$1.run(Dialog.java:1039)
at java.awt.Dialog$3.run(Dialog.java:1091)
at java.security.AccessController.doPrivileged(Native Method)
at java.awt.Dialog.show(Dialog.java:1089)
at java.awt.Component.show(Component.java:1419)
at java.awt.Component.setVisible(Component.java:1372)
at java.awt.Window.setVisible(Window.java:801)
at java.awt.Dialog.setVisible(Dialog.java:979)
at org.openmicroscopy.shoola.util.ui.UIUtilities.centerAndShow(UIUtilities.java:184)
at org.openmicroscopy.shoola.util.ui.TinyLoadingWin.setOnScreen(TinyLoadingWin.java:96)
at org.openmicroscopy.shoola.agents.util.archived.view.DownloaderControl.stateChanged(DownloaderControl.java:121)
at org.openmicroscopy.shoola.util.ui.component.AbstractComponent.fireStateChange(AbstractComponent.java:103)
at org.openmicroscopy.shoola.agents.util.archived.view.DownloaderComponent.download(DownloaderComponent.java:194)
at org.openmicroscopy.shoola.agents.util.archived.view.DownloaderControl.propertyChange(DownloaderControl.java:109)
at java.beans.PropertyChangeSupport.firePropertyChange(PropertyChangeSupport.java:339)
at java.beans.PropertyChangeSupport.firePropertyChange(PropertyChangeSupport.java:347)
at java.beans.PropertyChangeSupport.firePropertyChange(PropertyChangeSupport.java:276)
at java.awt.Component.firePropertyChange(Component.java:7865)
at org.openmicroscopy.shoola.util.ui.filechooser.FileChooser.setFolderPath(FileChooser.java:288)
at org.openmicroscopy.shoola.util.ui.filechooser.CustomizedFileChooser.approveSelection(CustomizedFileChooser.java:317)
at org.openmicroscopy.shoola.util.ui.filechooser.FileSaverUI.actionPerformed(FileSaverUI.java:440)
at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1995)
at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2318)
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:6038)
at javax.swing.JComponent.processMouseEvent(JComponent.java:3260)
at java.awt.Component.processEvent(Component.java:5803)
at java.awt.Container.processEvent(Container.java:2058)
at java.awt.Component.dispatchEventImpl(Component.java:4410)
at java.awt.Container.dispatchEventImpl(Container.java:2116)
at java.awt.Component.dispatchEvent(Component.java:4240)
at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4322)
at java.awt.LightweightDispatcher.processMouseEvent(Container.java:3986)
at java.awt.LightweightDispatcher.dispatchEvent(Container.java:3916)
at java.awt.Container.dispatchEventImpl(Container.java:2102)
at java.awt.Window.dispatchEventImpl(Window.java:2429)
at java.awt.Component.dispatchEvent(Component.java:4240)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:599)
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:273)
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:183)
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:177)
at java.awt.Dialog$1.run(Dialog.java:1039)
at java.awt.Dialog$3.run(Dialog.java:1091)
at java.security.AccessController.doPrivileged(Native Method)
at java.awt.Dialog.show(Dialog.java:1089)
at java.awt.Component.show(Component.java:1419)
at java.awt.Component.setVisible(Component.java:1372)
at java.awt.Window.setVisible(Window.java:801)
at java.awt.Dialog.setVisible(Dialog.java:979)
at org.openmicroscopy.shoola.util.ui.UIUtilities.centerAndShow(UIUtilities.java:184)
at org.openmicroscopy.shoola.agents.util.archived.view.DownloaderComponent.activate(DownloaderComponent.java:101)
at org.openmicroscopy.shoola.agents.imviewer.view.ImViewerComponent.download(ImViewerComponent.java:1683)
at org.openmicroscopy.shoola.agents.imviewer.actions.ArchivedAction.actionPerformed(ArchivedAction.java:82)
at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1995)
at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2318)
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:6038)
at javax.swing.JComponent.processMouseEvent(JComponent.java:3260)
at java.awt.Component.processEvent(Component.java:5803)
at java.awt.Container.processEvent(Container.java:2058)
at java.awt.Component.dispatchEventImpl(Component.java:4410)
at java.awt.Container.dispatchEventImpl(Container.java:2116)
at java.awt.Component.dispatchEvent(Component.java:4240)
at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4322)
at java.awt.LightweightDispatcher.processMouseEvent(Container.java:3986)
at java.awt.LightweightDispatcher.dispatchEvent(Container.java:3916)
at java.awt.Container.dispatchEventImpl(Container.java:2102)
at java.awt.Window.dispatchEventImpl(Window.java:2429)
at java.awt.Component.dispatchEvent(Component.java:4240)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:599)
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:273)
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:183)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:173)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:168)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:160)
at java.awt.EventDispatchThread.run(EventDispatchThread.java:121)
More information about the ome-users
mailing list