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<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>I have now tried shoola and get the following error message:<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'><o:p> </o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>Rendering Engine Exception: Can't load image metadata. Image id: 98<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>org.openmicroscopy.shoola.env.rnd.metadata.MetadataSourceException:
Can't retrieve the pixels metadata.<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'> at
org.openmicroscopy.shoola.env.rnd.metadata.MetadataSource.load(MetadataSource.java:210)<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'> at
org.openmicroscopy.shoola.env.rnd.metadata.MetadataSource.makeNew(MetadataSource.java:80)<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'> at
org.openmicroscopy.shoola.env.rnd.Renderer.makeNew(Renderer.java:114)<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'> at
org.openmicroscopy.shoola.env.rnd.RenderingManager.makeNew(RenderingManager.java:91)<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'> at
org.openmicroscopy.shoola.env.rnd.RenderingEngine.handleLoadImage(RenderingEngine.java:137)<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'> at
org.openmicroscopy.shoola.env.rnd.RenderingEngine.eventFired(RenderingEngine.java:242)<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'> at org.openmicroscopy.shoola.env.event.EventBusImpl.dispatch(EventBusImpl.java:185)<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'> at
org.openmicroscopy.shoola.env.event.EventBusImpl.post(EventBusImpl.java:165)<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'> at
org.openmicroscopy.shoola.agents.datamng.DataManager.viewImage(DataManager.java:1019)<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'> at org.openmicroscopy.shoola.agents.datamng.DataManagerCtrl.viewImage(DataManagerCtrl.java:333)<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'> at
org.openmicroscopy.shoola.agents.datamng.TreePopupMenuManager.view(TreePopupMenuManager.java:173)<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'> at
org.openmicroscopy.shoola.agents.datamng.TreePopupMenuManager.actionPerformed(TreePopupMenuManager.java:147)<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'> at
javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1849)<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'> at
javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2169)<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'> at
javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:420)<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'> at
javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:258)<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'> at
javax.swing.AbstractButton.doClick(AbstractButton.java:302)<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'> at
javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:1000)<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'> at
javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:1041)<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'> at
java.awt.Component.processMouseEvent(Component.java:5488)<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'> at
javax.swing.JComponent.processMouseEvent(JComponent.java:3126)<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'> at java.awt.Component.processEvent(Component.java:5253)<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'> at
java.awt.Container.processEvent(Container.java:1966)<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'> at
java.awt.Component.dispatchEventImpl(Component.java:3955)<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'> </span></font><span lang=FR>at
java.awt.Container.dispatchEventImpl(Container.java:2024)<o:p></o:p></span></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span lang=FR
style='font-size:10.0pt'> at
java.awt.Component.dispatchEvent(Component.java:3803)<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span lang=FR
style='font-size:10.0pt'> at
java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4212)<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span lang=FR
style='font-size:10.0pt'> </span>at
java.awt.LightweightDispatcher.processMouseEvent(Container.java:3892)<o:p></o:p></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'> at
java.awt.LightweightDispatcher.dispatchEvent(Container.java:3822)<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'> </span></font><span lang=FR>at
java.awt.Container.dispatchEventImpl(Container.java:2010)<o:p></o:p></span></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span lang=FR
style='font-size:10.0pt'> </span>at
java.awt.Window.dispatchEventImpl(Window.java:1774)<o:p></o:p></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'> at
java.awt.Component.dispatchEvent(Component.java:3803)<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'> at
java.awt.EventQueue.dispatchEvent(EventQueue.java:463)<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'> at
java.awt.EventDispatchThread.pumpOneEventForHierarchy(EventDispatchThread.java:242)<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'> at
java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:163)<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'> at
java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:157)<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'> at
java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:149)<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'> at
java.awt.EventDispatchThread.run(EventDispatchThread.java:110)<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>Caused by: org.openmicroscopy.is.ImageServerException:
org.apache.commons.httpclient.HttpRecoverableException: Error in parsing the
status line from the response: unable to find line starting with
"HTTP"<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'> at
org.openmicroscopy.is.HttpImageServer.executeCall(HttpImageServer.java:157)<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'> at
org.openmicroscopy.is.HttpImageServer.getPixelsInfo(HttpImageServer.java:360)<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'> at
org.openmicroscopy.is.HttpImageServer.getStackStatistics(HttpImageServer.java:1168)<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'> at
org.openmicroscopy.is.PixelsFactory.getStackStatistics(PixelsFactory.java:803)<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'> at
org.openmicroscopy.shoola.env.data.PixelsServiceAdapter.getStackStatistics(PixelsServiceAdapter.java:208)<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'> at org.openmicroscopy.shoola.env.rnd.metadata.MetadataSource.load(MetadataSource.java:198)<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'> ... 37 more<o:p></o:p></span></font></p>
<div style='mso-element:para-border-div;border:none;border-bottom:double windowtext 2.25pt;
padding:0in 0in 1.0pt 0in'>
<p class=MsoPlainText style='border:none;padding:0in'><font size=2
face="Courier New"><span style='font-size:10.0pt'>Exception in thread
"AWT-EventQueue-0"<o:p></o:p></span></font></p>
<p class=MsoPlainText style='border:none;padding:0in'><font size=2
face="Courier New"><span style='font-size:10.0pt'><o:p> </o:p></span></font></p>
</div>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'><o:p> </o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>When importing the metamorph images I get following output after import
(see the “unknown format”, is this correct???), and still cant see
the thumbnails:<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'><o:p> </o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>[bernd@BERND-HOME TestImages]$ ome import 011B1_Morph_*.TIF<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>Importing files<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'> </span></font><span
lang=DE>1/15: [IN PROGRESS] Starting import<o:p></o:p></span></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'> 14/15: [IN PROGRESS]
Importing<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>Use of uninitialized value in concatenation (.) or string at
/home/bernd/allOMEs/06_08_18/OME/src/perl2/OME/ImportEngine/AbstractFormat.pm
line 378.<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>Use of uninitialized value in concatenation (.) or string at
/home/bernd/allOMEs/06_08_18/OME/src/perl2/OME/ImportEngine/AbstractFormat.pm
line 378.<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>Use of uninitialized value in concatenation (.) or string at
/home/bernd/allOMEs/06_08_18/OME/src/perl2/OME/ImportEngine/AbstractFormat.pm
line 378.<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>Use of uninitialized value in concatenation (.) or string at /home/bernd/allOMEs/06_08_18/OME/src/perl2/OME/ImportEngine/AbstractFormat.pm
line 378.<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>Use of uninitialized value in concatenation (.) or string at
/home/bernd/allOMEs/06_08_18/OME/src/perl2/OME/ImportEngine/AbstractFormat.pm
line 378.<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>Use of uninitialized value in concatenation (.) or string at
/home/bernd/allOMEs/06_08_18/OME/src/perl2/OME/ImportEngine/AbstractFormat.pm
line 378.<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>Use of uninitialized value in concatenation (.) or string at
/home/bernd/allOMEs/06_08_18/OME/src/perl2/OME/ImportEngine/AbstractFormat.pm
line 378.<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>Use of uninitialized value in concatenation (.) or string at
/home/bernd/allOMEs/06_08_18/OME/src/perl2/OME/ImportEngine/AbstractFormat.pm
line 378.<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>Use of uninitialized value in concatenation (.) or string at
/home/bernd/allOMEs/06_08_18/OME/src/perl2/OME/ImportEngine/AbstractFormat.pm
line 378.<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>Use of uninitialized value in concatenation (.) or string at
/home/bernd/allOMEs/06_08_18/OME/src/perl2/OME/ImportEngine/AbstractFormat.pm
line 378.<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>Use of uninitialized value in concatenation (.) or string at
/home/bernd/allOMEs/06_08_18/OME/src/perl2/OME/ImportEngine/AbstractFormat.pm
line 378.<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>Use of uninitialized value in concatenation (.) or string at
/home/bernd/allOMEs/06_08_18/OME/src/perl2/OME/ImportEngine/AbstractFormat.pm
line 378.<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'> 15/15: [IN PROGRESS]
Executing import chain<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'> 15/15: [FINISHED]
Imported 16 images from 12 files. 12 scanned. <font color=red><span
style='color:red'>12 unknown format</span></font>, 0 duplicates, 0 errors.<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>Successfully Imported:<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>1345: 011B1_Morph_A01_s2<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>1346: 011B1_Morph_P01_s2<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>1347: 011B1_Morph_A01_s1<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>1348: 011B1_Morph_P01_s1<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>1349: 011B1_Morph_P01_s1_w2<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>1350: 011B1_Morph_A01_s1_w2<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>1351: 011B1_Morph_P01_s1_w3<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>1352: 011B1_Morph_P01_s1_w1<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>1353: 011B1_Morph_A01_s2_w2<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>1354: 011B1_Morph_A01_s1_w1<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>1355: 011B1_Morph_A01_s2_w3<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>1356: 011B1_Morph_P01_s2_w2<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>1357: 011B1_Morph_A01_s1_w3<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>1358: 011B1_Morph_A01_s2_w1<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>1359: 011B1_Morph_P01_s2_w3<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>1360: 011B1_Morph_P01_s2_w1<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>Exiting...<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>Exiting...<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'><o:p> </o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'><o:p> </o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'><o:p> </o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>Any ideas???<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'><o:p> </o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>Thanks,<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'><o:p> </o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>Bernd<o:p></o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'><o:p> </o:p></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|-----Original Message-----</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|From: ome-devel-bounces@lists.openmicroscopy.org.uk [mailto:ome-devel-</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|bounces@lists.openmicroscopy.org.uk] On Behalf Of Bernd Jagla</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|Sent: Friday, September 08, 2006 10:44 AM</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|To: 'Curtis Rueden'</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|Cc: ome-devel@lists.openmicroscopy.org.uk</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|Subject: Re: [ome-devel] image display problem</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|Curtis,</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|I can see the image even though I have to adjust the intensities...</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|I see this LDAP message in the error_log of httpd:</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|Can anyone make sense of this?</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|Here is the error log from the following steps:</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|Remove /OME (rm -rf)</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|Dropdb ome</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|Sudo perl install -y</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|ome import ~/allOMEs/inca/Screening.ome</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|(=> no problems)</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|ome import ~/test/Ai_compound_import.ome</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|=> problems with</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|OME::Tasks::LSIDManager::getRemoteObject() is not implemented. at</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|/usr/lib/perl5/site_perl/5.8.6/OME/ImportExport/ModuleImport.pm line
183</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|Could it be that this error comes up when doing the second import
within a</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|certain timeframe? There is no error log entry when this error occurs.</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|Thanks,</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|Bernd</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|Ok here is finally the snippet from the error_log:</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|[Fri Sep 08 09:31:21 2006] [notice] Digest: generating secret for
digest</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|authentication ...</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|[Fri Sep 08 09:31:21 2006] [notice] Digest: done</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|[Fri Sep 08 09:31:21 2006] [notice] LDAP: Built with OpenLDAP LDAP SDK</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|[Fri Sep 08 09:31:21 2006] [notice] LDAP: SSL support unavailable</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|[Fri Sep 08 09:31:22 2006] [notice] mod_python: Creating 4 session
mutexes</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|based on 150 max processes and 0 max threads.</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|[Fri Sep 08 09:31:22 2006] [notice] Apache/2.0.54 (Fedora) configured
--</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|resuming normal operations</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|Use of uninitialized value in print at</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|/home/bernd/allOMEs/06_08_18/OME/src/perl2/mod_perl_test.pl line 6.</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|Use of uninitialized value in print at</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|/home/bernd/allOMEs/06_08_18/OME/src/perl2/mod_perl_test.pl line 6.</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|[Fri Sep 08 09:31:22 2006] [error] [client 127.0.0.1] In PID 10585,
Error</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|calling OMEIS: Method parameter missing</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|[Fri Sep 08 09:31:26 2006] [error] [client 127.0.0.1] In PID 10601,
Error</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|calling OMEIS: Method parameter missing</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|[Fri Sep 08 09:31:44 2006] [notice] SIGHUP received. Attempting
to restart</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|[Fri Sep 08 09:31:44 2006] [warn] The ScriptAlias directive in</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|/OME/conf/httpd2.omeis-dev.conf at line 2 will probably never match
because</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|it overlaps an</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>| earlier ScriptAlias.</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|Use of uninitialized value in concatenation (.) or string at</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|/home/bernd/allOMEs/06_08_18/OME/src/perl2/OME/Install/ApacheConfigTask.pm</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|line 75.</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|Processing OME-startup.pl</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|DBD::Pg::st execute failed: ERROR: permission denied for
relation</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|experimenters</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|Tring to get a session as the Apache user...</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|Pre-loading SemanticTypes...</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|WARNING: Explicit deletion of OME::Session at /OME/conf/OME-startup.pl
line</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|76</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|OME::Session __destroySession: $self->__destroySession();</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>| at /OME/conf/OME-startup.pl line 76</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|Pre-loading classes for OME::Web...</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|[Fri Sep 08 09:31:47 2006] [notice] Digest: generating secret for
digest</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|authentication ...</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|[Fri Sep 08 09:31:47 2006] [notice] Digest: done</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|[Fri Sep 08 09:31:47 2006] [notice] LDAP: Built with OpenLDAP LDAP SDK</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|[Fri Sep 08 09:31:47 2006] [notice] LDAP: SSL support unavailable</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|[Fri Sep 08 09:31:48 2006] [notice] mod_python: Creating 4 session
mutexes</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|based on 150 max processes and 0 max threads.</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|[Fri Sep 08 09:31:48 2006] [notice] Apache/2.0.54 (Fedora) configured
--</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|resuming normal operations</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>||-----Original Message-----</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>||From: ctrueden.wisc@gmail.com [mailto:ctrueden.wisc@gmail.com] On
Behalf</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|Of</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>||Curtis Rueden</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>||Sent: Friday, September 08, 2006 9:40 AM</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>||To: Bernd Jagla</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>||Cc: ome-devel@lists.openmicroscopy.org.uk</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>||Subject: Re: [ome-devel] image display problem</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>||</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>||Hi Bernd,</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>||You could try reading the binary .ome files with VisBio from disk, to
see</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>||how things look.</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>||-Curtis</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>||</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>||</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>||On 9/7/06, Bernd Jagla < baj2107@columbia.edu</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|<mailto:baj2107@columbia.edu></span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>||> wrote:</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>||</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|| Hi there,</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>||</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>||</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>||</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|| I managed to get the images from the INCell
imported again with the</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>||new version of OME. The images are in OMEIS (verified). They 16 bit
Tiffs.</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>||</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|| The problem I have is that the images are not
displayed on the</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|screen.</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>||They cannot be exported to VisBio. I get an XML from the download
with</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|some</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>||binary data but can't confirm that this is what I want since I don't
know</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>||how to read them. I believe that the attached error log has something
to</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|do</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>||with this. I couldn't see anything interesting in the http error
logs.</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>||</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>||</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>||</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|| Please advise where look for possible solutions.</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>||</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>||</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>||</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|| Thanks,</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>||</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>||</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>||</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|| Bernd</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>||</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>||</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|| _______________________________________________</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|| ome-devel mailing list</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|| ome-devel@lists.openmicroscopy.org.uk</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|| http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>||</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>||</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>||</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>||</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>||</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|_______________________________________________</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|ome-devel mailing list</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|ome-devel@lists.openmicroscopy.org.uk</span></font></p>
<p class=MsoPlainText><font size=2 face="Courier New"><span style='font-size:
10.0pt'>|http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel</span></font></p>
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