[ome-users] Importing LEICA .lif files into OMERO beta4
Paulo Almeida
palmeida at igc.gulbenkian.pt
Thu Apr 2 16:18:00 BST 2009
Hi Caterina,
For what it's worth, I imported some Leica .lif files successfully (probably
from an SP5 confocal, but I'm not sure). I grabbed the metadata of one of
them in case it may be useful to determine why yours fail:
Dimensions (XY) [px] 512 x 512
Pixel size (XYZ) [µm] 0.16017677 x 0.16017677 x 0.50020266
Z-sections 39
Timepoints 1
I do have a problem. I imported several .lif files and they were all named
Series001 in Omero (actually, Omero generated a Series001 and a
Series001_ProjMax001 for each of them), which I suspect won't be convenient
for researchers. I don't know if that's a problem with my files, but I am
going to talk with a user this afternoon (she talked to Jean Marie when he
was here) and see how it works with hers.
Regards,
Paulo
On Thursday 02 April 2009 15:06:47 Caterina Strambio De Castillia wrote:
> Dear OMERO community,
>
> I have had problems importing Leica .lif files into the OMERO beta4
> DB using the latest release of the OMERO.importer.
>
> The error message I got is reported at the bottom of the message.
>
> Please advise
>
> Best
>
> Caterina
>
>
>
>
> ____________
>
> java.lang.RuntimeException: omero.InternalException
> serverStackTrace = "ome.conditions.InternalException: Wrapped
> Exception: (java.lang.IndexOutOfBoundsException):
> Index: 3, Size: 3
> at java.util.ArrayList.RangeCheck
> (ArrayList.java:546)
> at java.util.ArrayList.get(ArrayList.java:321)
> at ome.model.core.Pixels.getChannel
> (Pixels.java:1261)
> at ome.formats.OMEROMetadataStore.getChannel
> (OMEROMetadataStore.java:717)
> at ome.formats.OMEROMetadataStore.handle
> (OMEROMetadataStore.java:359)
> at
> ome.formats.OMEROMetadataStore.updateObject(OMEROMetadataStore.java:138)
> at ome.services.blitz.impl.MetadataStoreI
> $4.doWork(MetadataStoreI.java:144)
> at
> sun.reflect.GeneratedMethodAccessor526.invoke(Unknown Source)
> at
> sun.reflect.DelegatingMethodAccessorImpl.invoke
> (DelegatingMethodAccessorImpl.java:25)
> at java.lang.reflect.Method.invoke
> (Method.java:585)
> at
> org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(
> AopUtils.java:310)
> at
> org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinp
> oint(ReflectiveMethodInvocation.java:182)
> at
> org.springframework.aop.framework.ReflectiveMethodInvocation.proceed
> (ReflectiveMethodInvocation.java:149)
> at ome.services.util.Executor$Impl
> $Interceptor.invoke(Executor.java:377)
> at
> org.springframework.aop.framework.ReflectiveMethodInvocation.proceed
> (ReflectiveMethodInvocation.java:171)
> at ome.security.basic.EventHandler.invoke
> (EventHandler.java:116)
> at
> org.springframework.aop.framework.ReflectiveMethodInvocation.proceed
> (ReflectiveMethodInvocation.java:171)
> at
> org.springframework.orm.hibernate3.HibernateInterceptor.invoke
> (HibernateInterceptor.java:111)
> at
> org.springframework.aop.framework.ReflectiveMethodInvocation.proceed
> (ReflectiveMethodInvocation.java:171)
> at
> org.springframework.transaction.interceptor.TransactionInterceptor.invok
> e(TransactionInterceptor.java:106)
> at
> org.springframework.aop.framework.ReflectiveMethodInvocation.proceed
> (ReflectiveMethodInvocation.java:171)
> at ome.tools.hibernate.ProxyCleanupFilter
> $Interceptor.invoke(ProxyCleanupFilter.java:169)
> at
> org.springframework.aop.framework.ReflectiveMethodInvocation.proceed
> (ReflectiveMethodInvocation.java:171)
> at ome.services.util.ServiceHandler.invoke
> (ServiceHandler.java:97)
> at
> org.springframework.aop.framework.ReflectiveMethodInvocation.proceed
> (ReflectiveMethodInvocation.java:171)
> at
> org.springframework.aop.framework.JdkDynamicAopProxy.invoke
> (JdkDynamicAopProxy.java:204)
> at $Proxy55.doWork(Unknown Source)
> at ome.services.util.Executor$Impl.execute
> (Executor.java:307)
> at ome.services.throttling.Adapter.run
> (Adapter.java:50)
> at
> ome.services.throttling.InThreadThrottlingStrategy.runnableCall
> (InThreadThrottlingStrategy.java:51)
> at
> ome.services.blitz.impl.AbstractAmdServant.runnableCall
> (AbstractAmdServant.java:128)
> at
> ome.services.blitz.impl.MetadataStoreI.updateObjects_async
> (MetadataStoreI.java:129)
> at
> omero.api._MetadataStoreTie.updateObjects_async
> (_MetadataStoreTie.java:85)
> at
> omero.api._MetadataStoreDisp.___updateObjects(_MetadataStoreDisp.java:
> 166)
> at omero.api._MetadataStoreDisp.__dispatch
> (_MetadataStoreDisp.java:308)
> at IceInternal.Incoming.invoke
> (Incoming.java:166)
> at Ice.ConnectionI.invokeAll
> (ConnectionI.java:2045)
> at Ice.ConnectionI.message(ConnectionI.java:
> 977)
> at IceInternal.ThreadPool.run
> (ThreadPool.java:575)
> at IceInternal.ThreadPool.access$100
> (ThreadPool.java:12)
> at IceInternal.ThreadPool
> $EventHandlerThread.run(ThreadPool.java:951)
> "
> serverExceptionClass = "ome.conditions.InternalException"
> message = " Wrapped Exception:
> (java.lang.IndexOutOfBoundsException):
> Index: 3, Size: 3"
> at ome.formats.OMEROMetadataStoreClient.saveToDB
> (OMEROMetadataStoreClient.java:2247)
> at ome.formats.importer.ImportLibrary.importMetadata
> (ImportLibrary.java:239)
> at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:
> 328)
> at ome.formats.importer.ImportHandler.importImages
> (ImportHandler.java:181)
> at ome.formats.importer.ImportHandler.access$0(ImportHandler.java:107)
> at ome.formats.importer.ImportHandler$1.run(ImportHandler.java:88)
> Caused by: omero.InternalException
> serverStackTrace = "ome.conditions.InternalException: Wrapped
> Exception: (java.lang.IndexOutOfBoundsException):
> Index: 3, Size: 3
> at java.util.ArrayList.RangeCheck
> (ArrayList.java:546)
> at java.util.ArrayList.get(ArrayList.java:321)
> at ome.model.core.Pixels.getChannel
> (Pixels.java:1261)
> at ome.formats.OMEROMetadataStore.getChannel
> (OMEROMetadataStore.java:717)
> at ome.formats.OMEROMetadataStore.handle
> (OMEROMetadataStore.java:359)
> at
> ome.formats.OMEROMetadataStore.updateObject(OMEROMetadataStore.java:138)
> at ome.services.blitz.impl.MetadataStoreI
> $4.doWork(MetadataStoreI.java:144)
> at
> sun.reflect.GeneratedMethodAccessor526.invoke(Unknown Source)
> at
> sun.reflect.DelegatingMethodAccessorImpl.invoke
> (DelegatingMethodAccessorImpl.java:25)
> at java.lang.reflect.Method.invoke
> (Method.java:585)
> at
> org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(
> AopUtils.java:310)
> at
> org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinp
> oint(ReflectiveMethodInvocation.java:182)
> at
> org.springframework.aop.framework.ReflectiveMethodInvocation.proceed
> (ReflectiveMethodInvocation.java:149)
> at ome.services.util.Executor$Impl
> $Interceptor.invoke(Executor.java:377)
> at
> org.springframework.aop.framework.ReflectiveMethodInvocation.proceed
> (ReflectiveMethodInvocation.java:171)
> at ome.security.basic.EventHandler.invoke
> (EventHandler.java:116)
> at
> org.springframework.aop.framework.ReflectiveMethodInvocation.proceed
> (ReflectiveMethodInvocation.java:171)
> at
> org.springframework.orm.hibernate3.HibernateInterceptor.invoke
> (HibernateInterceptor.java:111)
> at
> org.springframework.aop.framework.ReflectiveMethodInvocation.proceed
> (ReflectiveMethodInvocation.java:171)
> at
> org.springframework.transaction.interceptor.TransactionInterceptor.invok
> e(TransactionInterceptor.java:106)
> at
> org.springframework.aop.framework.ReflectiveMethodInvocation.proceed
> (ReflectiveMethodInvocation.java:171)
> at ome.tools.hibernate.ProxyCleanupFilter
> $Interceptor.invoke(ProxyCleanupFilter.java:169)
> at
> org.springframework.aop.framework.ReflectiveMethodInvocation.proceed
> (ReflectiveMethodInvocation.java:171)
> at ome.services.util.ServiceHandler.invoke
> (ServiceHandler.java:97)
> at
> org.springframework.aop.framework.ReflectiveMethodInvocation.proceed
> (ReflectiveMethodInvocation.java:171)
> at
> org.springframework.aop.framework.JdkDynamicAopProxy.invoke
> (JdkDynamicAopProxy.java:204)
> at $Proxy55.doWork(Unknown Source)
> at ome.services.util.Executor$Impl.execute
> (Executor.java:307)
> at ome.services.throttling.Adapter.run
> (Adapter.java:50)
> at
> ome.services.throttling.InThreadThrottlingStrategy.runnableCall
> (InThreadThrottlingStrategy.java:51)
> at
> ome.services.blitz.impl.AbstractAmdServant.runnableCall
> (AbstractAmdServant.java:128)
> at
> ome.services.blitz.impl.MetadataStoreI.updateObjects_async
> (MetadataStoreI.java:129)
> at
> omero.api._MetadataStoreTie.updateObjects_async
> (_MetadataStoreTie.java:85)
> at
> omero.api._MetadataStoreDisp.___updateObjects(_MetadataStoreDisp.java:
> 166)
> at omero.api._MetadataStoreDisp.__dispatch
> (_MetadataStoreDisp.java:308)
> at IceInternal.Incoming.invoke
> (Incoming.java:166)
> at Ice.ConnectionI.invokeAll
> (ConnectionI.java:2045)
> at Ice.ConnectionI.message(ConnectionI.java:
> 977)
> at IceInternal.ThreadPool.run
> (ThreadPool.java:575)
> at IceInternal.ThreadPool.access$100
> (ThreadPool.java:12)
> at IceInternal.ThreadPool
> $EventHandlerThread.run(ThreadPool.java:951)
> "
> serverExceptionClass = "ome.conditions.InternalException"
> message = " Wrapped Exception:
> (java.lang.IndexOutOfBoundsException):
> Index: 3, Size: 3"
> at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native
> Method)
> at sun.reflect.NativeConstructorAccessorImpl.newInstance
> (NativeConstructorAccessorImpl.java:39)
> at sun.reflect.DelegatingConstructorAccessorImpl.newInstance
> (DelegatingConstructorAccessorImpl.java:27)
> at java.lang.reflect.Constructor.newInstance(Constructor.java:494)
> at java.lang.Class.newInstance0(Class.java:350)
> at java.lang.Class.newInstance(Class.java:303)
> at IceInternal.BasicStream$DynamicUserExceptionFactory.createAndThrow
> (BasicStream.java:2127)
> at IceInternal.BasicStream.throwException(BasicStream.java:1541)
> at IceInternal.Outgoing.throwUserException(Outgoing.java:442)
> at omero.api._MetadataStoreDelM.updateObjects
> (_MetadataStoreDelM.java:177)
> at omero.api.MetadataStorePrxHelper.updateObjects
> (MetadataStorePrxHelper.java:254)
> at omero.api.MetadataStorePrxHelper.updateObjects
> (MetadataStorePrxHelper.java:226)
> at ome.formats.OMEROMetadataStoreClient.saveToDB
> (OMEROMetadataStoreClient.java:2230)
> ... 5 more
>
>
>
>
> ____________________________
> Caterina Strambio De Castillia, Dottore in Biologia, PhD
>
> Biologiste 2 - Senior Research Scientist
> Laboratory of Viral replication, pathogenesis, and immunity
> http://www.mimo.unige.ch/luban_lab/
>
> Department of Microbiology and Molecular Medicine
> University of Geneva
> 1 Rue Michel Servet
> CH-1211 Geneva 4
> Switzerland
>
> Phone: +41-22-379-5720
> Fax: +41-22-379-5702
>
> ****
> Visiting Fellow
> Laboratory of Cellular and Structural Biology
> http://www.rockefeller.edu/labheads/rout/research_project_3.php
>
> The Rockefeller University
> 1230 York Avenue
> New York NY 10065
> ______________________________
> Caterina Strambio De Castillia
> via Monte Crenone 1
> 6500 Bellinzona
> Svizzera
>
> +41 91 8252701
> +41 78 7367537
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