[ome-users] (no subject)
Caterina Strambio De Castillia
strambc at mail.rockefeller.edu
Tue Apr 7 14:25:54 BST 2009
Hi Paulo
thank you for your reply and help.
As far as fixing my .lif import bug, I am not a developer (yet) and I
cannot think of solving it myself. I will have to rely on the OMERO
developers for this one.
As far as the more general .lif handling by OMERO, your post raises
two interesting points:
1) the .lif file is actually more like a directory file with multiple
"acquisitions" stored into it (each of which could be composed of
several actual image-plane files).
The ability for OMERO to sort through each "acquisition" and import
it as a separate, correctly named, OMERO-image would actually be
quite critical even though I am not sure how easy it is to implement.
It is clear though that with heavy SP5 usage users would be
discouraged from using OMERO if they have to go through renaming
their files once they have been imported into OMERO. I have found
myself in that position when importing into imageJ and it is really
hard especially because one looses all tracks of which image is which
without a meaningful file name matched with each image.
So solving this problem will be critical.
One possible way to implement would be to treat each .lif file at the
Project level with each "acquisition" stored as an image inside the
Project.
2) A related issue, did you notice if the metadata was imported
correctly for each "acquisition" in the .lif file?
In other words, did each image imported into OMERO have its own set
of correct metadata (some of the metadata would be shared, other such
as the specifics of each acquisition, would be clearly different).
Thank you for your imput
CIAO
Caterina
> 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
> > $4.doWork(MetadataStoreI.java:144)
> > at
> > sun.reflect.GeneratedMethodAccessor526.invoke(Unknown Source)
> > at
> > sun.reflect.DelegatingMethodAccessorImpl.invoke
> > (DelegatingMethodAccessorImpl.java:25)
> > at java.lang.reflect.Method.invoke
> > (Method.java:585)
> > at
> >
> org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflectio
> n(
> > AopUtils.java:310)
> > at
> >
> org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoi
> np
> > oint(ReflectiveMethodInvocation.java:182)
> > at
> > org.springframework.aop.framework.ReflectiveMethodInvocation.proceed
> > (ReflectiveMethodInvocation.java:149)
> > at ome.services.util.Executor$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.inv
> ok
> > 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
> > $4.doWork(MetadataStoreI.java:144)
> > at
> > sun.reflect.GeneratedMethodAccessor526.invoke(Unknown Source)
> > at
> > sun.reflect.DelegatingMethodAccessorImpl.invoke
> > (DelegatingMethodAccessorImpl.java:25)
> > at java.lang.reflect.Method.invoke
> > (Method.java:585)
> > at
> >
> org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflectio
> n(
> > AopUtils.java:310)
> > at
> >
> org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoi
> np
> > oint(ReflectiveMethodInvocation.java:182)
> > at
> > org.springframework.aop.framework.ReflectiveMethodInvocation.proceed
> > (ReflectiveMethodInvocation.java:149)
> > at ome.services.util.Executor$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.inv
> ok
> > 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
>
>
More information about the ome-users
mailing list