Unable to load DM3 file into OMERO 5.0.0

[rob.pumphrey]

Hi,

I have a DM3 file that I can load into OMERO 5.0.0 (and 4.4.8), but I am unable to view the image. The meta data is readable, but the Full Viewer (launched from the web UI) shows the message:
Min: 1.090737312E9 Max: 65535.0 Interval not supported.

I am able to view the DM3 file in ImageJ, and export a TIFF from ImageJ. The TIFF, when loaded into OMERO, shows an entirely black image.

I am not an expert in this area and I would appreciate suggestions as to how I can progress from here.

Thanks

Rob

[bramalingam]

Hi,

If the image was uploaded recently, there is a chance that the tiles are still being generated (shouldn't take more than a couple of hours). But if the error persists, it would be best if you could send the following file,

$OMERO_HOME/var/log/PixelData-0.log

Best,
Balaji

[rob.pumphrey]

Balaji,

Thank you for your response.

I am pretty sure the file has been fully ingested.

The relevant content of the Pixel log are:

Code: Select all

2014-03-13 16:26:17,553 INFO  [             ome.io.nio.FilePathResolver] (3-thread-1) Metadata only file, resulting path: /home/ome/apps/OMERO.data/ManagedRepository/root_0/2014-03/13/16-25-41.795/upload_tmpfile_13947279205645335469806574571870.tmp
2014-03-13 16:26:42,720 INFO  [                ome.io.nio.PixelsService] (3-thread-1) Creating BfPixelBuffer: /home/ome/apps/OMERO.data/ManagedRepository/root_0/2014-03/13/16-25-41.795/upload_tmpfile_13947279205645335469806574571870.tmp Series: 0
2014-03-13 16:26:42,734 INFO  [                ome.io.nio.PixelsService] (3-thread-1) Destination pyramid tile size: java.awt.Dimension[width=256,height=256]
2014-03-13 16:26:42,737 INFO  [                ome.io.nio.PixelsService] (3-thread-1) Pyramid creation for Pixels:202 1/176 (0%).
2014-03-13 16:26:46,224 INFO  [                ome.io.nio.PixelsService] (3-thread-1) Pyramid creation for Pixels:202 18/176 (9%).
2014-03-13 16:26:49,249 INFO  [                ome.io.nio.PixelsService] (3-thread-1) Pyramid creation for Pixels:202 35/176 (19%).
2014-03-13 16:26:52,415 INFO  [                ome.io.nio.PixelsService] (3-thread-1) Pyramid creation for Pixels:202 52/176 (28%).
2014-03-13 16:26:55,633 INFO  [                ome.io.nio.PixelsService] (3-thread-1) Pyramid creation for Pixels:202 69/176 (38%).
2014-03-13 16:26:58,687 INFO  [                ome.io.nio.PixelsService] (3-thread-1) Pyramid creation for Pixels:202 86/176 (48%).
2014-03-13 16:27:01,406 INFO  [                ome.io.nio.PixelsService] (3-thread-1) Pyramid creation for Pixels:202 103/176 (57%).
2014-03-13 16:27:03,958 INFO  [                ome.io.nio.PixelsService] (3-thread-1) Pyramid creation for Pixels:202 120/176 (67%).
2014-03-13 16:27:06,451 INFO  [                ome.io.nio.PixelsService] (3-thread-1) Pyramid creation for Pixels:202 137/176 (77%).
2014-03-13 16:27:08,957 INFO  [                ome.io.nio.PixelsService] (3-thread-1) Pyramid creation for Pixels:202 154/176 (86%).
2014-03-13 16:27:10,609 INFO  [                ome.io.nio.PixelsService] (3-thread-1) Pyramid creation for Pixels:202 171/176 (96%).
2014-03-13 16:27:11,049 INFO  [                ome.io.nio.PixelsService] (3-thread-1) SUCCESS -- Pyramid created for pixels id:202
2014-03-13 16:27:11,072 INFO  [       loci.formats.in.MinimalTiffReader] (3-thread-1) Reading IFDs
2014-03-13 16:27:11,075 INFO  [       loci.formats.in.MinimalTiffReader] (3-thread-1) Populating metadata
2014-03-13 16:27:11,192 INFO  [              loci.formats.in.TiffReader] (3-thread-1) Checking comment style
2014-03-13 16:27:11,198 INFO  [          loci.formats.in.BaseTiffReader] (3-thread-1) Populating OME metadata
2014-03-13 16:27:13,114 INFO  [ ome.services.pixeldata.PixelDataHandler] (3-thread-1) Added StatsInfo:251 for ome.model.core.Channel:Id_202 - C:0 Max:1.165283229E9 Min:1.090737312E9
2014-03-13 16:27:13,115 INFO  [ ome.services.pixeldata.PixelDataHandler] (3-thread-1) HANDLED EventLog:4381(entityId=202) [63345 ms.]
2014-03-13 16:27:13,118 ERROR [        ome.services.util.ServiceHandler] (3-thread-1) Method interface ome.services.util.Executor$Work.doWork invocation took 65052
2014-03-13 16:27:13,311 INFO  [             ome.io.nio.FilePathResolver] (3-thread-3) Metadata only file, resulting path: /home/ome/apps/OMERO.data/ManagedRepository/root_0/2014-03/13/16-25-41.795/upload_tmpfile_13947279205645335469806574571870.tmp
2014-03-13 16:27:13,317 ERROR [        ome.services.util.ServiceHandler] (3-thread-3) Method interface ome.services.util.Executor$Work.doWork invocation took 63546
2014-03-13 16:27:13,425 INFO  [             ome.io.nio.FilePathResolver] (3-thread-5) Metadata only file, resulting path: /home/ome/apps/OMERO.data/ManagedRepository/root_0/2014-03/13/16-25-41.795/upload_tmpfile_13947279205645335469806574571870.tmp
2014-03-13 16:27:13,476 INFO  [             ome.io.nio.FilePathResolver] (3-thread-1) Metadata only file, resulting path: /home/ome/apps/OMERO.data/ManagedRepository/root_0/2014-03/13/16-25-41.795/upload_tmpfile_13947279205645335469806574571870.tmp
2014-03-13 16:27:16,034 INFO  [             ome.io.nio.FilePathResolver] (3-thread-5) Metadata only file, resulting path: /home/ome/apps/OMERO.data/ManagedRepository/root_0/2014-03/13/16-25-41.795/upload_tmpfile_13947279205645335469806574571870.tmp
2014-03-13 16:27:16,141 INFO  [             ome.io.nio.FilePathResolver] (3-thread-4) Metadata only file, resulting path: /home/ome/apps/OMERO.data/ManagedRepository/root_0/2014-03/13/16-25-41.795/upload_tmpfile_13947279205645335469806574571870.tmp


When I try to preview the image, the stacktrace in OMEROWeb.log is

Code: Select all

2014-03-18 08:45:52,945 ERROR [                           omero.gateway] (proc.09397) getThumbnail:6414 Traceback (most recent call last):
  File "/home/ome/installations/OMERO/lib/python/omero/gateway/__init__.py", line 6409, in getThumbnail
    rv = thumb(*args)
  File "/home/ome/installations/OMERO/lib/python/omero/gateway/__init__.py", line 3541, in __call__
    return self.handle_exception(e, *args, **kwargs)
  File "/home/ome/installations/OMERO/lib/python/omeroweb/webclient/webclient_gateway.py", line 1894, in handle_exception
    e, *args, **kwargs)
  File "/home/ome/installations/OMERO/lib/python/omero/gateway/__init__.py", line 3538, in __call__
    return self.f(*args, **kwargs)
  File "/home/ome/installations/OMERO/lib/python/omero_api_ThumbnailStore_ice.py", line 215, in getThumbnailByLongestSide
    return _M_omero.api.ThumbnailStore._op_getThumbnailByLongestSide.invoke(self, ((size, ), _ctx))
ApiUsageException: exception ::omero::ApiUsageException
{
    serverStackTrace = ome.conditions.ApiUsageException: Min: 1.090737312E9 Max: 65535.0 Interval not supported
        at omeis.providers.re.quantum.QuantumStrategy.verifyInterval(QuantumStrategy.java:181)
        at omeis.providers.re.quantum.QuantumStrategy.setExtent(QuantumStrategy.java:294)
        at omeis.providers.re.QuantumManager.initStrategies(QuantumManager.java:114)
        at omeis.providers.re.Renderer.<init>(Renderer.java:352)
        at ome.services.ThumbnailBean.load(ThumbnailBean.java:341)
        at ome.services.ThumbnailBean.errorIfInvalidState(ThumbnailBean.java:692)
        at ome.services.ThumbnailBean.createScaledImage(ThumbnailBean.java:562)
        at ome.services.ThumbnailBean._createThumbnail(ThumbnailBean.java:818)
        at ome.services.ThumbnailBean.retrieveThumbnail(ThumbnailBean.java:1061)
        at ome.services.ThumbnailBean.retrieveThumbnailAndUpdateMetadata(ThumbnailBean.java:1016)
        at ome.services.ThumbnailBean.getThumbnailByLongestSide(ThumbnailBean.java:1094)
        at sun.reflect.GeneratedMethodAccessor1188.invoke(Unknown Source)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:606)
        at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307)
        at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183)
        at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150)
        at ome.security.basic.EventHandler.invoke(EventHandler.java:154)
        at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
        at ome.tools.hibernate.SessionHandler.doStateful(SessionHandler.java:218)
        at ome.tools.hibernate.SessionHandler.invoke(SessionHandler.java:202)
        at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)


Regards

Rob

[wmoore]

Hi Rob,

Please can you upload an example file at http://qa.openmicroscopy.org.uk/qa/upload/ and we'll take a look.

Thanks!

Will.

[wmoore]

Having read your error again, it seems likely that the issue is a long-standing known issue with handling very large pixel ranges: http://trac.openmicroscopy.org.uk/ome/ticket/3256

Unfortunately the rendering engine is highly optimised for smaller ranges and it will take some effort to address these issues, although it is on our TODO list.

[rob.pumphrey]

Thanks for the replies.

I have managed to work around this problem by opening the 32bit DM3 file in ImageJ, setting the image type to 16 bit and exporting as a TIFF.