Open Microscopy Environment

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

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

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

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.

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.

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.