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Curated metadata for all studies published in the Image Data Resource
https://idr.openmicroscopy.org
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idr0012 plates, Row C images have sizeZ=3 sizeC=1 instead of sizeZ=1 sizeC=3 #693

Open will-moore opened 5 months ago

will-moore commented 5 months ago

For all plates in idr0012, the Row C thumbnails appear greyscale and the images are not viewable: They have 1 Channel and sizeZ=3, instead of a single Z - 3-Channel as for the rest of the Images on each Plate.

E.g first Row C image of first plate: https://idr.openmicroscopy.org/webclient/?show=image-1811462

On idr-testing omeroreadwrite, trying to render tiles, e.g. http://localhost:1080/webgateway/render_image_region/1811462/1/0/?tile=1,0,0,512,512

Gives this in Blitz log

2024-04-19 08:47:19,676 INFO  [        ome.services.util.ServiceHandler] (Server-118)  Rslt:    null
2024-04-19 08:47:19,677 INFO  [        ome.services.util.ServiceHandler] (Server-142)  Meth:    interface omeis.providers.re.RenderingEngine.renderCompressed
2024-04-19 08:47:19,677 INFO  [        ome.services.util.ServiceHandler] (Server-142)  Args:    [Type: XY, z=1, t=0; Region: x=0 y=0 width=512 height=512, renderShapes=false, shapeIds=[]]
2024-04-19 08:47:19,677 INFO  [             omeis.providers.re.Renderer] (Server-142) Using: 'omeis.providers.re.GreyScaleStrategy' rendering strategy.
2024-04-19 08:47:19,678 INFO  [                 org.perf4j.TimingLogger] (Server-142) start[1713516439677] time[0] tag[omero.call.exception]
2024-04-19 08:47:19,679 WARN  [        ome.services.util.ServiceHandler] (Server-142) IllegalArgumentException thrown.

java.lang.IllegalArgumentException: Invalid Z index: 1/1
    at loci.formats.FormatTools.getIndex(FormatTools.java:474)
    at loci.formats.FormatTools.getIndex(FormatTools.java:409)
    at loci.formats.ChannelSeparator.getIndex(ChannelSeparator.java:266)
    at loci.formats.ReaderWrapper.getIndex(ReaderWrapper.java:498)
    at ome.io.bioformats.BfPixelsWrapper.getTile(BfPixelsWrapper.java:350)
    at ome.io.bioformats.BfPixelBuffer.getTile(BfPixelBuffer.java:499)
    at omeis.providers.re.data.PlaneFactory.createPlane(PlaneFactory.java:193)
    at omeis.providers.re.GreyScaleStrategy.renderAsPackedInt(GreyScaleStrategy.java:153)
    at omeis.providers.re.Renderer.renderAsPackedInt(Renderer.java:558)
    at ome.services.RenderingBean.renderAsPackedInt(RenderingBean.java:512)
    at ome.services.RenderingBean.renderCompressed(RenderingBean.java:542)
    at jdk.internal.reflect.GeneratedMethodAccessor1485.invoke(Unknown Source)
    at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.base/java.lang.reflect.Method.invoke(Method.java:566)
    at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)
    at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)

Rendering the first plane (Z=0, T=0) works OK: https://idr.openmicroscopy.org/webclient/render_image/1811462/0/0/

I can't see any pixel data for channels 2 and 3 (all black) http://localhost:1080/webgateway/render_image/1811462/0/0/?c=2|0:5$fff,3|0:5$fff