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Task #13270 (new)

Opened 8 years ago

Last modified 6 years ago

Bug: images not matching with well placement

Reported by: mtbcarroll Owned by: dgault
Priority: major Milestone: Unscheduled
Component: Bio-Formats Version: n.a.
Keywords: OMEXMLReader Cc: bf@…
Resources: n.a. Referenced By: n.a.
References: n.a. Remaining Time: n.a.
Sprint: n.a.


From inspecting the simple OME-XML for the attached plate one would expect the field names to describe their placement on the plate. However, if I import it and work around #13269 then the images aren't at all where I'd expect. Am I missing something simple?

Attachments (1)

problem-plate.ome.xml (5.1 KB) - added by mtbcarroll 8 years ago.
plate to import

Download all attachments as: .zip

Change History (7)

Changed 8 years ago by mtbcarroll

plate to import

comment:1 Changed 8 years ago by mtbcarroll

  • Version OMERO-5.2.0 deleted

comment:2 Changed 8 years ago by mtbcarroll

  • Cc bf@… added; ux@… removed
  • Component changed from Import to Bio-Formats
  • Keywords OMEXMLReader added

This mangling looks like it happens at the Bio-Formats level: compare the mapping from row & column to image name before and after the attached OME-XML goes through showinf -omexml. (If this is user error, please just point me to the doc I missed!)

comment:3 Changed 8 years ago by mtbcarroll

Ha, and it seems to work much better if I decrement the image numbers by 1 in both their actual IDs and the ImageRefs to them (leaving the abovementioned mapping unchanged).

Last edited 8 years ago by mtbcarroll (previous) (diff)

comment:4 Changed 7 years ago by mtbcarroll

  • Owner changed from jburel to dgault

comment:5 Changed 6 years ago by mtbcarroll

Just confirmed on current OMERO develop which I'm guessing is at least BF 5.7.3.

comment:6 Changed 6 years ago by mtbcarroll

I just ran into this bug again with problem-name.ome.xml from https://trello.com/c/fbJ6jMvZ/399-ignores-plate-names-in-naming-fields -

mtbc@ls28101:/tmp$ < problem-name.ome.xml grep Image:
        <ImageRef ID="Image:1"/>
        <ImageRef ID="Image:2"/>
  <Image ID="Image:1" Name="First Image">
  <Image ID="Image:2" Name="Second Image">
mtbc@ls28101:/tmp$ showinf -nopix -omexml-only problem-name.ome.xml | grep Image:
            <ImageRef ID="Image:1"/>
            <ImageRef ID="Image:1"/>
   <Image ID="Image:0" Name="First Image">
   <Image ID="Image:1" Name="Second Image">
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