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Task #11166 (closed)

Opened 7 years ago

Closed 6 years ago

Zeiss CZI metadata polishing

Reported by: mlinkert Owned by: mlinkert
Priority: minor Milestone: 5.0.2
Component: Bio-Formats Version: 4.4.8
Keywords: n.a. Cc: rleigh
Resources: n.a. Referenced By: n.a.
References: n.a. Remaining Time: n.a.
Sprint: n.a.

Description

From https://github.com/openmicroscopy/bioformats/pull/562:

Some minor issues with OME-XML consistency/correctness:

BPAE-cells_mitosis_3chZ(WF).czi ome-xml has FilterSet and Dichroic elements but these are not linked to internally in the ome-xml structure other than from some of the original metadata elements (and these are not true refs).

Mouse_kidney_VivaTome-1chTZ.czi: RefractiveIndex is "NaN" which isn't looking right. Likewise for PinholeSize.

Testimage_SYS169_CZMicroscopy.czi: LensNA is "-1.0". While this is possible for some materials, it's not that common in microscope objectives TTBOMK unless this is some fancy system with superlenses, so I just wanted to query its correctness. Same issues with FilterSet/Filter/Dichroic as above being defined but not linked.

Not related directly to the PR, but the space wastage from the XMLAnnotation blocks is far too much when you end up with several thousand annotations. It would be nice if key-value annotations could be stored in a single block, maybe with a uniqueness constraint on the keys.

Change History (5)

comment:1 Changed 7 years ago by mlinkert

  • Milestone changed from Unscheduled to Testing
  • Sprint set to Testing and Docs (1)
  • Version set to 4.4.8

comment:2 Changed 7 years ago by mlinkert

  • Milestone changed from Testing and Docs to OMERO-4.4.x
  • Sprint Testing and Docs (1) deleted

comment:3 Changed 6 years ago by mlinkert

  • Milestone changed from 5.x to 5.0.2

comment:4 Changed 6 years ago by mlinkert

The stored PinholeSize and RefractiveIndex for Mouse_kidney_VivaTome-1chTZ.czi really are NaN - see the original metadata table and Zen 2012.

comment:5 Changed 6 years ago by mlinkert

  • Resolution set to fixed
  • Status changed from new to closed

Fixed with https://github.com/openmicroscopy/bioformats/pull/1078; email forthcoming on ome-users/ome-devel with details of how to try this out prior to 5.0.2.

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