Task #11166 (closed)
Opened 11 years ago
Closed 10 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 11 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 11 years ago by mlinkert
- Milestone changed from Testing and Docs to OMERO-4.4.x
- Sprint Testing and Docs (1) deleted
comment:3 Changed 10 years ago by mlinkert
- Milestone changed from 5.x to 5.0.2
comment:4 Changed 10 years ago by mlinkert
comment:5 Changed 10 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.
Note: See
TracTickets for help on using
tickets.
You may also have a look at Agilo extensions to the ticket.
The stored PinholeSize and RefractiveIndex for Mouse_kidney_VivaTome-1chTZ.czi really are NaN - see the original metadata table and Zen 2012.