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Task #12935 (closed)

Opened 9 years ago

Closed 7 years ago

Updates for Zen 2.1+ data

Reported by: mlinkert Owned by: mlinkert
Priority: critical Milestone: Unscheduled
Component: Bio-Formats Version: 5.1.2
Keywords: ZeissCZIReader Cc: nikolaus.ehrenfeuchter@…
Resources: n.a. Referenced By: https://trello.com/c/y6KpD3sU/4-czi-tickets
References: n.a. Remaining Time: n.a.
Sprint: n.a.

Description

We now have the Zen 2.1/CZI 1.1 specification and corresponding example files. See data in team/mlinkert/From_*/

It's not entirely clear from the specification version history what has changed, so we will need to go through this page by page to note any differences. It doesn't look like any new compression/pixel types were added, so this may be limited to updating for new and/or changed metadata.

We are starting to receive community feedback based on the latest version of Zen (e.g. ​https://github.com/openmicroscopy/bioformats/issues/1840), so it's clear that some things are different now.

I will update the ticket as the specification review progresses, and as we start to make updates for any differences.

Change History (9)

comment:1 Changed 9 years ago by jamoore

  • Milestone changed from 5.1.4 to B-F-5.1.4

Splitting 5.1.4 due to milestone decoupling

comment:2 Changed 9 years ago by sbesson

  • Milestone changed from B-F-5.1.4 to BF-5.1.5

comment:4 Changed 8 years ago by mlinkert

My plan is to get as far as I can with this before the end of March, as it ties in with ongoing work in ​https://github.com/openmicroscopy/bioformats/pull/2268 and ​https://trello.com/c/QD5C8GH1/105-multi-scene-czi-file-from-basel. I will likely close this ticket at that time, and open a separate card for each specific remaining task.

comment:5 Changed 8 years ago by mtbcarroll

  • Cc nikolaus.ehrenfeuchter@… added

comment:6 Changed 8 years ago by mlinkert

  • Summary changed from Updates for Zen 2.1 data to Updates for Zen 2.1+ data

See also ​https://github.com/openmicroscopy/bioformats/issues/2370; file is being uploaded to inbox/zeiss-czi/sebi06/.

comment:7 Changed 8 years ago by sbesson

  • Milestone changed from B-F-5.2.0 to Unscheduled
  • Referenced By set to https://trello.com/c/y6KpD3sU/4-czi-tickets

comment:8 Changed 7 years ago by mlinkert

Most of this data is now working fine when tested with 5.3.3, and is now added to the repository for regular testing with: ​https://github.com/openmicroscopy/data_repo_config/pull/174

The outstanding concrete issues are listed below and can be addressed independently or as one PR; most should not affect configurations.

  1. PALM files in the ZEN black dataset collection do not open correctly; all are added to ​https://trac.openmicroscopy.org/ome/ticket/12469 and do not need to be addressed here.
  1. some files have incorrect stage positions: 
zeiss-czi/zeiss/ZEN 2.1 black LSM 880 -May 2015/Fluo#1_ZEN2-1-Airyscan.czi
zeiss-czi/zeiss/ZEN 2.1 black LSM 880 -May 2015/Lambda1.czi
zeiss-czi/zeiss/ZEN 2.1 black LSM 880 -May 2015/LambdaImage.czi
zeiss-czi/zeiss/ZEN 2.1 black LSM 880 -May 2015/LambdaImage_Linear unmixing.czi
zeiss-czi/zeiss/ZEN 2.1 black LSM 880 -May 2015/LambdaImage_Spectral channel extraction2CHannel.czi
zeiss-czi/zeiss/ZEN 2.1 black LSM 880 -May 2015/LAmbda+Rand+Tpmt.czi
zeiss-czi/zeiss/ZEN 2.1 black LSM 880 -May 2015/MT-Tilescan2-3stitched.czi
zeiss-czi/zeiss/ZEN 2.1 black LSM 880 -May 2015/MT-Tilescan2-3unstitched.czi
zeiss-czi/zeiss/ZEN 2.1 black LSM 880 -May 2015/MT-ZStack5_Position4_Time3.czi
zeiss-czi/zeiss/ZEN 2.1 black LSM 880 -May 2015/OnlineFingerprinting_2Channel.czi
zeiss-czi/zeiss/ZEN 2.1 black LSM 880 -May 2015/SIM_nicht verrechnet.czi
zeiss-czi/zeiss/ZEN 2.1 black LSM 880 -May 2015/SIM_verrechnet.czi
zeiss-czi/zeiss/ZEN 2.1 black LSM 880 -May 2015/Tile4-4Zstack5_Gestitchen.czi
zeiss-czi/zeiss/ZEN 2.1 black LSM 880 -May 2015/TileZstack5_Nicht Gestitchen.czi
zeiss-czi/zeiss/ZEN 2.1 black LSM 880 -May 2015/Time_Bleaching_Marker_BleachROI.czi
zeiss-czi/zeiss/ZEN 2.1 black LSM 880 -May 2015/Timeserie_GraphikElemente.czi
zeiss-czi/zeiss/ZEN 2.1 black LSM 880 -May 2015/WF.czi
  1. some files have one or more incorrect detector gains: 
zeiss-czi/zeiss/ZEN 2.1 black LSM 880 -May 2015/5Positionen.czi
zeiss-czi/zeiss/ZEN 2.1 black LSM 880 -May 2015/channel_3.czi
zeiss-czi/zeiss/ZEN 2.1 black LSM 880 -May 2015/HDR_Illu.czi
zeiss-czi/zeiss/ZEN 2.1 black LSM 880 -May 2015/HDRsampling.czi
zeiss-czi/zeiss/ZEN 2.1 black LSM 880 -May 2015/LAmbda+Rand+Tpmt.czi
zeiss-czi/zeiss/ZEN 2.1 black LSM 880 -May 2015/MT-Tilescan2-3stitched.czi
zeiss-czi/zeiss/ZEN 2.1 black LSM 880 -May 2015/MT-Tilescan2-3unstitched.czi
zeiss-czi/zeiss/ZEN 2.1 black LSM 880 -May 2015/MT-ZStack5_Position4_Time3.czi
zeiss-czi/zeiss/ZEN 2.1 black LSM 880 -May 2015/SIM_nicht verrechnet.czi
zeiss-czi/zeiss/ZEN 2.1 black LSM 880 -May 2015/SIM_verrechnet.czi
zeiss-czi/zeiss/ZEN 2.1 black LSM 880 -May 2015/Tile4-4Zstack5_Gestitchen.czi
zeiss-czi/zeiss/ZEN 2.1 black LSM 880 -May 2015/TileZstack5_Nicht Gestitchen.czi
zeiss-czi/zeiss/ZEN 2.1 black LSM 880 -May 2015/Time_Bleaching_Marker_BleachROI.czi
zeiss-czi/zeiss/ZEN 2.1 black LSM 880 -May 2015/Timeserie_GraphikElemente.czi
zeiss-czi/zeiss/ZEN 2.1 black LSM 880 -May 2015/WF.czi
  1. one file that sets "Label" on Modulo annotations fails the testValidXML automated test (testing disabled for this file): 
zeiss-czi/zeiss/ZEN 2.1 black LSM 880 -May 2015/SIM_nicht verrechnet.czi
  1. multiple detectors with same ID (causes OME-XML validation to fail, testing is disabled for these files): 
zeiss-czi/zeiss/ZEN 2.1 blue LSM 800 -May2015/LambdaCh10T3.czi
zeiss-czi/zeiss/ZEN 2.1 blue LSM 800 -May2015/LambdaCh10T3ConvertedForZENblack.czi
zeiss-czi/zeiss/ZEN 2.1 blue LSM 800 -May2015/LambdaCh10T1.czi
zeiss-czi/zeiss/ZEN 2.1 blue LSM 800 -May2015/LambdaCh10T1ConvertedForZENblack.czi
zeiss-czi/zeiss/ZEN 2.1 blue LSM 800 -May2015/AiryscanCh3T1Z1.czi
zeiss-czi/zeiss/ZEN 2.1 blue LSM 800 -May2015/AiryscanCh3T1Z5.czi
zeiss-czi/zeiss/ZEN 2.1 blue LSM 800 -May2015/AiryscanCh3T3Z1.czi
zeiss-czi/zeiss/ZEN 2.1 blue LSM 800 -May2015/AiryscanCh3T3Z5.czi
zeiss-czi/zeiss/ZEN 2.1 blue LSM 800 -May2015/AiryscanProcessedCh3T1Z1.czi
zeiss-czi/zeiss/ZEN 2.1 blue LSM 800 -May2015/AiryscanProcessedCh3T1Z5.czi
zeiss-czi/zeiss/ZEN 2.1 blue LSM 800 -May2015/AiryscanProcessedCh3T3Z1.czi
zeiss-czi/zeiss/ZEN 2.1 blue LSM 800 -May2015/AiryscanProcessedCh3T3Z5.czi
  1. incorrect channel names: 
zeiss-czi/zeiss/ZEN 2.1 blue LSM 800 -May2015/LambdaCh10T3ConvertedForZENblack.czi
zeiss-czi/zeiss/ZEN 2.1 blue LSM 800 -May2015/LambdaCh10T1ConvertedForZENblack.czi
  1. "spline contour"-type ROI missing: 
zeiss-czi/zeiss/ZEN 2.1 blue LSM 800 -May2015/ConfocalCh1T15Z1Bleaching2ROIS.czi
  1. questionable timestamps: 
zeiss-czi/zeiss/ZEN 2.1 blue LSM 800 -May2015/ConfocalCh1T15Z1Bleaching2ROIS.czi
  1. incorrect channel colors (added to ​https://trello.com/c/Ysnohq0T/42-zeiss-czi-channel-colors, does not need to be addressed here): 
zeiss-czi/zeiss/ZEN 2.1 blue LSM 800 -May2015/ConfocalCh3T1Z54BigFrameSize.czi

comment:9 Changed 7 years ago by mlinkert

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

With ​https://github.com/openmicroscopy/bioformats/pull/2881, everything except point 1 above is now addressed for 5.5.3.

Closing as fixed since point 1 is covered by ​https://trac.openmicroscopy.org/ome/ticket/12469

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