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Task #12469 (closed)

Opened 10 years ago

Closed 7 years ago

Bug: CZI: Problem with reading images from Elyra PALM system

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

Description

See: ​https://www.openmicroscopy.org/community/viewtopic.php?f=13&t=7569

QA: ​https://www.openmicroscopy.org/qa2/qa/feedback/9410/

CZI files containing images from Elyra PALM system are not correctly opened by Bioformats.
Image uploaded to QA contains 2 channels 1) HR: plane size: x: 1280, y: 1280 pixels and
2) WF: plane size: x: 128, y: 128 pixels, however image opened by Bioformats contains two channels with plane size: 128 x 128 pixels.

Change History (11)

comment:1 Changed 10 years ago by jamoore

  • Keywords ZeissCZIReader added

comment:2 Changed 9 years ago by mlinkert

  • Milestone changed from Unscheduled to 5.1.1

Moving to 5.1.1 for triage.

comment:3 Changed 9 years ago by mlinkert

  • Milestone changed from 5.1.1 to 5.2.0-m1

The HR dimensions are set in the 'storedSize' variable on DimensionEntry? - the 'size' variable is still set to 128 (I guess this is the display size?). Zen shows both channels at 128x128, and I don't see an option to view the full resolution HR channel.

Fixing this within the current model means splitting the channels into separate series; to do this completely properly will require model changes.

comment:4 Changed 9 years ago by mlinkert

See also QA 11007 and ​http://lists.openmicroscopy.org.uk/pipermail/ome-users/2015-April/005288.html; Sebastien tested and confirmed today.

comment:5 Changed 9 years ago by jamoore

  • Milestone changed from 5.2.0 to B-F-5.2.0

Splitting due to milestone decoupling.

comment:6 Changed 8 years ago by mlinkert

Current plan is to split the channels into separate series for 5.2.0 (in coordination with ​https://trac.openmicroscopy.org/ome/ticket/12935). How to model PALM data in general will need to be a separate discussion, and is added to ​https://trello.com/c/HmCOzJ8c/153-schema-changes-trac-tickets.

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

Other datasets from ​http://trac.openmicroscopy.org/ome/ticket/12935#comment:8 exhibit this problem:

zeiss-czi/zeiss/ZEN 2.1 black LSM 880 -May 2015/Image_5_PALM_verrechnet.czi
zeiss-czi/zeiss/ZEN 2.1 black LSM 880 -May 2015/PALM_OnlineVerrechnet.czi
zeiss-czi/zeiss/ZEN 2.1 black LSM 880 -May 2015/Palm_Source.czi

comment:10 Changed 7 years ago by bramalingam

  • Cc a.bruckbauer@… added

comment:11 Changed 7 years ago by mlinkert

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

PR open for 5.6.0 consideration: ​https://github.com/openmicroscopy/bioformats/pull/2897

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