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Task #12383 (closed)

Opened 10 years ago

Closed 9 years ago

Last modified 9 years ago

ZeissLSMReader may set indexed inappropriately

Reported by: mhiner-x Owned by: mlinkert
Priority: major Milestone: 5.1.2
Component: Bio-Formats Version: 5.0.2
Keywords: n.a. Cc:
Resources: n.a. Referenced By: n.a.
References: n.a. Remaining Time: 0.0d
Sprint: n.a.

Description

In the test dataset zeiss-lsm/QA images/10052011_R1_GR1_B1_L49.lsm there is a colorsOffset value (​https://github.com/openmicroscopy/bioformats/blob/develop/components/formats-gpl/src/loci/formats/in/ZeissLSMReader.java#L1028) so an 8-bit lookup table is parsed and indexed is set to true.

However, the dataset is uint16 so get8BitLookupTable returns null, and validChannels is never set so get16BitLookupTable returns null as well.

I'm not sure what the correct thing to do is when there seems to be an 8-bit lookup table for 16-bit data. But it seems like having indexed = true with no lookup table is incorrect.

Change History (6)

comment:1 Changed 10 years ago by mlinkert

  • Owner set to mlinkert
  • Type changed from Bug to Task

comment:2 Changed 10 years ago by mlinkert

  • Cc mlinkert removed
  • Component set to Bio-Formats
  • Milestone set to Unscheduled
  • Version set to 5.0.2

comment:3 Changed 9 years ago by mlinkert

  • Milestone changed from Unscheduled to 5.1.1

Moving to 5.1.1 for triage.

comment:4 Changed 9 years ago by mlinkert

  • Milestone changed from 5.1.1 to 5.1.2

comment:5 Changed 9 years ago by mlinkert

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

Fixed with ​https://github.com/openmicroscopy/bioformats/pull/1766

comment:6 Changed 9 years ago by Melissa Linkert <melissa@…>

  • Remaining Time set to 0

(In [41e40e1ef6d75259ef7f8c6b95f99cbd23bdb5b2/bioformats.git] on branch develop) Zeiss LSM: fix lookup tables for 16-bit data

Fixes #12383, fixes #12384.

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