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Task #12727 (closed)

Opened 9 years ago

Closed 9 years ago

Last modified 9 years ago

Leica SCN 400F file throws FormatException

Reported by:	sbesson	Owned by:	mlinkert
Priority:	major	Milestone:	5.1.0
Component:	Bio-Formats	Version:	5.0.6
Keywords:	Leica	Cc:
Resources:	n.a.	Referenced By:	n.a.
References:	n.a.	Remaining Time:	0.0d
Sprint:	n.a.

Description (last modified by sbesson)

See http://lists.openmicroscopy.org.uk/pipermail/ome-users/2015-February/005033.html and QA 10469. Bio-Formats initialization

Checking file format [Leica SCN]
Initializing reader
LeicaSCNReader initializing /ome/apache_repo/10469/Slide_907790L_DAPI_Ki67.scn
Reading IFDs
Populating metadata
Exception in thread "main" loci.formats.FormatException: Error setting core metadata for image number 25
	at loci.formats.in.LeicaSCNReader.initCoreMetadata(LeicaSCNReader.java:244)
	at loci.formats.in.LeicaSCNReader.initStandardMetadata(LeicaSCNReader.java:321)
	at loci.formats.in.BaseTiffReader.initMetadata(BaseTiffReader.java:95)
	at loci.formats.in.BaseTiffReader.initFile(BaseTiffReader.java:542)
	at loci.formats.FormatReader.setId(FormatReader.java:1396)
	at loci.formats.ImageReader.setId(ImageReader.java:835)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:651)
	at loci.formats.tools.ImageInfo.testRead(ImageInfo.java:988)
	at loci.formats.tools.ImageInfo.main(ImageInfo.java:1070)

References

Change History (5)

comment:1 Changed 9 years ago by sbesson

Description modified (diff)

comment:2 Changed 9 years ago by sbesson

Description modified (diff)

comment:3 Changed 9 years ago by sbesson

Description modified (diff)

comment:4 Changed 9 years ago by mlinkert

Resolution set to fixed
Status changed from new to closed

PR opened: https://github.com/openmicroscopy/bioformats/pull/1592

comment:5 Changed 9 years ago by Melissa Linkert <melissa@…>

Remaining Time set to 0

(In [63aa522e7b3e50b32b0fa2b0891819b25516b1ef/bioformats.git] on branch develop) Leica SCN: fix subresolution calculation to account for channel and Z counts

Not every plane corresponds to a new subresolution; this wasn't being
taken into account before.

Fixes #12727.

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