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Task #12756 (closed)

Opened 9 years ago

Closed 9 years ago

Bug: LIFReader has reverse plane order

Reported by:	rleigh	Owned by:	jburel
Priority:	minor	Milestone:	5.1.1
Component:	Bio-Formats	Version:	5.0.8
Keywords:	n.a.	Cc:	imagejlyd@…, mlinkert
Resources:	n.a.	Referenced By:	n.a.
References:	n.a.	Remaining Time:	n.a.
Sprint:	n.a.

Description

See: https://www.openmicroscopy.org/qa2/qa/feedback/10521/

Channel name order is: DAPI AF488 Cy3 Cy5

If you look at the pixel data with showinf, you'll see that the DAPI (nuclei) plane is the last plane, not the first.

Looking at the metadata in the LIF file, it looks like the channel name order is entirely correct, matching the MultiBand? channel order. So it looks like it's the mapping between plane number to image plane that might be at fault here--realChannel or getTileIndex perhaps?

References

Change History (5)

comment:1 Changed 9 years ago by mlinkert

Milestone changed from Unscheduled to 5.1.1

Moving to 5.1.1 for triage.

comment:2 Changed 9 years ago by jburel

Owner changed from mlinkert to jburel

comment:3 Changed 9 years ago by jburel

currently working on the reader as part of #12741

comment:4 Changed 9 years ago by jburel

Cc mlinkert added

comment:5 Changed 9 years ago by jburel

Resolution set to fixed
Status changed from new to closed

I looked at the image submitted. the planes seem to be correctly ordered.
Closing this ticket. Please re-open if required.

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