Task #12416 (closed)
Bug: InCell reader not filling WellSamples on plate
Reported by: | rleigh | Owned by: | mlinkert |
---|---|---|---|
Priority: | minor | Milestone: | 5.0.3 |
Component: | Bio-Formats | Version: | 5.0.2 |
Keywords: | n.a. | Cc: | wgeorgescu@… |
Resources: | n.a. | Referenced By: | n.a. |
References: | n.a. | Remaining Time: | 0.0d |
Sprint: | n.a. |
Description
See attached file. It looks like the InCell? reader isn't behaving correctly with this file. The original file has:
% grep "<Well" ~/Downloads/20x\ Z1\ 16fields\ Gr\ Rd\ DAPI\ Cy5_140610-3_fix_2.xdce | sort -g | uniq -c 64 <Well label="A - 1"> 64 <Well label="A - 10"> 64 <Well label="A - 11"> 64 <Well label="A - 12"> 64 <Well label="A - 2"> 64 <Well label="A - 3"> 64 <Well label="A - 4"> 64 <Well label="A - 5"> 64 <Well label="A - 6"> 64 <Well label="A - 7"> 64 <Well label="A - 8"> 64 <Well label="A - 9"> 64 <Well label="B - 1"> 64 <Well label="B - 10"> 64 <Well label="B - 11"> 64 <Well label="B - 12"> 64 <Well label="B - 2"> 64 <Well label="B - 3"> 64 <Well label="B - 4"> 64 <Well label="B - 5"> 64 <Well label="B - 6"> 64 <Well label="B - 7"> 64 <Well label="B - 8"> 64 <Well label="B - 9"> 64 <Well label="C - 1"> 64 <Well label="C - 10"> 64 <Well label="C - 11"> 64 <Well label="C - 12"> 64 <Well label="C - 2"> 64 <Well label="C - 3"> 64 <Well label="C - 4"> 64 <Well label="C - 5"> 64 <Well label="C - 6"> 64 <Well label="C - 7"> 64 <Well label="C - 8"> 64 <Well label="C - 9"> 64 <Well label="D - 1"> 64 <Well label="D - 10"> 64 <Well label="D - 11"> 64 <Well label="D - 12"> 64 <Well label="D - 2"> 64 <Well label="D - 3"> 64 <Well label="D - 4"> 64 <Well label="D - 5"> 64 <Well label="D - 6"> 64 <Well label="D - 7"> 64 <Well label="D - 8"> 64 <Well label="D - 9"> 64 <Well label="E - 1"> 64 <Well label="E - 10"> 64 <Well label="E - 11"> 64 <Well label="E - 12"> 64 <Well label="E - 2"> 64 <Well label="E - 3"> 64 <Well label="E - 4"> 64 <Well label="E - 5"> 64 <Well label="E - 6"> 64 <Well label="E - 7"> 64 <Well label="E - 8"> 64 <Well label="E - 9"> 64 <Well label="F - 1"> 64 <Well label="F - 10"> 64 <Well label="F - 11"> 64 <Well label="F - 12"> 64 <Well label="F - 2"> 64 <Well label="F - 3"> 64 <Well label="F - 4"> 64 <Well label="F - 5"> 64 <Well label="F - 6"> 64 <Well label="F - 7"> 64 <Well label="F - 8"> 64 <Well label="F - 9"> 64 <Well label="G - 1"> 64 <Well label="G - 10"> 64 <Well label="G - 11"> 64 <Well label="G - 12"> 64 <Well label="G - 2"> 64 <Well label="G - 3"> 64 <Well label="G - 4"> 64 <Well label="G - 5"> 64 <Well label="G - 6"> 64 <Well label="G - 7"> 64 <Well label="G - 8"> 64 <Well label="G - 9"> 64 <Well label="H - 1"> 64 <Well label="H - 10"> 64 <Well label="H - 11"> 64 <Well label="H - 12"> 64 <Well label="H - 2"> 64 <Well label="H - 3"> 64 <Well label="H - 4"> 64 <Well label="H - 5"> 64 <Well label="H - 6"> 64 <Well label="H - 7"> 64 <Well label="H - 8"> 64 <Well label="H - 9">
Dimensionality:
16 fields
4 channels
21 z
1 t
The reader is correctly picking up the wells, but it's not filling them with WellSamples? (fields), so they are as a result appearing empty. There's nothing added after A5.
Attachments (1)
Change History (5)
Changed 10 years ago by rleigh
comment:1 Changed 10 years ago by mlinkert
comment:2 Changed 10 years ago by mlinkert
- Milestone changed from Unscheduled to 5.0.3
And one more update: https://www.openmicroscopy.org/community/viewtopic.php?f=4&t=7545#p14250
That's sufficient information to get this done for 5.0.3, I think.
comment:3 Changed 10 years ago by mlinkert
- Resolution set to fixed
- Status changed from new to closed
Pretty sure this is sorted out now with https://github.com/openmicroscopy/bioformats/pull/1212.
comment:4 Changed 10 years ago by Melissa Linkert <melissa@…>
- Remaining Time set to 0
(In [d595dd18c27cfa1a173df672445c2b3121290cf1/bioformats.git] on branch develop) InCell?: correct for Z/T recording oddities in InCell? 6000
Fixes #12416.
See follow-up: https://www.openmicroscopy.org/community/viewtopic.php?f=4&t=7545#p14182