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Task #12416 (closed)

Opened 10 years ago

Closed 10 years ago

Last modified 10 years ago

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: https://www.openmicroscopy.org/community/posting.php?mode=reply&f=4&t=7545&sid=dbf7c3e209bc694f58d6faac5a28fc3c#pr14168

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)

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.

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