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Task #13230 (closed)

Opened 6 years ago

Closed 3 years ago

Bug: Cellomics plate view column index off

Reported by: wmoore Owned by: sbesson
Priority: critical Milestone: Unscheduled
Component: Bio-Formats Version: OMERO-5.2.0
Keywords: n.a. Cc: bramalingam
Resources: n.a. Referenced By: n.a.
References: n.a. Remaining Time: n.a.
Sprint: n.a.

Description

See http://lists.openmicroscopy.org.uk/pipermail/ome-users/2016-May/006006.html

"I uploaded some Thermo CellInsight? plate data to OMERO 5.2.3, and noticed that there is a problem with the well column index. The wells are numbered A01 -> H12, but OMERO webclient viewer seems to think the index starts from A00, and shifts the wells to the right."

Sample file submitted: QA 17183

Change History (7)

comment:1 Changed 6 years ago by sbesson

  • Milestone changed from B-F-5.2.0 to Unscheduled
  • Owner mlinkert deleted

comment:2 Changed 5 years ago by sbesson

Also submitted as #13297 - see QA 17350.

comment:3 Changed 5 years ago by sbesson

  • Cc bramalingam added

comment:4 Changed 5 years ago by sbesson

  • Owner set to sbesson

Assuming the column well semantics is meant to be 1-based instead of 0-based, then we could update the reader accordingly and fix both the index and the generated Image Name to comply with the semantics. This change would require test configuration PRs and would be suitable for Bio-Formats 5.3.0. I could not find any example of Cellomics plates with A00. Melissa, have you encountered such cases?

comment:5 Changed 5 years ago by sbesson

While looking at this with Andrea, I realized the origin of the issue was https://github.com/openmicroscopy/bioformats/pull/923 (motivated by https://github.com/CellProfiler/CellProfiler/issues/1043) which also modified the column indexing (-1 dropped) hence the data layout.

comment:7 Changed 3 years ago by mlinkert

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

Closing based upon https://github.com/openmicroscopy/bioformats/pull/3086#issuecomment-369646712, so this should have been fixed in 5.9.0. Feel free to reopen if there was more left to do though.

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