Task #13230 (closed)
Opened 8 years ago
Closed 5 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 8 years ago by sbesson
- Milestone changed from B-F-5.2.0 to Unscheduled
- Owner mlinkert deleted
comment:2 Changed 7 years ago by sbesson
comment:3 Changed 7 years ago by sbesson
- Cc bramalingam added
comment:4 Changed 7 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 7 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:6 Changed 6 years ago by mlinkert
Possibly related PR: https://github.com/openmicroscopy/bioformats/pull/3086
comment:7 Changed 5 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.
Also submitted as #13297 - see QA 17350.