Task #2433 (closed)
Opened 9 years ago
Closed 9 years ago
BUG: lei filter not populating cutin cutout
| Reported by: | wmoore | Owned by: | bwzloranger |
|---|---|---|---|
| Priority: | major | Milestone: | OMERO-Beta4.2 |
| Component: | Import | Version: | n.a. |
| Keywords: | n.a. | Cc: | cxallan |
| Resources: | n.a. | Referenced By: | n.a. |
| References: | n.a. | Remaining Time: | n.a. |
| Sprint: | 2010-05-13 (9) |
Description
For example, leica/joel/sequential_scan_2.lei [three channel sequen] imported to nightshade (fourtwo) under Will's tests/lei:
The first channel has emission filter "SP Mirror 4" with cut-in: 665 cut-out: 800. These values are missing from an import with BioFormats 6360.
Change History (6)
comment:1 Changed 9 years ago by wmoore
- Owner changed from mlinkert-x to bwzloranger
comment:2 Changed 9 years ago by mlinkert
I checked all of the Filter/TransmittanceRange/EmissionFilterRef? values in 'sequential scan 2.lei' using bio-formats:r6388, and all matched up with the values from 4.1. The only suspicious thing was that EmissionFilterRef? was being populated multiple times for several Channels; that has been fixed in bio-formats:r6389. Not sure if that could have caused linkage issues in OMERO, but it might be worth seeing if updating solves the problem.
comment:3 Changed 9 years ago by wmoore
I think this is due to another bug that Chris knows about, where the transmittance range indexes are getting mixed up between different filters.
comment:4 Changed 9 years ago by wmoore
- Cc cxallan added
- Component changed from General to Import
Chris: I think you were talking about this yesterday and wanted me to test if it was fixed today?
I am still seeing the same bug in BF revision 6389.
comment:5 Changed 9 years ago by cxallan
comment:6 Changed 9 years ago by cxallan
- Resolution set to fixed
- Status changed from new to closed
Not sure if this is a bio-formats or OMERO issue, since the loci_tools.jar in ImageJ seems to populate "SP Mirror 4" with the correct cutIn and cutOut values.