Task #11399 (closed)
Opened 11 years ago
Closed 9 years ago
Bug: ImageJ scale units are not preserved
| Reported by: | omero-qa | Owned by: | rleigh |
|---|---|---|---|
| Priority: | minor | Milestone: | 5.1.1 |
| Component: | Bio-Formats | Version: | 4.4.8 |
| Keywords: | n.a. | Cc: | lunelli@… |
| Resources: | n.a. | Referenced By: | n.a. |
| References: | n.a. | Remaining Time: | n.a. |
| Sprint: | n.a. |
Description
https://www.openmicroscopy.org/qa2/qa2/qa/feedback/7589/
Comment: Two AFM files calibrated in ImageJ using nm as units.
Once uploaded in Omero pixel units are interpreted as microns
The imagej metadata obtained with parseCommentImageJ in components/scifio/src/loci/formats/in/TiffReader.java contains a "Unit" property describing the scale units. We currently ignore this and treat all units as microns. We can probably do a better job here for a certain set of standard units. ImageJ units are entirely freeform, so we can't cope with arbitrary unit names. This is related to #7951 in that a standard means of getting a scaling factor for a conversion of $unit to µm would be necessary in order to implement this.
Change History (3)
comment:1 Changed 11 years ago by rleigh
- Component changed from from QA to Bio-Formats
comment:2 Changed 9 years ago by mlinkert
- Milestone changed from Unscheduled to 5.1.1
comment:3 Changed 9 years ago by mlinkert
- Resolution set to fixed
- Status changed from new to closed
This was fixed with: https://github.com/openmicroscopy/bioformats/pull/1716
Note: See
TracTickets for help on using
tickets.
You may also have a look at Agilo extensions to the ticket.
Moving to 5.1.1 for triage.