Task #11276 (closed)
Opened 11 years ago
Closed 11 years ago
Bug: LIFReader scale of PoxX/PosY is out by 10^6
| Reported by: | omero-qa | Owned by: | rleigh |
|---|---|---|---|
| Priority: | minor | Milestone: | Unscheduled |
| Component: | Bio-Formats | Version: | 4.4.8 |
| Keywords: | n.a. | Cc: | teague@… |
| 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/7464/
Comment: Leica LIF images from LAS AF ver 2.3.1 (Confocal scanner TCS SP5, DMI 6000B stand). The metadata extraction for PositionX and PositionY are incorrect by a factor of 106 (ie, they're reported in meters but should be in um.)
The two attached images demonstrate this. "corners.lif" is 4 images taken at the x/y limits of our stage, approximately the dimensions of a 96-well plate (128mm x 85mm). (There was no sample on the stage, so the images themselves are black.)
The second, "grid.lif", is a 4x4 mosaic of some GFP-positive yeast cells taken on the same instrument; overlap of the images is ~50%.
Change History (4)
comment:1 Changed 11 years ago by rleigh
- Component changed from from QA to Bio-Formats
- Status changed from new to accepted
comment:2 Changed 11 years ago by rleigh
https://github.com/rleigh-dundee/bioformats/tree/lif-physicalsize
Needs testing. I haven't yet been able to observe usage of XPos/YPos in the provided examples, so still needs more testing.
comment:3 Changed 11 years ago by rleigh
Works fine as far as I can see. PR opened. https://github.com/openmicroscopy/bioformats/pull/604
comment:4 Changed 11 years ago by rleigh
- Resolution set to fixed
- Status changed from accepted to closed
Patch committed on https://github.com/rleigh-dundee/bioformats/tree/lif-physicalsize