Task #12214 (closed)
Bug: LIF import results in incorrect channel colours
| Reported by: | rleigh | Owned by: | mlinkert |
|---|---|---|---|
| Priority: | major | Milestone: | 5.0.3 |
| Component: | Import | Version: | 5.0.1 |
| Keywords: | n.a. | Cc: | matthew.couchman@… mlinkert |
| Resources: | n.a. | Referenced By: | n.a. |
| References: | n.a. | Remaining Time: | 0.0d |
| Sprint: | n.a. |
Description
QA image: #9185
Original mail: http://lists.openmicroscopy.org.uk/pipermail/ome-users/2014-April/004382.html
Bio-Formats shows this as a multi-series set of RGB images with the channel colour -1 (0xFFFFFFFF). ImageInfo? renders this correctly. However, perhaps Bio-Formats should not be setting a channel colour if the image is RGB in addition to this? (I'm not certain how channel colour and RGB subchannels are intended to interact in the data model; this might be perfectly valid.)
Import into OMERO (5.0 dev_5_0 build) shows the RGB images as magenta (the channel colours for R, G and B are white, green and blue, respectively). It looks like this might be due to the channel colour from the original file only being applied to the first channel, with the second two being assigned heuristically. Maybe it needs a special case to ignore the channel colour for RGB channels since it's implicit?
Change History (3)
comment:1 Changed 10 years ago by mlinkert
- Milestone changed from Unscheduled to 5.0.3
- Owner set to mlinkert
comment:2 Changed 10 years ago by mlinkert
- Resolution set to fixed
- Status changed from new to closed
comment:3 Changed 10 years ago by Melissa Linkert <melissa@…>
- Remaining Time set to 0
(In [f29c5dfbc10e3ee6c695bc30b1cb052632afd614/bioformats.git] on branch develop) Leica LIF: do not set Channel.Color for RGB images
The stored color will usually (always?) be 0xffffffff, which causes the
displayed colors to be inaccurate (since the 'R' component will be shown
as white).
Fixes #12214.
PR opened: https://github.com/openmicroscopy/bioformats/pull/1193