Task #11233 (closed)
Opened 11 years ago
Closed 10 years ago
Bug: CZI BGR24/BGR48 RGB image pixel data not handled correctly
Reported by: | rleigh | Owned by: | mlinkert |
---|---|---|---|
Priority: | minor | Milestone: | 5.0.2 |
Component: | Bio-Formats | Version: | 4.4.8 |
Keywords: | ZeissCZIReader | Cc: | ayako.nakayama@…, l.maier@…, organelas@…, martin.huettinger@…, ebbwdan@… |
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/2013-July/003829.html which contains a sample image and jpeg of how it should look.
The sample image is correctly parsed as pixelType==3 (BGR_24), but this is not correctly displayed by showinf. Tested with current dev_4_4 and develop. The image x/y size is correct.
showinf does show " RGB mismatch " so it does look like there's an inconsistency in the RGB/channel count here.
Attachments (1)
Change History (9)
comment:1 Changed 11 years ago by rleigh
- Cc ayako.nakayama@… added
comment:2 Changed 11 years ago by rleigh
- Cc l.maier@… added
comment:3 Changed 11 years ago by mlinkert
comment:4 Changed 11 years ago by mlinkert
- Cc organelas@… added
comment:5 Changed 11 years ago by rleigh
- Cc martin.huettinger@… added
http://qa.openmicroscopy.org.uk/qa/feedback/7601/
See also the images in /ome/team/rleigh/7601 which include the original images uploaded, plus exports of the images from zen (blue) 2012 and zen.txt containing my notes on the image size and pixel type of each image as shown in zen.
Greyscale images are handled correctly. RGB 24- and 48-bit images are not. There are obvious problems incorrectly processing the pixel data here seen when viewing with showinf; it looks like we're not using the correct pixel type.
I can attach screenshots of the bioformats rendering if needed.
comment:6 Changed 11 years ago by rleigh
- Cc ebbwdan@… added
- Summary changed from Bug: CZI BGR24 RGB image pixel data not handled correctly to Bug: CZI BGR24/BGR48 RGB image pixel data not handled correctly
See also QA#7891 and attached image for RBG48 with 14(42)bpp.
Changed 11 years ago by rleigh
QA#7891; note the pixel type is shown as uint8 *not* 16, which is wrong
comment:7 Changed 10 years ago by mlinkert
- Milestone changed from Unscheduled to 5.0.2
comment:8 Changed 10 years ago by mlinkert
- Resolution set to fixed
- Status changed from new to closed
Fixed with https://github.com/openmicroscopy/bioformats/pull/1078; email forthcoming on ome-users/ome-devel with details of how to try this out prior to 5.0.2.
This appears to be the same problem: http://lists.openmicroscopy.org.uk/pipermail/ome-users/2013-September/003944.html