Task #3124 (closed)
Bug: OME-TIFF export
| Reported by: | omero-qa | Owned by: | cxallan |
|---|---|---|---|
| Priority: | major | Milestone: | OMERO-Beta4.3 |
| Component: | from QA | Version: | n.a. |
| Keywords: | n.a. | Cc: | Jay_Copeland@…, jburel, jamoore, cxallan, mlinkert |
| Resources: | n.a. | Referenced By: | n.a. |
| References: | n.a. | Remaining Time: | 0.0d |
| Sprint: | 2011-02-10 (5) |
Description (last modified by jburel)
http://qa.openmicroscopy.org.uk/qa/feedback/2901/
Comment: When I attempt to export to ome.tiff I get a tiff stack which ImageJ interprets as a tiff with 600 z slices. The correct structure is 2 channels, 12 z slices, and 25 t time points. I can set these manually in ImageJ. But I was hoping that ImageJ would interpret the ome.tiff correctly and I could avoid this step. Any suggestions?
I have been working on this issue some more and have some additional information. There seems to be a problem with how omero implements the ome.tif export. When I use the most recent LOCI plugin for ImageJ to export to ome.tif the resulting file is correct. When I use omero to export the file to ome.tif C and Z get mixed up. It appears that as you scroll through Z the images alternate between C. Also, I should mention that opening images in ImageJ using the LOCI Bio-Formats Importer resolves the stack order issue I mentioned originally in this comment. That was a psuedo-issue. The real problem is that the omero export functionality appears to be broken.
Change History (9)
comment:1 Changed 9 years ago by jburel
- Description modified (diff)
- Priority changed from minor to major
comment:2 Changed 9 years ago by jmoore
comment:3 Changed 9 years ago by jmoore
- Cc cxallan mlinkert-x added
- Milestone changed from Unscheduled to OMERO-Beta4.3
- Summary changed from OME-TIFF export to Bug: OME-TIFF export
comment:4 Changed 9 years ago by cxallan
- Sprint set to 2011-02-10 (5)
comment:5 Changed 9 years ago by cxallan
- Status changed from new to accepted
comment:6 Changed 9 years ago by cxallan
- Remaining Time set to 0.75
comment:7 Changed 9 years ago by Chris Allan <callan@…>
- Remaining Time changed from 0.75 to 0
- Resolution set to fixed
- Status changed from accepted to closed
(In [bd43082c72a4079add928031fa270dc7e6dc6bdf/ome.git]) Enforce XYZCT dimension order. (Fixes #3124)
In order to ensure that the changes made in ([8867/omero]) (See #3718)
remain valid and that exports have the correct dimension order (Closes
order set in the OMERO database. The server relies on an XYZCT order and
all interactions happen as such, it must be enforced throughout.
comment:8 Changed 8 years ago by Chris Allan <callan@…>
(In [c60d1c673de9ece42501b7b5709ccaeeada99c70/ome.git] on branch dev_4_2) Enforce XYZCT dimension order. (Fixes #3124)
In order to ensure that the changes made in ([8867/omero]) (See #3718)
remain valid and that exports have the correct dimension order (Closes
order set in the OMERO database. The server relies on an XYZCT order and
all interactions happen as such, it must be enforced throughout.
(cherry picked from commit bd43082c72a4079add928031fa270dc7e6dc6bdf)
comment:9 Changed 5 years ago by dpwrussell <douglas.russell@…>
(In [b01bc7842963fabeef2148cb5798404d8fea9a9b/ome.git] on branch develop) Handle broken image links in public shares correctly as before #3124
Referencing ticket #3473 has changed sprint.