Task #12642 (accepted)
Opened 9 years ago
Last modified 8 years ago
BUG: Export as OME-TIFF broken
Reported by: | pwalczysko | Owned by: | jburel |
---|---|---|---|
Priority: | blocker | Milestone: | OME-Files |
Component: | Export | Version: | 5.1.0-m1 |
Keywords: | n.a. | Cc: | ux@…, bf@… |
Resources: | n.a. | Referenced By: | n.a. |
References: | n.a. | Remaining Time: | n.a. |
Sprint: | n.a. |
Description
On the sample image
the Export as OME-TIFF gives wrong result (compare with the original on the screenshot and the "Save as Tiff" result)
Happens the same both in Web and Insight
Attachments (2)
Change History (26)
Changed 9 years ago by pwalczysko
comment:1 Changed 9 years ago by pwalczysko
- Cc mlinkert added
comment:2 Changed 9 years ago by pwalczysko
comment:3 Changed 9 years ago by pwalczysko
- Owner changed from web-team@… to mlinkert
comment:4 Changed 9 years ago by pwalczysko
Changed the ownership to mlinkert - sorry if this is not the right course of action, but I understand we need at least your opinion at this stage.
comment:5 Changed 9 years ago by pwalczysko
- Component changed from Web to Export
Note that the problem happens in Insight as well as Web.
comment:6 Changed 9 years ago by jamoore
- Resolution set to invalid
- Status changed from new to closed
comment:7 Changed 9 years ago by pwalczysko
Note that similar noise problems with our readers were reported for SCN files http://lists.openmicroscopy.org.uk/pipermail/ome-users/2014-December/004938.html
comment:8 Changed 9 years ago by pwalczysko
@jamoore : Not sure what is happening here. The ticket was closed on the strength of it being replaced by the Trello. Then the Trello card was archived on the strenght of not being relevant to the board. ????
comment:9 Changed 9 years ago by pwalczysko
- Resolution invalid deleted
- Status changed from closed to reopened
comment:10 Changed 9 years ago by jburel
- Owner changed from mlinkert to jburel
- Status changed from reopened to accepted
It is b/c it was not related to units.
I will have a look
it could be related to the RE
comment:11 Changed 9 years ago by jamoore
Thanks for catching that, Petr!
comment:12 Changed 9 years ago by jamoore
- Milestone changed from 5.1.0-m2 to 5.1.0
comment:13 Changed 9 years ago by pwalczysko
The important thing is that the image must be small
- create in Fiji an image "New -> Imege"
- use size 10 x 10 and use "Ramp"
- then, still in Fiji, save the newly created image as tiff (do not use Bio-Formats)
- import the image to OMERO (looks as expected)
- export it from OMERO using the latest schema
- view the image using the default Preview program on Mac - it is completely scrambled
- reimport the scrambled .ome.tiff into OMERO
- the image looks okay
- examine the oritinally created .tiff using tiffinfo - the info says
Subfile Type: (0 = 0x0) Image Width: 10 Image Length: 10
- examine the exported .ome.tiff using tiffinfo
Image Width: 10 Image Length: 10 Tile Width: 128 Tile Length: 128
- obviously a Bio-Formats problem
See user-3, ID 26356, trout merge.
Changed 9 years ago by pwalczysko
comment:14 Changed 9 years ago by pwalczysko
- Milestone changed from 5.1.0 to 5.1.1
comment:15 Changed 9 years ago by jburel
- Milestone changed from 5.1.1 to 5.1.3
OME-TIFF work scheduled for 5.1.3. Moving to 5.1.3.
comment:16 Changed 9 years ago by jburel
- Milestone changed from 5.1.3 to 5.1.4
comment:17 Changed 9 years ago by jamoore
- Milestone changed from 5.1.4 to OMERO-5.1.4
Splitting 5.1.4 due to milestone decoupling
comment:18 Changed 9 years ago by jburel
- Milestone changed from OMERO-5.1.4 to 5.x
The work on export has been pushed
comment:19 Changed 8 years ago by jamoore
- Milestone changed from 5.x to OMERO-5.2.1
Bumping for review.
comment:20 Changed 8 years ago by jburel
- Milestone changed from OMERO-5.2.1 to OMERO-5.2.2
Milestone OMERO-5.2.1 deleted
comment:21 Changed 8 years ago by jburel
- Milestone changed from OMERO-5.2.2 to OMERO-5.2.1
Milestone OMERO-5.2.2 deleted
comment:22 Changed 8 years ago by jburel
- Milestone changed from OMERO-5.2.2 to Metadata
comment:23 Changed 8 years ago by jburel
- Milestone changed from Metadata to OME-Files
comment:24 Changed 8 years ago by mtbcarroll
- Cc bf@… added; ajpatterson mlinkert removed
There has been work lately on the OME-TIFF reading and writing I think. I don't quite know what's been done nor what's planned but it might be appropriate to include this ticket if there is work on those anyway. Are we sure it's a Bio-Formats problem; maybe a workflow with bfconvert or somesuch also evinces the bug? Is it incorrect to have a tile size larger than image size?
Further investigation with ajpatterson revealed that: