Task #12548 (new)
Opened 10 years ago
Last modified 9 years ago
BUG: ND2 reader issue — at Version 5
Reported by: | bramalingam | Owned by: | mlinkert |
---|---|---|---|
Priority: | major | Milestone: | 5.1.0 |
Component: | Bio-Formats | Version: | 5.0.3 |
Keywords: | n.a. | Cc: | aryeh@…, wel@… |
Resources: | n.a. | Referenced By: | n.a. |
References: | n.a. | Remaining Time: | n.a. |
Sprint: | n.a. |
Description (last modified by wmoore)
Original E-mail:
Bio-formatds no longer properly reads nd2 multifield files. I just noticed it today.
I will try to upload an example. Bsically, ir gets the frames, z-size, etc wrong.
I tried both the version distributed with Fiji, and the cersion I get when I select the bio-formats update site.
I hae not founda way to fall bakc to previous versions of bio-formats to see where things changed, I am abroad so Ido not have access to backups.
I will try to upload an image.
ok -- I verified the following:
- A fresh download of the newest Fiji reproduces the problem
- The June 2014 lifeline version works
- pasting the Jars/Bio?=formats directory from lifeline to latest fixes the problem.
I uploaded an nd2 multifield image set called control003.nd2. using the Fiji Help>Upload a Sample Image utility. It should be about 2 GB in size.
http://lists.openmicroscopy.org.uk/pipermail/ome-users/2014-September/004680.html QA9507
The issue was reproducible.
There is a mismatch in the metadata, between NIS elements and Bio-formats.
Change History (5)
comment:1 Changed 10 years ago by mlinkert
- Milestone changed from Unscheduled to 5.1.0
- Priority changed from minor to major
comment:2 Changed 10 years ago by crueden-x
comment:3 Changed 10 years ago by rleigh
Also see:
https://www.openmicroscopy.org/qa2/qa2/qa/feedback/10100/
https://www.openmicroscopy.org/community/viewtopic.php?f=13&t=7651
Confirmed with current develop--dimensionality is wrong as described in the forum post above.
comment:4 Changed 10 years ago by rleigh
- Cc wel@… added
comment:5 Changed 10 years ago by wmoore
- Description modified (diff)
See also https://github.com/imagej/imagej/issues/99, which might be related.