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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:

  1. A fresh download of the newest Fiji reproduces the problem
  2. The June 2014 lifeline version works
  3. 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

See also ​https://github.com/imagej/imagej/issues/99, which might be related.

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)
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