[ome-users] Bio-Formats ND2 importer bug

[Cammer, Michael]

We gave up on BioFormats for opening ND2 files more than a few hundred MB.  We now have files that are 10+ GB and they don't open, or maybe they do but we don't have the patience to wait.  It's  faster to export folders of TIFs from Elements and reassemble.

We'd love to see ND2 importer working for large files.

Michael Cammer, Sr Research Scientist, DART Microscopy Laboratory
NYU Langone Health, 540 First Avenue, SK2 Microscopy Suite, New York, NY  10016
C: 914-309-3270  Michael.Cammer at med.nyu.edu<mailto:Michael.Cammer at med.nyu.edu>  http://nyulmc.org/micros  http://microscopynotes.com/


From: ome-users [mailto:ome-users-bounces at lists.openmicroscopy.org.uk] On Behalf Of Paul-Gilloteaux Perrine
Sent: Thursday, February 8, 2018 9:31 AM
To: ome-users at lists.openmicroscopy.org.uk
Cc: francois.paris at univ-nantes.fr; perrine.paul-gilloteaux at univ-nantes.fr; Isabelle.Delias at nikon.com; manon.pietri at univ-nantes.fr
Subject: [ome-users] Bio-Formats ND2 importer bug


Dear Bio-Formats team,

Im also reporting a bug on nd2 with bioformat (tested on last release 5.7.3 snapshot and previous)

Disabling the chunkmap option does not solve the problem.

I ve uploaded a short example data set here: https://www.openmicroscopy.org/qa2/qa/feedback/20512/?token=1f4ad9c32a8ea3de4f0c34d2c4add35c<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.openmicroscopy.org_qa2_qa_feedback_20512_-3Ftoken-3D1f4ad9c32a8ea3de4f0c34d2c4add35c&d=DwMFAw&c=j5oPpO0eBH1iio48DtsedbOBGmuw5jHLjgvtN2r4ehE&r=oU_05LztNstAydlbm5L5GDu_vAdjXk3frDLx_CqKkuo&m=wOsSGQja4TLs56sXa1P8sT_q6DdHNaWJvRr50dHM4U4&s=LH49R6mHp1j5M6bwJ4YyuzFZ7TNHPps6IrWr_9OqwIs&e=>

In a few words (see my comments on the link above), time and positions are shuffled, while NIS element correcty read the file metadata.
Series corresponds to time when it should be position, and time to what should be position.
It only happens when there is several channels (no problem if the movie is 1 channel multi-t, multi pos)
It only happens with acquisitions generated with the last version of NIS 4.5.0.00 (but read correctly by previous version of NIS element).
Best regards,
Perrine

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