[ome-users] Bio-Formats ND2 importer bug

[Perrine PAUL-GILLOTEAUX]

They do open, (we have long multi pos of about 200Gb each), but indeed 
you need to be patient ...
Data conversion/processing /analysis takes about 1 day with Fiji.

Le 08-02-2018 15:42, Cammer, Michael a écrit :
> 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 http://nyulmc.org/micros
> [1] http://microscopynotes.com/ [2]
> 
> 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
> [3]
> 
> 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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> Links:
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> [1] http://nyulmc.org/micros
> [2] http://microscopynotes.com/
> [3]
> 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=

-- 
Perrine Paul-Gilloteaux, IR CNRS
Ingénieur en gestion et analyse de données images

SFR Santé François Bonamy UMS 3556
IRS-UN, 8 quai Moncousu, BP 70721
44007 Nantes cedex 1, France

perrine.paul-gilloteaux at univ-nantes.fr
tel: 02 28 08 03 43