[ome-users] Bioformats only imports parts of .nd2 file

Mon Aug 27 14:58:20 BST 2018

Hi Anna-Lena,

Thank you for testing that option and providing the further details. We have an existing Trello card for incorrect time points with the chunk map enabled but I have added the details you provided showing that time points are also incorrect when it is disabled.
https://trello.com/c/UtugDbmG/31-nd2-incorrect-sizet-when-chunkmap-enabled

Would it be possible to send the sample file for us to use in testing? If so I will arrange FTP details to be sent to you privately as the file size is large.

With Thanks,
David Gault

On 27 Aug 2018, at 00:27, Anna-Lena Merten <anna-lena.merten at fau.de<mailto:anna-lena.merten at fau.de>> wrote:

Hi David,

up to now the Chunkmap option was ticked. I unticked it and now Bio-Formats opens 6.8GB instead of 2GB (screenshot attached, ComparisonChunkmap). This also results in 874 timestamps instead of 256 and the first timestamp actually starts at 0s instead of 84s (screenshot attached, ComparisonTimestamp). It is very close now, but the original file has 7.2GB and 1200 timestamps (we took a picture every 100ms for 2min).

Thank you for your help!

Best

Anna-Lena

Am 24.08.2018 um 19:11 schrieb David Gault (Staff):
Hi Ann-Lena,

What is the dimension size you are seeing when you open the file with Bio-Formats?

Does the same behaviour occur with and without the ND2 chunk map option selected?
This can be set in: Plugins > Bio-Formats > Bio-Formats Plugins Configuration > Formats > Nikon ND2 > Chunkmap

With Thanks,
David Gault

On 24 Aug 2018, at 00:09, Anna-Lena Merten <anna-lena.merten at fau.de<mailto:anna-lena.merten at fau.de>> wrote:

Hi Romain,

thank you for your quick reply!

As you can see in the attached screenshot, there should be enough RAM available for ImageJ.

I tried using the virtual stack option (Plugins -> Bio-Formats -> Bio-Formats Importer, ticked the box 'Use virtual stack' in the dialog box), but the same problem occurs.

Best regards,

Anna-Lena

Am 23.08.2018 um 16:45 schrieb Josh Moore:
CC Anna-Lena since she was previously not on the list.
~J.

On Thu, Aug 23, 2018 at 8:20 AM Romain Guiet <romain.guiet at epfl.ch<mailto:romain.guiet at epfl.ch>> wrote:
Hi Anna-Lena,

ImageJ only indicates 2GB but does not respond with an error message
How much RAM have you set for your ImageJ  (EDIT > Options > Memory & Threads) ?
If you want to open the whole 7 Gb file, it should be (at least) more than 8 GB even 12GB (if you computer can offered it)

Alternatively, you could use the virtual stack option, just to verify if bio-formats can read all the slice.

Best,

Romain

---------------------------------------------------------------
Dr. Romain Guiet
Bioimaging and Optics Platform (PT-BIOP)
Ecole Polytechnique Fédérale de Lausanne (EPFL)
Faculty of Life Sciences
Station 19, AI 0140
CH-1015 Lausanne

Phone: [+4121 69] 39629
http://biop.epfl.ch/
---------------------------------------------------------------

-----Original Message-----
From: ome-users <ome-users-bounces at lists.openmicroscopy.org.uk><mailto:ome-users-bounces at lists.openmicroscopy.org.uk> On Behalf Of Anna-Lena Merten
Sent: jeudi, 23 août 2018 07:57
To: ome-users at lists.openmicroscopy.org.uk<mailto:ome-users at lists.openmicroscopy.org.uk>
Subject: [ome-users] Bioformats only imports parts of .nd2 file

Hi everyone,

using the NIS Elements software we recorded stacks of images (time lapse, interval: 100ms, duration: 2 min, Loops: 1201; 1 position, 1
channel) which resulted in .nd2-files bigger than 7GB.

Bioformats 5.9.1 does not open the complete stack, there are obviously images missing from the end of the stack (NIS Elements still opens the whole time lapse). Even though the files are bigger than 7GB, ImageJ only indicates 2GB but does not respond with an error message (screenshots in appendix). There do not seem to be problems with files smaller than 2GB.

I am working with Windows 10, ImageJ 1.52e and Java 1.8.0_66 (64-bit).

Thank you for your help!

Best regards,

Anna-Lena

--
Anna-Lena Merten

Institute of Medical Biotechnology
Friedrich-Alexander-University Erlangen-Nuremberg Ulrich-Schalk-Str.3, 91056 Erlangen, Germany

phone: +49 9131 85 69643
FAX: +49 9131 85 23002
web: http://www.mbt.tf.uni-erlangen.de/

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--
Anna-Lena Merten

Institute of Medical Biotechnology
Friedrich-Alexander-University Erlangen-Nuremberg
Ulrich-Schalk-Str.3, 91056 Erlangen, Germany

phone: +49 9131 85 69643
FAX: +49 9131 85 23002
web: http://www.mbt.tf.uni-erlangen.de/

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--
Anna-Lena Merten

Institute of Medical Biotechnology
Friedrich-Alexander-University Erlangen-Nuremberg
Ulrich-Schalk-Str.3, 91056 Erlangen, Germany

phone: +49 9131 85 69643
FAX: +49 9131 85 23002
web: http://www.mbt.tf.uni-erlangen.de/

<ComparisonChunkmap.PNG><ComparisonTimestamp.PNG>

The University of Dundee is a registered Scottish Charity, No: SC015096
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