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

[Anna-Lena Merten]

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> On 
>>>> Behalf Of Anna-Lena Merten
>>>> Sent: jeudi, 23 août 2018 07:57
>>>> To: 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/
>>>>
>>>> _______________________________________________
>>>> ome-users mailing list
>>>> ome-users at lists.openmicroscopy.org.uk
>>>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>>
>> --
>> 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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>
>
> The University of Dundee is a registered Scottish Charity, No: SC015096 

-- 
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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