[ome-users] ND2 opening issue in MATLAB

[Pramukta Kumar]

Hi Dan,

I would also be interested in looking at your nd2 files.  I wrote the 
bf-tools scripts and while they have been working adequately for us 
here, I would definitely like to see about speeding them up when I have 
a bit of time.  Could you share them via Dropbox or Google Drive or 
whatever is easiest for you?

Thanks,
Pramukta

On 12/20/2012 01:56 PM, Daniel Dickinson wrote:
> Hi again Melissa,
>
> I forgot to mention that I also tried opening these images using the 
> BioFormats Importer plugin in ImageJ, and import failed.  The Fiji 
> status bar displays "Parsing Block 'ImageMetadat' 0%" but seems to be 
> hung up there, and the image never displays.
>
> If you think it would help, I'd be happy to figure out how to get you 
> one of the problematic nd2 files so that you can try to reproduce the 
> problem.
>
> Best,
> Dan
>
>
> On Dec 20, 2012, at 12:42 PM, Melissa Linkert 
> <melissa at glencoesoftware.com <mailto:melissa at glencoesoftware.com>>
>  wrote:
>
>> Hi Dan,
>>
>>> I suspect I may have discovered a bug or memory leak in the LOCI 
>>> MATLAB toolbox.  I'm using the bfopen.m script to read Nikon ND2 
>>> files in MATLAB R2011a on Mac OSX 10.8.  I'm able to read a 63MB ND2 
>>> file without any problem.  However, when I attempt to read a 120MB 
>>> file, the program crashes with an "out of memory" error (full text 
>>> of the error message is below).  However, I don't believe this is an 
>>> issue of not enough memory being available, because increasing the 
>>> maximum java heap memory from 256MB to 2GB in the MATLAB settings 
>>> had no effect on the problem.  Also, I am able to read the files 
>>> successfully using a different script (bfread.m from 
>>> https://github.com/prakatmac/bf-tools/wiki/about), though it is 
>>> slower than bfopen.m.
>>
>> Based upon the error message, it looks like bfopen.m was using an older
>> version of Bio-Formats.  The Matlab scripts from here:
>>
>> https://github.com/prakatmac/bf-tools
>>
>> will download the latest version of loci_tools.jar and place it in an
>> 'ext' folder, so it's likely that you now have two copies of
>> loci_tools.jar (one that is an old version and one that is the latest
>> version).
>>
>> Could you please try updating the copy of loci_tools.jar that is in your
>> Matlab work folder?  bfUpgradeCheck.m should be able to do this, or 
>> you can
>> manually download loci_tools.jar from:
>>
>> http://www.openmicroscopy.org/site/products/bio-formats/downloads
>>
>> The output of 'version = loci.formats.FormatTools.VERSION' should then
>> be "4.4.5" (if you downloaded the stable version) or "4.5.0-DEV" (if you
>> downloaded the trunk or daily build).
>>
>> Regards,
>> -Melissa
>>
>> On Thu, Dec 20, 2012 at 03:07:28PM +0000, Daniel Dickinson wrote:
>>> Hi,
>>>
>>> I suspect I may have discovered a bug or memory leak in the LOCI 
>>> MATLAB toolbox.  I'm using the bfopen.m script to read Nikon ND2 
>>> files in MATLAB R2011a on Mac OSX 10.8.  I'm able to read a 63MB ND2 
>>> file without any problem.  However, when I attempt to read a 120MB 
>>> file, the program crashes with an "out of memory" error (full text 
>>> of the error message is below).  However, I don't believe this is an 
>>> issue of not enough memory being available, because increasing the 
>>> maximum java heap memory from 256MB to 2GB in the MATLAB settings 
>>> had no effect on the problem.  Also, I am able to read the files 
>>> successfully using a different script (bfread.m from 
>>> https://github.com/prakatmac/bf-tools/wiki/about), though it is 
>>> slower than bfopen.m.
>>>
>>> Thanks for any suggestions.
>>> -Dan Dickinson
>>>
>>>
>>>>> imageCell=bfopen(['/Users/danieldickinson/Documents/Postdoc/Data/Exp139/139_mChCtrl 
>>>>> nd2/139_mChCtrl_002.nd2']);
>>> ??? Java exception occurred:
>>> java.lang.OutOfMemoryError: Java heap space
>>> at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1486)
>>> at loci.formats.in.NativeND2Reader.iterateIn(NativeND2Reader.java:1515)
>>> at loci.formats.in.NativeND2Reader.initFile(NativeND2Reader.java:403)
>>> at loci.formats.FormatReader.setId(FormatReader.java:1178)
>>> at loci.formats.DelegateReader.setId(DelegateReader.java:259)
>>> at loci.formats.ImageReader.setId(ImageReader.java:727)
>>> at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:529)
>>> at loci.formats.ChannelFiller.setId(ChannelFiller.java:263)
>>> at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:529)
>>> at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:274)
>>>
>>> Error in ==> bfGetReader at 57
>>> r.setId(id);
>>> Error in ==> bfopen at 92
>>> r = bfGetReader(id, stitchFiles);
>>>
>>>
>>> **/.*********************************************
>>> Daniel J. Dickinson, Ph.D.
>>> Postdoctoral fellow, Goldstein Lab
>>> University of North Carolina
>>> 650-815-1923
>>> ddickins at live.unc.edu<mailto:ddickins at live.unc.edu>
>>>
>>
>>> _______________________________________________
>>> ome-users mailing list
>>> ome-users at lists.openmicroscopy.org.uk
>>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>>
>>
>
> ***********************************************
> Daniel J. Dickinson, Ph.D.
> Postdoctoral fellow, Goldstein Lab
> University of North Carolina
> 650-815-1923
> ddickins at live.unc.edu <mailto:ddickins at live.unc.edu>
>
>
>
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> ome-users at lists.openmicroscopy.org.uk
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