[ome-users] ND2 opening issue in MATLAB

[Daniel Dickinson]

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>

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-users/attachments/20121220/7bc15242/attachment.html>