[ome-users] Bug report: Cannot open jp2 file created by StereoInvestigator

[Kouichi C. Nakamura]

To whom it may concern,

This is a report that I could not open a |*.jp2|file created by 
StereoInvestigator 11 with Bioformats MATLAB toolbox 5.7.1.

Best regards,

Kouichi

Bioformats MATLAB toolbox 5.7.1

Windows 7

MATLAB R2017b

*Non-working data:*

https://www.openmicroscopy.org/qa2/qa/feedback/18265/?token=8cf0204d2e89b851340d51ae107504bd

*Format detailts:*This .jp2 file was created by StereoInvestigator 11. I 
was able to open it with Bioformats plugin with Fiji. Although I got a 
warning, I did not get a |OutOfMemory|or |NegativeArraySize|error 
message when trying to open the file with MATLAB. With the same command 
I was able to open a |*.jpg|file successfully.

my code

filename = 'Z:\Images from Otto\Images\20171018 Qudro, Rb CR Gt 
CB\Rb-CR(A488) Gt-CB(Frontier,Cy3)_5x_AR-_01.jp2';
​
data = bfopen(filename);

Error message


data = bfopen(filename);
​
Warning: *** Insufficient memory detected. ***
*** 368m found ***
*** 512m or greater is recommended ***
*** See http://www.mathworks.com/matlabcentral/answers/92813 ***
*** for instructions on increasing memory allocation. ***

> In bfCheckJavaMemory (line 53)
In bfGetReader (line 47)
In bfopen (line 114)
Reading series #1
   .Error using bfGetPlane (line 78)
Java exception occurred:
java.lang.RuntimeException:
jj2000.j2k.fileformat.reader.FileFormatReader.<init>(Ljj2000/j2k/io/RandomAccessIO;Lcom/sun/media/imageioimpl/plugins/jpeg2000/J2KMetadata;)V
​
   at 
com.sun.media.imageioimpl.plugins.jpeg2000.J2KReadState.initializeRead(J2KReadState.java:729)
​
   at 
com.sun.media.imageioimpl.plugins.jpeg2000.J2KReadState.<init>(J2KReadState.java:241)
​
   at 
com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageReader.readRaster(J2KImageReader.java:551)
​
   at 
ome.codecs.services.JAIIIOServiceImpl.readRaster(JAIIIOServiceImpl.java:177)
​
   at ome.codecs.JPEG2000Codec.decompress(JPEG2000Codec.java:296)
​
   at ome.codecs.JPEG2000Codec.decompress(JPEG2000Codec.java:267)
​
   at loci.formats.codec.WrappedCodec.decompress(WrappedCodec.java:132)
​
   at loci.formats.codec.JPEG2000Codec.decompress(JPEG2000Codec.java:63)
​
   at loci.formats.in.JPEG2000Reader.openBytes(JPEG2000Reader.java:182)
​
   at loci.formats.ImageReader.openBytes(ImageReader.java:457)
​
   at loci.formats.ChannelFiller.openBytes(ChannelFiller.java:156)
​
   at loci.formats.ChannelFiller.openBytes(ChannelFiller.java:148)
​
   at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:198)
​
   at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:159)
​
Caused by: java.lang.NoSuchMethodError:
jj2000.j2k.fileformat.reader.FileFormatReader.<init>(Ljj2000/j2k/io/RandomAccessIO;Lcom/sun/media/imageioimpl/plugins/jpeg2000/J2KMetadata;)V
​
   at 
com.sun.media.imageioimpl.plugins.jpeg2000.J2KReadState.initializeRead(J2KReadState.java:450)
​
   ... 13 more
​
Error in bfopen (line 150)
       arr = bfGetPlane(r, i, varargin{:});
78 plane = r.openBytes(...


-- 
Kouichi C. Nakamura, PhD
Senior Postdoctoral Neuroscientist
MRC Brain Network Dynamics Unit
University of Oxford
Mansfield Road, Oxford OX1 3TH, United Kingdom
+44-1865-271582 (office)
http://www.mrcbndu.ox.ac.uk/people/dr-kouichi-c-nakamura
kouichi.c.nakamura at gmail.com
kouichi.nakamura at pharm.ox.ac.uk

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