Open Microscopy Environment

Making my first attempts to import a file to Matlab using Bioformats. The file is generated by Aperio, has a .svs extension, and is large. It also has several ancillary files (metadata) that should be brought in at the same time. Here is how it goes (below). Any thoughts on how to fix this? Thanks. Paul

>> A=bfopen('E:\data\Theresa\Aperio Scans from tmz\83806.svs');
Reading IFDs

Populating metadata

Populating OME metadata

Expected positive value for PhysicalSizeX; got 0.0

Expected positive value for PhysicalSizeY; got 0.0

Reading series #1
.??? Java exception occurred:
java.lang.OutOfMemoryError: Java heap space

at loci.common.DataTools.allocate(DataTools.java:863)

at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:157)

at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:143)


Error in ==> bfGetPlane at 38
plane = r.openBytes(iPlane - 1);

Error in ==> bfopen at 93
arr = bfGetPlane(r, i);

Hi Paul,

Thank you very much for the error report.

The problem is that bfopen tries to open the complete image, even though it is very large. There is now a ticket on our issue tracking system to fix this:

http://trac.openmicroscopy.org.uk/ome/ticket/9777

In the meantime, if the image contains less than 2 GB of pixel data then you may be able to read it by increasing the amount of memory allocated to Matlab's JVM.

Regards,
-Melissa

I did increase memory, and it works.

Thanks

P