Open Microscopy Environment

Hello

I'm trying out bfmatlab but cannot initialize a reader for large image files (100+GB).

Specifically, Matlab hangs or throws a java heap exception when I call bfGetReader. The problem happens at line 89: r.setId(id);

Is there an alternative way to initialize a reader? Can bfmatlab handle large files, and if so what's the right way to read them?

Thanks,

Alex

Hi Alex,

in general, bfmatlab should be able to cope with large image files without throwing Java heap exceptions.
Some information is necessary for us to help you with your issue:
- which version of Bio-Formats are you using?

Code: Select all

>> char(loci.formats.FormatTools.VERSION)


- which file format are you opening?
- how much Java memory is there available on MATLAB?

Code: Select all

java.lang.Runtime.getRuntime().maxMemory/(1024*1024)


Best,
Sebastien

Hi Sebastien
Thanks for the quick reply. Here's more info:
1. ver: 5.0.3
2. file format: PCORAW. No problem reading files up to 50 GB, but problems with bigger files.
3. 500 MB java heap. Does initialization require space only for metadata, or more?
Thanks,
Alex

Hi Alex,

for very large files (~100GB), could you try increase your heap size to a larger value e.g. 1024MB and see if this fixes the error?

Best
Sebastien

Yes -- that fixed it. Thank you. Is there any other method to read large files that's less memory intensive?

Thanks again,

Alex

Hi Alex,

no, to be able to read files with Bio-Formats, initializing the reader with `setId()` is mandatory. For many formats, including TIFF for instance, the memory requirements are expected to scale linearly with the size of the file so upping the JVM heap size to ~1G is expected for files of this order of magnitude.

Best,
Sebastien