[ome-users] big data processing with bfopen

[Yuanyuan Jiang]

Dear All,

 

I have a big stream data from the Hamamatsu sCMOS camera. The file size is
more than 10GB and the format can be .BTF(big tiff) or the .HIS format
(Hamamatsu format). I tried to use the bioformats library (bfopen) to load
in the MATLAB or the ImageJ, in both cases, the latest jar files are added
to the path of the software. 

 

However, for the HIS format, it only read portion of the data.  That is
probably due to the memory restriction of the bioformats only read 2 GB 

    error(['Image plane too large. Only 2GB of data can be extracted '...

        'at one time. You can workaround the problem by opening '...

        'the plane in tiles.']);

One suggest from the link
http://www.openmicroscopy.org/site/support/bio-formats5.2/about/bug-reportin
g.html

But I do not find any examples to use it : openBytes(int, int,int, int, int)


 

If I use the big tiff format, the bio-formats can read the small dataset,
but the larger dataset (>4GB), there is error to ask the Java advanced
Imaging, which I have no clue to install or include. 

 

Error using bfGetReader (line 84)

Java exception occurred:

loci.formats.MissingLibraryException: Java Advanced Imaging

(JAI) is required to read some TIFF files. Please install JAI

from https://jai.dev.java.net/

 

 

Can someone help me to find a solution. Really thanks a lot.

 

 

Best regards,

 

Yuanyuan

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