jpg2000 and mxrs in imagej

Posted by Filip Bochner on Dec 06, 2015; 1:56pm
URL: http://imagej.273.s1.nabble.com/jpg2000-and-mxrs-in-imagej-tp5015148.html

Hi,

I'm struggling with export of very large .mrxs (mirax) files. These are scans from a slide scanner that I intend to analyze further in ImageJ.

I found a tool called JP2 WSI converter. It seems really good, because it can batch-convert huge mrxs files into jpg2000.

The problem is that even if ImageJ2 data structures and SCIFIO are enabled, the program cannot load the files.

Before I enabled them I was getting a following message: java.lang.IllegalArgumentException: Array size too large: 33280 x 105216 x 1

After enabling ImageJ2 data structures and SCIFIO the memory gets flooded and the software gets stuck (work on a workstation with 6 cores, 6 threads and 64 GB of memory).

Thanks for help!

Filip


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