Posted by
ctrueden on
Dec 07, 2015; 3:54am
URL: http://imagej.273.s1.nabble.com/jpg2000-and-mxrs-in-imagej-tp5015148p5015154.html
Hi Filip,
> After enabling ImageJ2 data structures and SCIFIO
It sounds like you are running an old version of Fiji. For various reasons,
I suggest you upgrade to the latest version. However, in this case doing so
will not solve the issue at hand.
> IllegalArgumentException: Array size too large: 33280 x 105216 x 1
ImageJ only supports planes up to 2Gpix. See also
http://imagej.net/Troubleshooting#NegativeArraySizeException.
As a workaround, I second Herbie's suggestion to work with your image in
tiles. You can use the "Crop on import" option on the Bio-Formats Import
Options dialog.
Regards,
Curtis
On Sun, Dec 6, 2015 at 7:56 AM, Filip Bochner <
[hidden email]>
wrote:
> 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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