Posted by
Filip Bochner on
Dec 07, 2015; 10:03am
URL: http://imagej.273.s1.nabble.com/jpg2000-and-mxrs-in-imagej-tp5015148p5015159.html
Hi Curtis and Herbie,
> 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.
This is what I just did. I downloaded FIJI again and updated it through the update tool. Still I get the same error about the array size.
> 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
Unfortunately "Crop on import still doesn't work. As I understand X Coordinate 1 and Y Coordinate 1 are the coordinates that specify where to start cropping the matrix. Width 1 and Height 1 are probably the sizes of the single tile? It still doesn't work with such input I get the same error about the array size. I suspect that FIJI has to load it first in order to crop it, so it leads to the same problem. What do you think?
> if, as Curtis tells us, ImageJ-2/SCIFIO shows the same limited array size as ImageJ-1, that actually is a limitation due to "classic" Java, then I see no chance for handling images as large as yours
Is this problem going to be addressed in the future? I understand for now there is no way to do it? If not the only option is to use the python library called "openslide" and then maybe MATLAB? Would MATLAB handle such a big maps?
Thanks
Filip
-----Original Message-----
From: ImageJ Interest Group [mailto:
[hidden email]] On Behalf Of Curtis Rueden
Sent: Monday, December 07, 2015 5:55 AM
To:
[hidden email]
Subject: Re: jpg2000 and mxrs in imagej
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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