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Re: jpg2000 and mxrs in imagej

Posted by Herbie on Dec 07, 2015; 9:18am
URL: http://imagej.273.s1.nabble.com/jpg2000-and-mxrs-in-imagej-tp5015148p5015157.html

Good day Curtis,

I'm a bit surprised that ImageJ-2/SCIFIO is limited to the same amount
of pixels (array size) as ImageJ-1. I thought that it uses the newer
Java BIG number formats that should allow for much larger arrays. Do I
confuse or did I miss something?

In my response to Filip I thought that the problem only concerns the
io-section of ImageJ-2, i.e. "Bio-Formats" or the like.

Eager to learn more about this aspect of ImageJ-2

Herbie

:::::::::::::::::::::::::::::::::::::::::::
Am 07.12.15 um 04:54 schrieb Curtis Rueden:

> 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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>>
>
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