http://imagej.273.s1.nabble.com/jpg2000-and-mxrs-in-imagej-tp5015148p5015239.html
> 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
The limitation is on the ImageJ 1.x side. ImageJ2 and Fiji still use ImageJ
1.x as the default user interface. Image data structures must be translated
> 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
>>>
>>>
>>> --
>>> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html>>>
>>>
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>> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html>>
>>
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