Re: jpg2000 and mxrs in imagej

Posted by ctrueden on
URL: http://imagej.273.s1.nabble.com/jpg2000-and-mxrs-in-imagej-tp5015148p5015239.html

Hi Herbie,

> 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?

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
between IJ1 and IJ2, so the 2 Gpix bottleneck still applies.

The ImgLib2 library and ImageJ common data model support N-dimensional
images in an extensible interface-driven way, with N<=2^31-1 and of length
2^63-1 each.

Regards,
Curtis

On Mon, Dec 7, 2015 at 3:26 AM, Herbie <[hidden email]> wrote:

> 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
>>>
>>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>
>>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html