Login  Register

Re: jpg2000 and mxrs in imagej

Posted by Herbie on Dec 07, 2015; 5:03pm
URL: http://imagej.273.s1.nabble.com/jpg2000-and-mxrs-in-imagej-tp5015148p5015163.html

Dear Kees,

thanks for chiming in but Filip has to deal with much larger images of
about 33k x 105k pixels. I'm sure that this is beyond classic Java's
array size.

Have a good day

Herbie

:::::::::::::::::::::::::::::::::::::::::::::::::::
Am 07.12.15 um 18:03 schrieb Straatman, Kees (Dr.):

> Dear Curtis, Herbie and Filip,
>
> Did not follow this discussion closely but I thought that TrackEM2
> plugin is able to open large datasets? Found on their website "•Very
> large images (like 21k x 21k) are now handled much better; only
> waiting time is for loading the file."
>
> Best wishes
>
> Kees
>
>
> Dr Ir K.R. Straatman Senior Experimental Officer Advanced Imaging
> Facility Centre for Core Biotechnology Services University of
> Leicester
> http://www2.le.ac.uk/colleges/medbiopsych/facilities-and-services/cbs/lite/aif
>
>
>
> -----Original Message----- From: ImageJ Interest Group
> [mailto:[hidden email]] On Behalf Of Filip Bochner Sent: 07
> December 2015 10:06 To: [hidden email] Subject: Re: jpg2000 and
> mxrs in imagej
>
> 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
>>
>>
>> -- 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
>

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