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Re: jpg2000 and mxrs in imagej

Posted by Herbie on Dec 06, 2015; 3:18pm
URL: http://imagej.273.s1.nabble.com/jpg2000-and-mxrs-in-imagej-tp5015148p5015150.html

Filip,

evidently, RGB 0 bit doesn't make sense -- no?

Usually, RGB means 24bit per pixel which results in about 10.5 GByte for
your image.
I don't know why ImageJ2 can't deal with 10.5 GByte images, but I know
that the old data structures of Java, hence ImageJ, are can't.

"[...] the program cannot load the files"
I guess with "program" you mean "Fiji".

BTW, which _slide_ scanner provides "33280 x 105216" pixels per image?
What kind of slides (format?) do have such spatial resolution?

Best

Herbie

:::::::::::::::::::::::::::::::::::::::::::
Am 06.12.15 um 16:04 schrieb Filip Bochner:

> Hi Herbie,
>
> "x 1" means that this is just one image. If it was a stack with let's
> say 13 images it would say "x 13".
>
> NIS-elements viewer (which just opens the images) shows RGB 0 bit.
>
> Filip
>
> -----Original Message----- From: ImageJ Interest Group
> [mailto:[hidden email]] On Behalf Of Herbie Sent: Sunday,
> December 06, 2015 4:46 PM To: [hidden email] Subject: Re:
> jpg2000 and mxrs in imagej
>
> Filip,
>
> I've no experience with ImageJ2 data structures and don't know about
> their limits, but what does "x 1" mean in "33280 x 105216 x 1"? Does
> it indicate a single image, i.e. no stack, or does it stand for a
> binary-valued image?
>
> If it is not a binary-valued image, what is its bit-depth?
>
> Best
>
> Herbie
>
> ::::::::::::::::::::::::::::::::::::::::::: Am 06.12.15 um 14:56
> schrieb Filip Bochner:
>> 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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