http://imagej.273.s1.nabble.com/jpg2000-and-mxrs-in-imagej-tp5015148p5015151.html
images you are dealing with.
the file format.
> Herbie,
>
> Of course you're right. I couldn't see what is the bit depth in
> properties of the file. I would also guess it's 24bit. Apparently
> Image Viewer displayed it incorrectly. And I trusted it
> unfortunately.
>
> Yes, we keep talking about Fiji :)
>
> The slide scanner' name's Panoramic Midi. It saves the files in .mrxs
> format. Each .mrxs is accompanied with a folder of .dat files. In
> principle it's a tiled image that can be viewed by free Panoramic
> Viewer (that doesn't have a batch export and it's poorly written so
> the conversion of single ROI takes forever and I have tens of slides
> with tens of ROIs and will have even more). A single scan gives
> 4096x4096 resolution images, but there is an array of them, which
> after export gives a huge matrix.
>
> I don't think it's a size (gb) problem, since I opened much larger
> files in Fiji. It could be an array-size problem. It might not be
> even related to the format, but I'm not sure whether .tiff of similar
> size would give the same error (or crash).
>
> Filip
>
> Wysłane z iPada
>
> Dnia 06.12.2015 o godz. 17:26 Herbie <
[hidden email]> napisał(a):
>
>> 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
>