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Re: jpg2000 and mxrs in imagej

Posted by Herbie on Dec 07, 2015; 9:25am
URL: http://imagej.273.s1.nabble.com/jpg2000-and-mxrs-in-imagej-tp5015148p5015158.html

Filip,

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.

Best

Herbie

:::::::::::::::::::::::::::::::::::::::::::
Am 06.12.15 um 20:06 schrieb Filip Bochner:

> Herbie, thanks for your input. There is no way to get into the single
> tiles. Probably some programing must be involved there, and that for
> now exceeds my capabilities. I'm a biologist trying to get the stuff
> done in the simplest way possible. I hope there is a simple way, and
> the imagej problem can be solved.
>
> Any other ideas?
>
>
>
> Wysłane z iPada
>
> Dnia 06.12.2015 o godz. 19:37 Herbie <[hidden email]> napisał(a):
>
>> Filip,
>>
>> I found your explanations quite helpful and I hope that those on
>> the list who may help further, also get a better impression of the
>> kind of images you are dealing with.
>>
>> If you can separately access the 4096x4096 images, my
>> recommendation is to do the tiling in Fiji which more or less
>> implies to rely on TIF as the file format.
>>
>> HTH
>>
>> Herbie
>>
>> :::::::::::::::::::::::::::::::::::::::::::
>>> Am 06.12.15 um 18:22 schrieb Filip Bochner: 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
>>
>> -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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