Posted by
ctrueden on
May 28, 2014; 6:00pm
URL: http://imagej.273.s1.nabble.com/Apparent-Bio-formats-error-tp5007899p5007960.html
Hi Thomas,
> I tried to open it with LOCI, full resolution (46080*41728, 3 planes),
> I got "java.lang.ArrayIndexOutOfBoundsException: 1473511424" error.
> The 11520*10432 resolution open, but the quality is not here.
If you crop your image (using the "Crop on import" checkbox) such that the
opened plane is less than 2 gigapixels in size (width times height),
Bio-Formats should be open the full resolution data one tile at a time.
You could also try converting to TIFF in one shot using the Bio-Formats
command line tools [1] ("bfconvert" command), though I have not tested this
with image planes exceeding 2 GPix.
Regards,
Curtis
[1]
https://www.openmicroscopy.org/site/support/bio-formats5/users/comlinetools/On Wed, May 28, 2014 at 2:16 AM, Thomas GUILBERT
<
[hidden email]>wrote:
> Dear all,
>
> I used to work on my old computer with "large" NDPI files from Hamamatsu
> Nanozoomer acquisitions.
> To treat this kind of large files, I use NDPI tools plugin :
> - PreviewNDPI
> - Selection of small ROI (I asume entire image too big)
> - Extract to TIFF
> - then, my processing.
>
> Selection of ROIs is time consuming.
> I actually use new 64bits Win7 32GbRAM 3GbRAM Graphic Card's computer.
> Well, if I want to convert an _entire NDPI image_ to tiff (full
> resolution), I only get this error message : "Illegal page requested from a
> TIFF file."
>
> I tried to open it with LOCI, full resolution (46080*41728, 3 planes), I
> got
> "java.lang.ArrayIndexOutOfBoundsException: 1473511424" error.
> The 11520*10432 resolution open, but the quality is not here.
>
> Could anyone tell me what are the limits ?
>
> Thanks all,
>
> --
> Thomas GUILBERT, PhD
> Plate-Forme Cochin Imagerie,
> Institut Cochin - INSERM U1016
> Bât. Gustave Roussy 5ème étage
> 22 rue Méchain, 75014 PARIS
> tel: 01 40 51 66 55
>
>
http://www.cochin.inserm.fr/>
[hidden email]
>
> --
> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html>
--
ImageJ mailing list:
http://imagej.nih.gov/ij/list.html