Posted by
Rasband, Wayne (NIH/NIMH) [E] on
Oct 17, 2014; 1:27am
URL: http://imagej.273.s1.nabble.com/Problems-with-Saving-Tiff-greater-than-4-GB-bigTiff-exporter-tp5010074p5010087.html
On Oct 16, 2014, at 4:33 AM, T.J. Wardill wrote:
> Dear ImageJ list,
>
> Can someone tell me exactly which format is a multipage-tif file that
> ImageJ/Fiji saves when the total size is over 4GB?
Stacks larger than 4GB are saved in "raw" format, as if you had used File>Save As>Raw except the raw data is preceded by a small header. You can find the header size (offset) by opening the file in ImageJ with debugging enabled in Edit>Options>Misc. Matlab should be able to open the files if it has the ability to open raw files. When saving stacks larger than 4GB, the latest ImageJ daily build (1.49j3) displays the information needed to open the stack as raw data. Here is an example of the information displayed:
Stack is larger than 4GB. Most TIFF readers will only open the first image. Use this information to open as raw:
name=Untitled, dir=, width=1024, height=1024, nImages=2050, offset=203, type=ushort, byteOrder=little, format=0, url=, whiteIsZero=f, lutSize=0, comp=1, ranges=null, samples=1
-wayne
> I have a problem that
> Matlab cannot load subframes from these large files. I also tried using
> the bioformats exporter to get a bigTiff formatted file but found this
> would not work. I tried the tif and OME-Tif extensions but got the log
> error that stated loci.formats.FormatException: File is too large; call
> setBigTiff(true), and the saving up to 4gb when the log error occurred
> was quite slow. There does not seem to be anywhere easy to set this
> parameter within Fiji. This is probably a simple error but any help
> would be most appreciated.
>
> Best, Trevor
> --
>
> DR TREVOR WARDILL (BBSRC David Phillips Fellow)
> Department of Physiology, Development and Neuroscience
> Physiology Building, University of Cambridge
> Downing Street, Cambridge, CB2 3EG
> (M): 07914 945 555 (W): 01223 746 919
>
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>
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