Re: Problems with Saving Tiff greater than 4 GB & bigTiff exporter

Posted by Djoere Gaublomme on Mar 17, 2015; 4:22pm
URL: http://imagej.273.s1.nabble.com/Problems-with-Saving-Tiff-greater-than-4-GB-bigTiff-exporter-tp5010074p5012017.html

Hi,

I was wondering if there is an update to this.
I am trying to save a  >4GB file as OME-TIFF via the BioFormats  
exporter in a macro, but I get this error as well.  I want to import  
the file into Imaris with timing metadata still attached (which works  
with ome-tiff).  I have tried saving as raw, but Imaris doesn't accept  
this format.

I read that SCIFIO should already automatically handle the  
bigTiff=true setting, yet I still get the error.
My IT knowledge currently doesn't go much further than writing a  
simple macro, so I have to admit feeling somewhat confused when  
reading explanations about this bug.

The macro command I tried is:
run("Bio-Formats Exporter", "save="+ outputfolder + name +".ome.tif  
compression=Uncompressed");

I tried with an updated version of Fiji (ImageJ  1.49p)

Is there a simple solution to this problem yet?

Thanks

Djoere




Quoting "Rasband, Wayne (NIH/NIMH) [E]" <[hidden email]>:

> 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
>> [hidden email]
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html