http://imagej.273.s1.nabble.com/Problems-with-Saving-Tiff-greater-than-4-GB-bigTiff-exporter-tp5010074p5012033.html
Unfortunately, I can't really offer any useful hints either. From my
> 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>>>
>>
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