http://imagej.273.s1.nabble.com/Problems-with-Saving-Tiff-greater-than-4-GB-bigTiff-exporter-tp5010074p5012152.html
> Hi,
>
> I'd be curious as well as we are basically having the same issue here...
>
> Unfortunately, I can't really offer any useful hints either. From my
> experience, the combination with Imaris is even more tricky as they can't
> read BigTIFFs - at least none that I tried.
>
> Best
> ~Niko
>
>
> On 17.03.2015 17:22, Djoere Gaublomme wrote:
>
>> 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>>
>
> --
> Niko Ehrenfeuchter | Image Analysis Specialist | Biozentrum, University of
> Basel | Klingelbergstr. 50/70 | CH-4056 Basel
> Phone: +41 (61) 26 72673 |
[hidden email] |
> www.biozentrum.unibas.ch | www.microscopynetwork.unibas.ch
>
>
> --
> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html>