Re: Opening .btf files

Posted by Johannes-P. Koch on Nov 27, 2009; 12:10pm
URL: http://imagej.273.s1.nabble.com/Opening-btf-files-tp3690296p3690301.html

Concerning btif and tif, maybe we can get some feedback from
specialists, but I have already opened bigtiff files (appr. 7gb) in
ImageJ (using LOCI) and saved them as tiff (which is of about the same
file size in order to import those in Huygens (because Huygens cannot
read 64-bit offsets at the moment, but again, they are working on that).
So, I think the limitation comes from the CellR software and is not due
to an inherent size limit of tiff files?! Correct?

I will write you ASAP about the CellR version I am using.

Still, it should be possible with LOCI to read such bigtiff files, maybe
again, we could get a feedback here from the developpers?

Best,
Johannes


Colin Rickman schrieb:

> Dear Johannes
>
> Thanks for getting in touch. I don't think it is possible to save such
> large files as a .tif file given the inherent limit on file size. I
> think that is where the big tiff (.btf) format is preferable. As I
> said in my message I have tried the most recent version of Bioformats
> but it cannot open the file. Maybe the way CellR wites the .btf file
> is incompatible. Which version of CellR are you using?
>
> At the moment I am exporting the data using CellR to individual
> Z-stack .tif files to restitch together.
>
> Colin
>
> Johannes-P. Koch wrote:
>> Dear Colin,
>>
>> I have the same problem; First, I have to mention that the handling
>> of big files is not sophisticated in the Olympus software. I am in
>> contact with Olympus, they are currently working on that.
>> Specifially, I suppose, that it should be possible to save big files
>> (>2gb) in tif. Now, the program simply does not allow this action.
>>
>> What you need to open such files in ImageJ is the LOCI Bioformats
>> plugin; works perfectly. An alternative would be to not save your
>> files as bigtiff, but as split tifs and import the series in ImageJ
>> via File->Import->Image Sequence.
>>
>> Best,
>> Johannes
>>
>> Colin Rickman schrieb:
>>> Hi
>>>
>>> I have acquired some large 4D widefield datasets using an Olympus
>>> microscope running the CellR software. The files are very large and
>>> have been saved in a .btf file format. I have the most stable
>>> version of bioformats installed but can't open them using imagej. Is
>>> this file format supproted in any way by imagej?
>>>
>>> Hope someone can help
>>>
>>> Regards
>>>
>>> Colin
>>>
>>> --
>>> Dr Colin Rickman
>>> School of Engineering and Physical Sciences Heriot-Watt University
>>> Edinburgh
>>> EH14 4AS
>>>
>>> Tel: [phone]
>>> Fax: [phone]
>>>
>>
>>
>
>

--
Mag. Johannes-P. KOCH
Department of Biochemistry and Cell Biology
MFPL, University of Vienna
Dr. Bohrgasse 9/5
A-1030 Vienna
Austria

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