Posted by
Johannes-P. Koch on
Nov 28, 2009; 2:04pm
URL: http://imagej.273.s1.nabble.com/Opening-btf-files-tp3690296p3690299.html
I got some info concerning the tiff file size limits; actually, I could
have made the calculations by myself anyway, but indeed, if you use
32-bit offsets, your are limited to something of 4gb. However, the big
problem with Olympus now is, that Olympus softwares handle these offsets
using signed integers, therefore supporting files sizes of up to only
2gb. I checked the file I mentioned as converted to tif with a size of
about 7gb. Actually, what I did was to split the channels, thus getting
below 2gb (each channel). I am sorry about this wrong statement in my
last mail.
Still, LOCI should work...have not got an answer on that, yet.
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: +44 131 6511512
>>> Fax: +44 131 6503128
>>>
>>
>>
>
>