Opening .btf files

[Colin Rickman-3]

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]

[Johannes-P. Koch]

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

phone: [phone]
fax: [phone]

mail to: [hidden email]

[Colin Rickman-3]

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]
>>
>
>

--
--
Dr Colin Rickman
School of Engineering and Physical Sciences Heriot-Watt University Edinburgh
EH14 4AS

Tel: [phone]
Fax: [phone]

[Johannes-P. Koch]

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

phone: [phone]
fax: [phone]

mail to: [hidden email]

[Johannes-P. Koch]

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: [phone]
>>> Fax: [phone]
>>>
>>
>>
>
>

[ctrueden]

Hi Colin & Johannes,

The Bio-Formats Importer plugin does support the BigTIFF format (recognized
with various extensions: .tif, .tiff, .btf, .tf2, .tf8). If your files do
not work, it is probably a bug. We would need to know the exact error
message (if any) and ideally get a sample file from you, since we do not
have the CellR software at LOCI.

If you need a place to put a sample dataset, we can send you our server
information off-list.

Regards,
Curtis

On Sat, Nov 28, 2009 at 8:04 AM, Johannes-P. Koch <
[hidden email]> wrote:

> 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: [phone]
>>>> Fax: [phone]
>>>>
>>>>
>>>
>>>
>>
>>