Big Tiff (.btf) file format

[Oliver Biehlmaier]

Hi everyone,

Our Olympus CellR system generates “Big Tiff”-files (.btf) instead of conventional Tiff-files if a multidimensional acquisition experiment exceeds 4GB.
Bitplane’s Imaris does not recognize the btf. ImageJ tries to open but freezes...
Does anyone know which programs can open and handle these files?

Many thanks in advance,
Oliver


<><><><><><><><><><><><><><><><><><><><><><><><>

Oliver Biehlmaier, PhD

Advanced Microscopy
Light Microscopy Centre (LMC)
Schafmattstr. 18
ETH-Hönggerberg, HPM F16
8093 Zürich
Switzerland

Phone:  [phone]
Fax:    [phone]
Email:  oliver.biehlmaier@...
URL:    http://www.lmc.ethz.ch/People/Oliver
<><><><><><><><><><><><><><><><><><><><><><><><>

[Shalin Mehta]

Hi Oliver,
If you are using 32-bit version of ImageJ that may  not be able to
load files larger than 4 GB. 64-bit ImageJ should be able to do so. I
think when RAM is low, one can use virtual stacks to load only those
slices that are being processed. LOCI bioformats  supports files from
CellR but no mention of big-tiffs.
http://www.loci.wisc.edu/bio-formats-format/olympus-cellrapl
A post here  suggests that big tiffs are supported:
http://n2.nabble.com/Opening-btf-files-td4074793.html

hope this helps
Shalin


On Mon, Nov 30, 2009 at 7:42 PM, Oliver Biehlmaier
<[hidden email]> wrote:

> Hi everyone,
>
> Our Olympus CellR system generates “Big Tiff”-files (.btf) instead of
> conventional Tiff-files if a multidimensional acquisition experiment exceeds
> 4GB.
> Bitplane’s Imaris does not recognize the btf. ImageJ tries to open but
> freezes...
> Does anyone know which programs can open and handle these files?
>
> Many thanks in advance,
> Oliver
>
>
> <><><><><><><><><><><><><><><><><><><><><><><><>
>
> Oliver Biehlmaier, PhD
>
> Advanced Microscopy
> Light Microscopy Centre (LMC)
> Schafmattstr. 18
> ETH-Hönggerberg, HPM F16
> 8093 Zürich
> Switzerland
>
> Phone:  [phone]
> Fax:    [phone]
> Email:  [hidden email]
> URL:    http://www.lmc.ethz.ch/People/Oliver
> <><><><><><><><><><><><><><><><><><><><><><><><>
>
>

[Julio Vazquez]

I'm not sue, but perhaps the Aperio ImageScope viewer or the Olympus/Hamamatsu Nanozoomer viewer (NDPview) will do that.... I believe both instruments acquire data in big tiff format; both viewers are downloadable, so it should be easy to try them out and see...

http://www.aperio.com/download-imagescope-viewer.asp

http://www.olympusamerica.com/seg_section/seg_vm_downloads.asp

--

Julio Vazquez, 

Fred Hutchinson Cancer Research Center

Seattle, WA 98109-1024

http://www.fhcrc.org/

On Nov 30, 2009, at 3:42 AM, Oliver Biehlmaier wrote:

Hi everyone,

Our Olympus CellR system generates “Big Tiff”-files (.btf) instead of conventional Tiff-files if a multidimensional acquisition experiment exceeds 4GB.
Bitplane’s Imaris does not recognize the btf. ImageJ tries to open but freezes...
Does anyone know which programs can open and handle these files?

Many thanks in advance,
Oliver


<><><><><><><><><><><><><><><><><><><><><><><><>

Oliver Biehlmaier, PhD

Advanced Microscopy
Light Microscopy Centre (LMC)
Schafmattstr. 18
ETH-Hönggerberg, HPM F16
8093 Zürich
Switzerland

Phone:  [phone]
Fax:    [phone]
Email:  oliver.biehlmaier@...
URL:    http://www.lmc.ethz.ch/People/Oliver
<><><><><><><><><><><><><><><><><><><><><><><><>

[Rickman, Colin]

Hi Oliver

I have had similar issues with Bigtiff files from Olympus CellR. I
posted to the ImageJ list last week and Curtis Rueden (OME Loci) is
having a look at why I can't open them using the Bioformats plugin. My
solution at present is to use the CellR software to split the file in to
a tif image sequence and load the sequence in ImageJ (64bit Java in
Linux with 6Gb RAM allocated). Imaris should also be able to import the
sequence (on a 64bit computer with plenty of RAM) but you will have to
check the channel, Z and T dimensions after import .

Regards

Colin

> On Nov 30, 2009, at 3:42 AM, Oliver Biehlmaier wrote:
>
>> Hi everyone,
>>
>> Our Olympus CellR system generates “Big Tiff”-files (.btf) instead of
>> conventional Tiff-files if a multidimensional acquisition experiment
>> exceeds 4GB.
>> Bitplane’s Imaris does not recognize the btf. ImageJ tries to open
>> but freezes...
>> Does anyone know which programs can open and handle these files?
>>
>> Many thanks in advance,
>> Oliver
>>
>>
>> <><><><><><><><><><><><><><><><><><><><><><><><>
>>
>> Oliver Biehlmaier, PhD
>>
>> Advanced Microscopy
>> Light Microscopy Centre (LMC)
>> Schafmattstr. 18
>> ETH-Hönggerberg, HPM F16
>> 8093 Zürich
>> Switzerland
>>
>> Phone:  [phone]
>> Fax:    [phone]
>> Email:  [hidden email]
>> URL:    http://www.lmc.ethz.ch/People/Oliver
>> <><><><><><><><><><><><><><><><><><><><><><><><>
>>
>

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

Tel: [phone]
Fax: [phone]