opening of 64-bit TIFF files

[Johannes-P. Koch]

Dear all,

I saved quite a big file (~3GB) in a 64-bit TIFF file format. My ImageJ gives an error response. Does anybody have written an input plugin making this format available for opening in ImageJ? Or does such a plugin exist at all?

Best regards,
Johannes
_________________________________
Johannes-P. KOCH
University of Vienna
MFPL, Center of Molecular Biology
Department of Biochemistry
Dr. Bohrg. 9/5
A-1030 Vienna
Austria
phone [phone]
fax [phone]

[hidden email]




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[Albert Cardona]

Johannes-P. Koch wrote:
> Dear all,
>
> I saved quite a big file (~3GB) in a 64-bit TIFF file format. My ImageJ gives an error response. Does anybody have written an input plugin making this format available for opening in ImageJ? Or does such a plugin exist at all?
>  


ImageJ supports short (16-bit) and float (32-bit), but not 64-bit images
that I know of.
You could create a LongProcessor or a DoubleProcessor to implement
64-bit support, but they would not interact fully inside ImageJ -- would
need lots of tweaks all over.

Alternatively, you can create your own importer and represent them in
32-bit, doing some scaling.

Albert

--
Albert Cardona
http://albert.rierol.net

[Michael Schmid]

Hi Johannes,

ImageJ supports reading 64-bit images as raw data (and converts these  
to 32 bit).

If it is a one-time problem and you know the image size, you could  
try to open it as raw data. You have to play with the offset. A  
starting point might be Image size (in bytes) minus width*height*8;  
then you have to vary the value until the image appears centered.

This won't work for all tiff images, only if the image data is one  
big chunk.

Michael
________________________________________________________________

On 19 Dec 2008, at 16:34, Albert Cardona wrote:

> Johannes-P. Koch wrote:
>> Dear all,
>>
>> I saved quite a big file (~3GB) in a 64-bit TIFF file format. My  
>> ImageJ gives an error response. Does anybody have written an input  
>> plugin making this format available for opening in ImageJ? Or does  
>> such a plugin exist at all?
>>
>
>
> ImageJ supports short (16-bit) and float (32-bit), but not 64-bit  
> images that I know of.
> You could create a LongProcessor or a DoubleProcessor to implement  
> 64-bit support, but they would not interact fully inside ImageJ --  
> would need lots of tweaks all over.
>
> Alternatively, you can create your own importer and represent them  
> in 32-bit, doing some scaling.
>
> Albert
>
> --
> Albert Cardona
> http://albert.rierol.net

[Mario Emmenlauer-3]

Hi,

Johannes-P. Koch wrote:
> I saved quite a big file (~3GB) in a 64-bit TIFF file format. My ImageJ gives an error response. Does anybody have written an input plugin making this format available for opening in ImageJ? Or does such a plugin exist at all?

Just to be sure, you are saying your data is 64bit, or your file-offsets
are 64bit? I'm just asking, because you mention the file is huge (>2GB).
 >2GB tiff is a problem to some tiff-readers, and >4GB is a problem to
most tiff-readers.

But that is not what you mean, you mean your image data (inside the tiff
file structure) is 64bit?

Cheers,

    Mario

[ctrueden]

Hi Johannes,

If you mean the file offsets are 64bit, you are presumably using the BigTIFF
format:
http://www.aperio.com/bigtiff/

Bio-Formats supports BigTIFF, so please give it a try if you have not
already:
http://www.loci.wisc.edu/ome/formats.html

If Bio-Formats cannot read your file, we would be interested in fixing the
problem. Let us know, and I will send you our FTP information off-list.

-Curtis

On Fri, Dec 19, 2008 at 1:39 PM, Mario Emmenlauer <[hidden email]>wrote:

> Hi,
>
> Johannes-P. Koch wrote:
>
>> I saved quite a big file (~3GB) in a 64-bit TIFF file format. My ImageJ
>> gives an error response. Does anybody have written an input plugin making
>> this format available for opening in ImageJ? Or does such a plugin exist at
>> all?
>>
>
> Just to be sure, you are saying your data is 64bit, or your file-offsets
> are 64bit? I'm just asking, because you mention the file is huge (>2GB).
> >2GB tiff is a problem to some tiff-readers, and >4GB is a problem to
> most tiff-readers.
>
> But that is not what you mean, you mean your image data (inside the tiff
> file structure) is 64bit?
>
> Cheers,
>
>   Mario
>

[Johannes-P. Koch]

Thanks to all the replies, I am sorry for answering such late!

Anyway, the Bioformats plugin helped a lot. With this plugin I was able to
read the file format, which is indeed Bigtiff (64-bit off-sets).

Thanks again and happy new year.

Johannes


On Mo, 22.12.2008, 23:19, Curtis Rueden wrote:

> Hi Johannes,
>
> If you mean the file offsets are 64bit, you are presumably using the
> BigTIFF
> format:
> http://www.aperio.com/bigtiff/
>
> Bio-Formats supports BigTIFF, so please give it a try if you have not
> already:
> http://www.loci.wisc.edu/ome/formats.html
>
> If Bio-Formats cannot read your file, we would be interested in fixing the
> problem. Let us know, and I will send you our FTP information off-list.
>
> -Curtis
>
> On Fri, Dec 19, 2008 at 1:39 PM, Mario Emmenlauer
> <[hidden email]>wrote:
>
>> Hi,
>>
>> Johannes-P. Koch wrote:
>>
>>> I saved quite a big file (~3GB) in a 64-bit TIFF file format. My ImageJ
>>> gives an error response. Does anybody have written an input plugin
>>> making
>>> this format available for opening in ImageJ? Or does such a plugin
>>> exist at
>>> all?
>>>
>>
>> Just to be sure, you are saying your data is 64bit, or your file-offsets
>> are 64bit? I'm just asking, because you mention the file is huge (>2GB).
>> >2GB tiff is a problem to some tiff-readers, and >4GB is a problem to
>> most tiff-readers.
>>
>> But that is not what you mean, you mean your image data (inside the tiff
>> file structure) is 64bit?
>>
>> Cheers,
>>
>>   Mario
>>
>
>

--