Posted by
T.J. Wardill on
Oct 16, 2014; 2:20pm
URL: http://imagej.273.s1.nabble.com/Problems-with-Saving-Tiff-greater-than-4-GB-bigTiff-exporter-tp5010074p5010082.html
Thanks Johannes,
So my original post asked about the bioformats plugin, noting it will
not save tif files larger than 4 GB. I cannot use ImageJ2 as it has too
many bugs for my purposes. I do not want to use single files for each
frame as I have many 10,000's of frames from dual high speed cameras. I
can currently use 2GB chunks as tifs but wanted to manage my data in
single takes which are about 15-20 GB.
SCIFIO seems to be integrated with the save function in ImageJ, but the
file format for large tiffs, is not readable by Matlab, so at the moment
there is no solution that I can find in standard ImageJ/Fiji that will
save a multipage tiff that is about 15-20GB and can be read by Matlab.
Now it may just be that Matlab is useless with bigtif file formats but I
am not sure this is the case.
If anyone can please tell the file format for the large tifs saved with
ImageJ standard I would be most grateful. This may help me diagnose why
Matlab cannot read them.
Best regards, Trevor
On 2014-10-16 15:01, Johannes Schindelin wrote:
> Hi Trevor,
>
> please do not cut out the community of the conversation. I re-Cc:ed the
> mailing list. The question you asked could have been easily answered by
> other users than myself.
>
> On Thu, 16 Oct 2014, T.J. Wardill wrote:
>
>> Unfortunately in my version of Fiji & ImageJ, I do not have these save as options. Are these a plugin?
>
> Yes. The Bio-Formats and SCIFIO plugins, respectively. If you want to use
> plain ImageJ 1.x, you will have to get them from somewhere and install
> them manually. In Fiji, Bio-Formats is included since 2008 and SCIFIO is
> included since sometime last year.
>
> Ciao,
> Johannes
>
> Thanks Johannes, look like good ideas, are these in ImageJ?
>
> Unfortunately in my version of Fiji & ImageJ, I do not have these save as options. Are these a plugin?
>
> Regards, Trevor
>
> On 2014-10-16 14:04, Johannes Schindelin wrote:
>
> Hi Trevor,
>
> On Thu, 16 Oct 2014, T.J. Wardill wrote:
> Can someone tell me exactly which format is a multipage-tif file that ImageJ/Fiji saves when the total size is over 4GB?
>
> There are unfortunately multiple ways to save .tiff files. In your case,
> you might want to use File>Save As>SCIFIO... or File>Save As>Bio-Formats...
>
> Ciao,
> Johannes
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