[ome-users] FW: Extract individual tiles from huge tiled tiff file

[Melissa Linkert]

Hi Ofra,

> Is there a way to use bfconvert or other utility to extract automatically all the tiles into different files?
> The tile size is written in the file.

Not at the moment, unfortunately.  I have filed a ticket on our issue
tracking system to do this:

http://trac.openmicroscopy.org.uk/ome/ticket/10292

You have been CC'd, and so will receive an automated email when we
update the status of that ticket.  If you prefer not to receive those
emails, please let me know.

Regards,
-Melissa

On Mon, Jan 28, 2013 at 03:53:00PM +0000, Ofra Golani wrote:
> Dear Melissa
> 
> Thanks for your answer.
> Is there a way to use bfconvert or other utility to extract automatically all the tiles into different files?
> The tile size is written in the file.
> 
> Thanks,
> Ofra
> 
> PS:I tried to send this question to the mailing list a week ago but it didn't get through.
> 
> 
> Melissa Linkert <melissa at glencoesoftware.com> ëúá:
> Hi Ofra,
> 
> > I have a huge tiled tif files which was created by saving scan of whole slide histology from Panoramic Viewer software.
> > I can read the file using LOCI-Importer in Fiji, but I want to extract the individual tiles instead of the huge stitched image for further processing.
> >
> > Using bfconvert (using -separate) I can only split the 3 channels of the image, but not the tiles.
> > What flags do I need to use in order to get (all) the individual tiles ?
> 
> The '-crop x,y,w,h' flag should do this, so to extract the
> upper-left-most 512x512 tile you would do something like this:
> 
> $ bfconvert -crop 0,0,512,512 input-file.tiff output-file.tiff
> 
> In Fiji/ImageJ, you can also open tiles by selecting the "Crop on import"
> option.
> 
> Regards,
> -Melissa
> 
> P.S. For future, it is a little better to ask this sort of question on
> the ome-users mailing list (in CC):
> 
> http://www.openmicroscopy.org/site/community/mailing-lists
> 
> as that ensures a response even if I am away.
> 
> On Sun, Jan 27, 2013 at 01:11:09PM +0000, Ofra Golani wrote:
> > Dear Melissa,
> >
> > I have a huge tiled tif files which was created by saving scan of whole slide histology from Panoramic Viewer software.
> > I can read the file using LOCI-Importer in Fiji, but I want to extract the individual tiles instead of the huge stitched image for further processing.
> >
> > Using bfconvert (using -separate) I can only split the 3 channels of the image, but not the tiles.
> > What flags do I need to use in order to get (all) the individual tiles ?
> >
> > I'm attaching small example file.
> >
> > Thanks,
> > Ofra Golani
> >
> > BioImaging Informatics
> > Biological Services Unit
> > Weizmann Institute of Science
> > Tel: +972-8-934-5177
> > ofra.golani at weizmann.ac.il<mailto:ofra.golani at weizmann.ac.il>
> > http://bioservices.weizmann.ac.il/bioinformatics/about.html
> > http://www.weizmann.ac.il/vet/IC/informatics
> >
> 
>