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

[Melissa Linkert]

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
>