MRXS huge white borders

[Benjamin Gilbert]

On 07/28/2014 04:21 PM, Tom N. wrote:
> I am using "vips dzsave" pyramid builder to convert an MRXS slide to
> Zoomify on Ubuntu. Vips uses OpenSlide to read the MRXS slide.  The
> conversion is working fine, but the resulting Zoomify slide has huge
> white borders.

Hi Tom,

OpenSlide uses the coordinate system of the original slide file.  For 
MRXS files, this means that the image includes the entire original 
slide, not just the region for which pixels were recorded.

If you are using OpenSlide >= 3.4.0, you can read the 
openslide.bounds-{x,y,width,height} properties to get the level-0 
coordinates of the non-empty portion of the slide.  You should be able 
to use VIPS to crop to these bounds before generating your Zoomify pyramid.

John, what do you think of adding an option to VIPS openslideload to 
automatically crop using the bounds properties?

--Benjamin Gilbert