MRXS huge white borders

[jcupitt at gmail.com]

On 28 July 2014 22:38, Benjamin Gilbert <bgilbert at cs.cmu.edu> wrote:
> 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.
>
>
> 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?

Yes, that's probably a good idea.

It could even be the default behaviour. Would anyone ever want huge
areas of blank image? The bounds would still be in the metadata so the
extra blank stuff could easily be added back.

John