Z-stack in MRXS

Tibor Gyuris gyurist at gmail.com
Mon Dec 15 05:17:31 EST 2014

Hi Benjamin,

Thanks for the reply!

You can grab the sample from the following url although it's going to be a
massive 106GB download:



On Mon Dec 15 2014 at 05:58:04 CET Benjamin Gilbert <bgilbert at cs.cmu.edu>

> On 12/13/2014 12:52 PM, Tibor Gyuris wrote:
> > We are working on a web based virtual microscopy service and we have
> > received a couple of a huge ( 100GByte+ ) mrxs images which contain not
> > only a single image but also 20+ additional layers with different focal
> > plane scans.
> >
> > Have you encountered such an mrxs before and if yes do you know how
> > these additional ZStackLevel layers are stored and what would be the
> > simplest way to add support for these?
> >
> > I suspect each of these should point to a structure which is identical
> > to the zoom level hierarchy.
> I haven't seen such files myself, but that would be my guess as well.
> The larger issue is that the OpenSlide API doesn't provide a way to
> refer to more than one focal plane:
>      https://github.com/openslide/openslide/issues/31
> so even if we added support to the driver, there would be no way to
> exercise it.  This limitation affects several formats and will need to
> be addressed at some point.
> > I can share one of the example mrxs files we have if you are interested.
> That would be very helpful.
> --Benjamin Gilbert
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