Z-stack in MRXS

Benjamin Gilbert bgilbert at cs.cmu.edu
Sun Dec 14 23:57:59 EST 2014

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:


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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