Z-stack in MRXS
gyurist at gmail.com
Sat Dec 13 12:52:15 EST 2014
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. OpenSlide reads the default layer fine but we would like to
show the additional layers too.
The Panoramic Viewer show these very nicely as you can see on the examples
I've checked the OpenSlide.ini and these additional layers look something
like this there:
HIER_2_NAME = Microscope focus level
HIER_2_COUNT = 20
HIER_2_DEFAULT = 0
HIER_2_SECTION = LAYER_2_SECTION
HIER_2_VAL_0 = ExtFocusLevel
HIER_2_VAL_0_SECTION = LAYER_2_LEVEL_0_SECTION
HIER_2_VAL_1 = ZStackLevel_(-9)
HIER_2_VAL_1_SECTION = LAYER_2_LEVEL_1_SECTION
HIER_2_VAL_2 = ZStackLevel_(-8)
HIER_2_VAL_2_SECTION = LAYER_2_LEVEL_2_SECTION
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've also checked the openslide-vendor-mirax.c source file and it seemed to
me only the zoom level hierarchy is processed, the others are simply
I can share one of the example mrxs files we have if you are interested.
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