Nanozoomer annotation coordinate system to openslide pixels
bgilbert at cs.cmu.edu
Mon Nov 10 05:27:59 EST 2014
On 11/10/2014 02:27 AM, Ahmed Bassiouni wrote:
> The NDP annotations seems to use their own coordinate system which I can
> not convert to the openslide pixel based system to extract the pictures.
There are several other coordinate values in NDPI and VMS slides which
seem consistent with yours:
and in VMS only:
The values of PhysicalMacroWidth/Height imply that the units are nm.
Playing around in GIMP, I found that the OffsetFromSlideCentre values
are the offset of the center of the main image relative to the center of
the macro image (i.e., the slide), with +x pointing right and +y
> (some of the point coordinates are actually negative!! weird! see
> example below)
More specifically, all of your X coordinates are negative. Perhaps the
origin is the center of the physical slide (or the center of the main
If the coordinates are relative to the main image, you can use the
openslide.mpp-x/y properties to compute the correct scaling factor.
If the coordinates are relative to the entire slide, there's a problem,
since NDPI doesn't seem to provide an equivalent of the VMS-only
properties above. In order to convert the annotation coordinates to
main image coordinates, you would need to know the size of the slide,
which would need to be either hardcoded or calculated from (a) the
downsample of the macro image and (b) its pixel dimensions. The
downsample, in turn, can be calculated from (c) the X/YResolution tags
of the macro IFD, which OpenSlide does not expose right now. However,
the resulting slide dimensions would be fairly inaccurate because of the
low resolutions of (b) and (c).
I could add properties to expose the downsample of the macro image if
needed, but I'm hoping there's a better solution. Please let us know
what you find.
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