<font size=2 face="sans-serif">Hello,</font>
<br>
<br><font size=2 face="sans-serif">I concur with Benjamin that this is
mostly hardware (scanning device and camera) related information. I've
asked one of our engineers for his 'best guess' estimation of what the
parameters mean and here's what he came up with:</font>
<br>
<br><font size=2 face="sans-serif">XYImagePos => Possible a location
within the WSI that may be linked back to the position of the slideholder
in the device (see also XYZMotorPos)</font>
<br><font size=2 face="sans-serif">XYZMotorPos => The effectieve location
of the slideholder in the Miraxdevice when a picture is taken. Whether
these axis are also used to define additional locations within the WSI,
is unknown</font>
<br><font size=2 face="sans-serif">XYZMotorError => Correction error
(and suggests the possibility to compensate) to XYZMotorPos.</font>
<br><font size=2 face="sans-serif">ObjectLevel => Perhaps the level
in the 'tiled pyramid'?</font>
<br><font size=2 face="sans-serif">OpticalFocusLevel => Autofocus-related
(helps explain why the zoom-level is never exactly 40x, but e.g. 39.8x)</font>
<br><font size=2 face="sans-serif">LaserFocusLevel => Autofocus-related</font>
<br><font size=2 face="sans-serif">FocusingType => What algorithm was
used for autofocus</font>
<br><font size=2 face="sans-serif">Neighbours => What pixels and images
are next to each other</font>
<br><font size=2 face="sans-serif">FocalPlane => Name of the focus level
(an alternate name for ZMotorPos perhaps?)</font>
<br><font size=2 face="sans-serif">ImageAcquisitionTime => exposure
time for a picture</font>
<br>
<br><font size=2 face="sans-serif">If would seem that the Neighbours information
at least may be useful to help stitch the respective tiles back together.
Do you find this information for each tile? Or just once for a single WSI?</font>
<br>
<br><font size=2 face="sans-serif">hth,</font>
<br>
<br><font size=2 face="sans-serif">Yves</font>
<br>
<br>
<br>
<br><font size=1 color=#5f5f5f face="sans-serif">From:
</font><font size=1 face="sans-serif">"Benjamin Gilbert
(OpenSlide)" <bgilbert@cs.cmu.edu></font>
<br><font size=1 color=#5f5f5f face="sans-serif">To:
</font><font size=1 face="sans-serif">openslide-users@lists.andrew.cmu.edu</font>
<br><font size=1 color=#5f5f5f face="sans-serif">Date:
</font><font size=1 face="sans-serif">20-08-12 01:58</font>
<br><font size=1 color=#5f5f5f face="sans-serif">Subject:
</font><font size=1 face="sans-serif">Re: Opinions
regarding MIRAX data file contents</font>
<br><font size=1 color=#5f5f5f face="sans-serif">Sent by:
</font><font size=1 face="sans-serif">openslide-users-bounces+sucaet=histogenex.com@lists.andrew.cmu.edu</font>
<br>
<hr noshade>
<br>
<br>
<br><tt><font size=2>On Fri, August 17, 2012 1:08 am, John Minnie wrote:<br>
> <scaninfo XImagePos="8" YImagePos="115"<br>
> XMotorPos="3006" YMotorPos="47110" ZMotorPos="1356"
XMotorError="0"<br>
> YMotorError="0" ZMotorError="0" ObjectLevel="0.0143"<br>
> OpticalFocusLevel="-1"<br>
> LaserFocusLevel="-1.0000" FocusingType="OptPartialRange"<br>
> Neighbours="1:(26;132)" FocalPlane="(26;132)"
ImageAcquisitionTime="<br>
> 4616.000 ms"/><br>
><br>
> Does anybody have any idea what this data is and if there is any relation<br>
> between this data and the so-called "slide position file"?<br>
<br>
I'd guess that this is the ScanInfoLayer_XMLInfoLevel hierarchical<br>
section, but I haven't verified that.<br>
<br>
The XImagePos and YImagePos appear to correspond to camera positions<br>
(i.e., the tile coordinates in the position map dumped by parse-mirax.py,<br>
divided by CameraImageDivisionsPerSide). I didn't find a clear<br>
relationship between the XMotorPos/YMotorPos and the values in the slide<br>
position map. Regardless, the values are not large enough to give
pixel<br>
precision in level 0, so I don't think this data will help us.<br>
<br>
BTW, while investigating this, I modified parse-mirax.py to dump<br>
file/offset/length tuples for all non-hierarchical sections. The
new<br>
version is in Git.<br>
<br>
--Benjamin Gilbert<br>
<br>
<br>
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