Opinions regarding MIRAX data file contents

Yves Sucaet sucaet at histogenex.com
Mon Aug 20 05:34:52 EDT 2012


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 

XYImagePos => Possible a location within the WSI that may be linked back 
to the position of the slideholder in the device (see also XYZMotorPos)
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
XYZMotorError => Correction error (and suggests the possibility to 
compensate) to XYZMotorPos.
ObjectLevel => Perhaps the level in the 'tiled pyramid'?
OpticalFocusLevel => Autofocus-related (helps explain why the zoom-level 
is never exactly 40x, but e.g. 39.8x)
LaserFocusLevel => Autofocus-related
FocusingType => What algorithm was used for autofocus
Neighbours => What pixels and images are next to each other
FocalPlane => Name of the focus level (an alternate name for ZMotorPos 
ImageAcquisitionTime => exposure time for a picture

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?



From:   "Benjamin Gilbert (OpenSlide)" <bgilbert at cs.cmu.edu>
To:     openslide-users at lists.andrew.cmu.edu
Date:   20-08-12 01:58
Subject:        Re: Opinions regarding MIRAX data file contents
Sent by:        
openslide-users-bounces+sucaet=histogenex.com at lists.andrew.cmu.edu

On Fri, August 17, 2012 1:08 am, John Minnie wrote:
> <scaninfo XImagePos="8" YImagePos="115"
> XMotorPos="3006" YMotorPos="47110" ZMotorPos="1356" XMotorError="0"
> YMotorError="0" ZMotorError="0" ObjectLevel="0.0143"
> OpticalFocusLevel="-1"
> LaserFocusLevel="-1.0000" FocusingType="OptPartialRange"
> Neighbours="1:(26;132)" FocalPlane="(26;132)" ImageAcquisitionTime="
> 4616.000 ms"/>
> Does anybody have any idea what this data is and if there is any 
>  between this data and the so-called "slide position file"?

I'd guess that this is the ScanInfoLayer_XMLInfoLevel hierarchical
section, but I haven't verified that.

The XImagePos and YImagePos appear to correspond to camera positions
(i.e., the tile coordinates in the position map dumped by parse-mirax.py,
divided by CameraImageDivisionsPerSide).  I didn't find a clear
relationship between the XMotorPos/YMotorPos and the values in the slide
position map.  Regardless, the values are not large enough to give pixel
precision in level 0, so I don't think this data will help us.

BTW, while investigating this, I modified parse-mirax.py to dump
file/offset/length tuples for all non-hierarchical sections.  The new
version is in Git.

--Benjamin Gilbert

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