[ome-users] VMS file format: incorrect image dimension

[Matthias Baldauf]

Hello Melissa,

Thank you for your response!

 > Thank you for the bug report.  I assume that you see the same problem
 > with 5.0.0-beta1 (from 
http://www.openmicroscopy.org/site/products/ome5/bio-formats)?

I tried to read the CMU files with LOCI Tools 5.0.0-beta1, but the 
problem remains.

 > What would you expect the overall image dimensions to be for CMU-1 (or
 > CMU-2 or CMU-3)?  My understanding for each of those is that there are
 > 2x2 tiles, so 122880x122880 seems to make sense; if that's incorrect
 > though please let us know.

The *.vms files do not contain the image dimensions in pixels. However, 
the overall image dimensions can be obtained by looking at the 
dimensions of all JPEG "tile" files (the number of tiles depends on the 
overall image size and is not always 2x2) - e.g. the dimensions of CMU-1 
are 102400x76288 (wxh). Those JPEG files are - in contrast to the NDPI 
JPEG-images - valid as they are close to, but not exceeding the maximum 
JPEG dimensions. As the scanned area is most likely rectangular, not all 
tiles have a square shape: the tiles in edge regions (right & bottom) 
are also rectangular.

Going back to the *.vms file: I may found a solution to get the overall 
image dimensions in pixels without having to look at all tiles. It seems 
that the "PhysicalHeight" and "PhysicalWidth" metadata elements contain 
the physical size of the image in nanometer. I came to this assumption 
by dividing the physical width and height by the overall width and 
height in pixels -> The width-quotient is 228.198242187 and the 
height-quotient is 227.53125. I think those numbers represent the size 
of one pixel in nanometer in X and Y direction, because they are pretty 
close to the 40x scanning resolution of 0.23 microns/pixel (as stated by 
the manufacturer) - and the CMU test images were acquired at 40x 
magnification. I am not sure if the quotients are equal for every 
scanner, but I am pretty sure that the physical size unit is nanometer 
as converting the "PhysicalMacroWidth" and "PhysicalMacroHeight" from 
nanometers to millimeters gives the size of the microscopy slide (76x26 mm).

I hope this information is helpful for you!

Regards,
Matthias