[ome-users] (no subject)

[Jose Faro]

Hi,
I am an immunologist working in the field of Germinal Centers and I 
find FindSpots very useful, because it can pinpoint automatically all 
GCs in a lymph node or in a spleen and estimate their volumes. 
However, there is a scarcity of specific info about the output 
tables, which makes me uncertain on how to correctly interpret the 
results.

The main questions I have are the following:

A) The meaning of the majority of column headings in output tables is 
not explained in the user guide nor, to my knowledge, in the OME 
menus. Although I can figure out the meaning of some of them, other 
headings are obscure to me:

A1) 1st table, Signals, has headings:
Feature, Mean, GeometricSigma, Background, GeometricMean, Integral, 
CentroidZ, Sigma, CentroidY, TheC, CentroidX

-what is the meaning of "Background", "Integral", "TheC"?

A2) 2nd table, Extent, has headings:
Feature, Volume, MinX, MinZ, MinY, MaxZ, SigmaZ, FormFactor, MaxX, 
Perimeter, SurfaceArea, SigmaX, SigmaY

-what is the meaning of "Volume", "MinX", "MinZ", "MinY", "MaxZ", 
"FormFactor", "MaxX", "Perimeter", "SurfaceArea"?
-does Volume refer to the number of voxels in the corresponding spot? 
If so, does every voxel counted in the volume have neccessarily an 
intensity above the threshold? or it counts every voxel within the 
spot surface, irrespective of their intensity?
-does SurfaceArea refer to the number of voxels in the spot surface?

A3) 3rd table, Location, has headings:
Feature, TheX, TheY, TheZ

-what is the meaning of "TheX", "TheY", "TheZ"? It seems redundant 
with CentroidX, CentroidY, CentroidZ.

A4) how to transform "Volume" and "SurfaceArea" into figures with 
physical units (eg, micron^3, micron^2).

B) for any particular 3D image, is it possible to visualize 
slice-by-slice the spot areas determined by FindSpots superimposed to 
the corresponding slice image? (This would be required to decide if 
the spots as determined by FindSpots capture or not the image 
features of interest, which is required in turn to adjust the 
threshold and minimum volume parameters...)

Thanks a lot for your help.
Jose
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Jose Faro
University of Vigo
Department of Biochemistry, Genetics and Immunology
Edificio de Ciencias Experimentales
Campus As Lagoas-Marcosende
36310 Vigo
SPAIN

Phone:	(34) 986 812625
Fax:	(34) 986 812556
Email:	jfaro at uvigo.es

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