SAMA documentation  Quantities
Documentation for Software for Automated Morphological Analysis : quantities evaluated and their interpretation.
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Summary of the relevant quantities, by order of appearance in the pdf produced.
Basic morphometrics
Note: axis refers to the axis when fitting the structure to an ellipsoid.
 "Quality" Elon1Elon2 without lumen analysis. Elon1Elon2+5*lumenosity with lumen analysis.
Proportions of the structure:
 "Elon1" elongation: length of the main axis of the structure/length of the second axis of the structure
 "logElon1" Logarithm of Elon11 .
 "Elon2" flatness: length of the second axis of the structure/length of the third axis of the structure
 "logElon2" Logarithm of Elon2 1.
Sizes
 "logvol" Logarithm of the volume of the structure, in units (ex: µm³).
 "logEll_MajRad" logarithm of the length of the largest axis of the structure.
 "logFerret" logarithm of the largest distance between two points of the structure.
Comparison with other shapes
 "Sphericity" ratio of volume to area set to 1 for spheres (and smaller for any other shape). That is S³=36 pi V²/A³.
 "RatioVolEllipsoid" volume of the structure / volume of the embeding ellipsoid. Describes how convoluted the structure is that is to say how different from en ellipsoid it is.
 "logRatioVolEllipsoid" Logarithm of 1RatioVolEllipsoid.
 "RatioVolbox" Volume of the structure/ Volume of its bounding box.
 "logRatioVolbox" Logarithm 1RatioVolbox.
 "logMoment1" "logMoment2" "logMoment3" logarithms of the three moments invariant by rotation and translation discussed in Sadjadi, Firooz A.; Hall, Ernest L., "ThreeDimensional Moment Invariants," in Pattern Analysis and Machine Intelligence, IEEE Transactions on , vol.PAMI2, no.2, pp.127136, March 1980 doi: 10.1109/TPAMI.1980.4766990
http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=4766990&isnumber=4766983  "logMoment4" "logMoment5" Moments also invariant by scaling.
Thickness measures (from bonej)
Thickness is a quantity that can be computed for every point inside a structure: it is the radius of the largest ball which contains this point and that fit inside the structure.
 "Thickness_Mean" Each structure is represented by its mean thickness.
 "Thickness_SD" Each structure is represented by the standard deviation of its thickness.
 "Thickness_Max" Each structure is represented by the thickness of its thickest point.
 "logThickness_Mean", "logThickness_SD", "logThickness_Max" Logarithm of the above.
 "rThickness_Mean" reduced thickness: Mean Thickness / volume of the structure (power 1/3, to compare a length with a length)
 "rThickness_SD" same for standard deviation.
 "rThickness_Max" same for maximum.
 "rbThickness_SD" standard deviation / mean
 "rbThickness_Max" max/ mean
Lumen analysis
 "lumenosity" volume of lumen / volume of the structure
 "lumen" 1 if there is a lumen 0 otherwise. (when the mean is applied, it is the proportion of structures with lumena).
Branching analysis
 "complexity" logarithm of the number of branches of the skeleton.
 "complexity2" 0 if there is one branch and 1 if there is 2 branches or more.
 "complexity3" logarithm of the cumulative length of branches.
 "complexity4" "entropy" of the branches (sum p log(p) with p=length of the branch/ cumulative length of branches).
PCA analysis
 "Dim.1" "Dim.2" "Dim.3" "Dim.4" "Dim.5" The first 5 dimension from pca analysis. The variable taken into account depend on the analysis options (with or without lumen analysis, branching analysis, etc.).
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