High content analysis tools


Meier et.al. paper supplementary

List of selected features

Every feature value was measured both on the detected cell and the surrounding region using CellProfiler. For detailed explanation see [1] and [2].


Intensity features

Nucleus Cytoplasm Whole cell
DAPI mean, std mean, std
GFP mean, std mean, std mean, std




Texture (Haralick) features

  • Angular second moment
  • Contrast
  • Correlation
  • Variance
  • Inverse difference moment
  • Sum average
  • Sum variance
  • Sum entropy
  • Entropy
  • Difference variance
  • Difference entropy
  • Info meas 1-2
  • Gabor X&Y

Shape features of the nucleus

  • Area
  • Eccentricity
  • Solidity 
  • Extent 
  • Euler number
  • Perimeter 
  • Form factor 
  • Major and minor axis length 
  • Orientation 


[1] Carpenter, A. E.; Jones, T. R.; Lamprecht, M. R.; Clarke, C.; Kang, I. H.; Friman, O.; Guertin, D. A.; Chang, J. H.; Lindquist, R. A.; Moffat, J.; et al. CellProfiler: Image Analysis Software for Identifying and Quantifying Cell Phenotypes. Genome Biol. 2006, 7(10), R100.

[2] Haralick. Textural Features for Image Classification. IEEE Transaction on Systems Man, Cybernetics, 1973














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