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Topic Title: Can I get a measure of the irregularity of cell shape?
Topic Summary: Calculating compactness
Created On: 1/5/2017 9:13 AM
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 1/5/2017 9:13 AM
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Posts: 75
Joined: 5/16/2014

Usually this is defined by cell compactness given as circumference normalized to area but this isn't readily available as a morphology readout in Columbus.

Compactness is available as one of the STAR features, but that only allows you to use thresholds between 30 – 60% and not 0 or 100% (whatever would be equivalent to not applying a threshold at all).

A method to dervive compactness is shown below.

1) Find Nuclei

2) Find Cytoplasm

3) Select Population

a. Common filters

b. Remove Border Objects (to get rid of any incomplete cells/cells on edges so that the measurement is more accurate

4) Calculate Morphology

a. Membrane

b. Standard

i. Area

** because the membrane is 1px wide, calculating the area is essentially calculating the circumference

5) Calculate Morphology Properties

a. Cell

b. Standard

i. Area

6) Calculate Properties

a. By Formula

b. A/B

c. Variable A = Membrane Area

d. Variable B = Cell Area

e. Output property = compactness



Edited: 1/5/2017 at 9:22 AM by RAH

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