Re: Colocalization analysis w/ ICA and JACoP

Posted by sibert on Jun 10, 2010; 8:00pm
URL: http://imagej.273.s1.nabble.com/Colocalization-analysis-w-ICA-and-JACoP-tp3687953p3687956.html

A few more notes on some differences between the ICA and JACoP plugins:

Pearson's coefficient

-The Pearson correlation for ICA does not include 0-0 pairs, JACoP does.

-A manual threshold can be applied to the Pearson correlation for ICA, only the automatic Costes' threshold can be applied for JACoP.

Mander's coefficients (M1 & M2)

-Thresholds in ICA are inclusive (>=), thresholds in JACoP are exclusive (>).

-ICA calculates M1 by calculating the sum of all ch1 pixels that overlap with ch2 pixels > ch2 threshold divided by the sum of all ch1 pixels; the minimum threshold ('use threshold' unchecked) is 1.

-JACoP v.2 calculates M1 by calculating the sum of ch1 pixels > ch1 threshold that overlap with ch2 pixels > ch2 threshold divided by the sum of ch1 pixels > ch1 threshold.

-JACoP v.1 calculates M1 similar to ICA.

Veronica Labrador Cantarero wrote

     I also compared Overlap and K coefficients obtained for several images with MS
Excel and with JACoP plugin. When no threshold was applied the results were
exactly the same but as I applied thresholds values became different (see the
document "Test 2").

Overlap Coefficients (Overlap, K1, & K2)

-When thresholds are applied JACoP will only include pixels that are above threshold for both channels.  This includes the numerator values (A*B) and the denominator values (A^2 and B^2).

-I have not observed any differences between the ICA and JACoP Overlap coefficient other than the difference in handling thresholds (inclusive vs. exclusive respectively) which is usually insignificant.

In the document 'Test 2' the denominator values contain pixels that are below threshold in the other channel, deleting these will give you the same values as the JACoP plugin.