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amorante1 / TripleColocalization

Program used to calculate the colocalization between three color channels during immunofluoresence micoscopy. Program will calculate the percentage of overlap of channel 1 to both channels 2 and 3 together. Output colocalization is based on Manders' Colocalization Coefficient
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ask for the property of this program #1

Open wanghao1991217 opened 10 months ago

wanghao1991217 commented 10 months ago

This program will calculate the percentage of overlap of channel 1 to both channels 2 and 3 together.

1: is ch1 overlap to ch2, and ch1 overlap to ch3 simultaneously? or 2: ch1 overlap to the merged ch of ch2 and ch3?

amorante1 commented 9 months ago

The program is based on the Manders' colocalization formula: m1

where Ri is the pixel value of a given pixel in channel 1 where the pixel value in channel 2 > 0. The sum of these Ri values is then divided by the sum of all channel 1 pixel values to give a percentage of overlap of channel 1 to channel 2.

This program uses a modified version of this formula: mm1

In this case, the formula is still calculating the sum of pixel values in channel 1, but instead of only using channel 2, it also uses channel 3. So it is the sum of pixel values in channel 1 where the pixel value of channel 2 and the pixel value of channel 3 are both > 0.

So this would more closely fit your second question where it is comparing the channel 1 to the merge of channels 2 and 3.