Ripley K-Function

[James Sanders]

Hi All,

when computing the Ripley K-function, a .txt file is printed. The .txt file has no column headers and I'm unsure of what all the values are, other than the first column which is the bin size. Could someone let me know?  

Thanks,

James.

[James Sanders]

After some searching and guessing a few things I've worked out what most of the columns relate to:

Col 1: Bin size

Col 2: Complete spatial randomness i.e. no cluster and homogeneous structure#

Col 3: Possibly n^2?

Col 4: Lambda?

Col 5: Ripley's K(r) value

Col 6: Normalized K-function L(r) = sqrt(K(r)/pi)

Col 7: Normalized L-function H(r) = L(r)-r

If any of these are incorrect then let me know, otherwise hopefully this will be of use to others.

Great bit of software by the way Steve. We had previously tried many other open source software but this has by far been both the easiest to use and the most robust.  It actually gives meaningful results, which is always useful! 

[Steve Wolter]

Thanks for the flowers.

https://github.com/stevewolter/rapidSTORM/blob/master/ripley_k/RipleyK.cpp#L140 gives the columns' meaning.

Col 1 is the distance histogram bin's position (say, 5 mum), and 2 is the area covered by a ring with the bin's position and width (say, Pi*(5+0.5)^2 - Pi (5-0.5)^2 for a bin 1 mum wide), in square micrometers. 3 is the number of molecules that have a neighbor within the bin, noncumulative. 4 is the relative density of localizations in the bin, compared to the overall expected density (1 for expected density). The rest is correct, as far as I remember the theory.

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