In the paper "ThunderSTORM: a comprehensive ImageJ plug-in for PALM and STORM data analysis and super-resolution imaging" in Fig. 6 the problem is graphically described: 

The red dots mark the ground truth (GT), in Matlab a matrix of coordinates [x1 y1;y1 y2;... ] and a second matrix contains the same type but with detected coordinates. Then you compare both and pair the GT coordinates with the detected coordinates within a confidence interval that defines the least distance to count as pair or correctly detected coordinate. 

There are 2 ways of pairing one described in c) and one in d).

Does anyone know if there exists a matlab implementation of d) (or c) including the classification of TP, FP and FN?

Thanks, Danny