Merging of reappearing molecules

In some SMLM experiments, a single photoactivated molecule may appear in several sequential images, then disappear for a while, appear again, and finally bleach completely. If this is the case, ThunderSTORM identifies such sequences of molecular locations and combines them into one single molecule. The new position, imaged size, and the background offset of the resulting signal is calculated as the mean value of the original data, while the intensity and the background signal level is calculated as the sum. The localization uncertainty of the merged molecule is calculated from the new values. The distance within which molecules are merged together in the subsequent frames, as well as the allowed number of frames in which the molecule can disappear, are user-specified values. Users can also specify a maximum number of consecutive frames such that a repeating event is still considered a single molecule. The merging algorithm is based on finding nearest-neighbors between active molecules from the previous frame and the current frame.