A method for single molecule tracking using a conventional single-focus confocal setup

One way to achieve spatial resolution using fluorescence imaging - and track single molecules - is to use wide-field illumination and collect measurements over multiple sensors (camera pixels). Here we propose another way that uses confocal measurements and a single sensor. Traditionally, confocal microscopy has been used to achieve high temporal resolution at the expense of spatial resolution. This is because it utilizes very few, and commonly just one, sensors to collect data. Yet confocal data encode spatial information. Here we show that non-uniformities in the shape of the confocal excitation volume can be exploited to achieve spatial resolution. To achieve this, we formulate a specialized hidden Markov model and adapt a forward filtering-backward sampling Markov chain Monte Carlo scheme to efficiently handle molecular motion within a symmetric confocal volume characteristically used in fluorescence correlation spectroscopy. Our method can be used for single confocal volume applications or incorporated into larger computational schemes for specialized, multi-confocal volume, optical setups.