Single molecule tracking provides unprecedented insights into diffusional processes of systems in life and material sciences. Determination of molecule positions with high accuracy and correct connection of the determined positions to tracks is a challenging task with, so far, no universal solution for single fluorescing molecules tackling the challenge of low signal-to-noise ratios, frequent blinking and photo bleaching. Thus, the development of novel algorithms for automatic single molecule fluorescence tracking is essential to analyse the huge amount of diffusional data obtained with single molecule widefield fluorescence microscopy. Here, we present a novel tracking model using a top-down polyhedral approach which can be implemented effectively using standard linear programming solvers. The results of our tracking approach are compared to the ground truth of simulated data with different diffusion coefficients, signal-to-noise ratios and particle densities. We also determine the dependency of blinking on the analysed distribution of diffusion coefficients. To confirm the functionality of our tracking method, the results of automatic tracking and manual tracking by a human expert are compared and discussed.

A highly stable setup for stimulated Raman scattering (SRS) microscopy is presented. It is based on a two-branch femtosecond Er:fiber laser operating at a 40 MHz repetition rate. One of the outputs is directly modulated at the Nyquist frequency with an integrated electro-optic modulator (EOM). This compact source combines a jitter-free pulse synchronization with a broad tunability and allows for shot-noise limited SRS detection. The performance of the SRS microscope is illustrated with measurements on samples from material science and cell biology.

We have investigated passive mode-locking of Tm,Ho:YAG lasers with GaInAs- and GaSb-based semiconductor saturable absorber mirrors (SESAMs). With a GaInAs-based SESAM, stable dual-wavelength mode-locking operation was achieved at 2091 nm and 2097 nm, generating pulses with duration of 56.9 ps and a maximum output power of 285 mW. By using the GaSb-based SESAMs, we could generate mode-locked pulses as short as 21.3 ps at 2091 nm with a maximum output power of 63 mW. We attribute the shorter pulse duration obtained with the GaSb SESAMs to the ultrafast recovery time of the absorption and higher nonlinearity compared to standard GaInAs SESAMs.

A passively mode-locked Tm,Ho:YAP laser around 2.1 μm wavelength employing a semiconductor saturable absorber mirror is demonstrated. Stable continuous wave mode-locking operation was achieved at variable center wavelengths of 2036.5 nm, 2064.5 nm, 2095.5 nm, 2103.5 nm, and 2130 nm, respectively. Pulses as short as 40.4 ps were obtained at 2064.5 nm with a spectral FWHM of 0.5 nm at output powers of 132 mW and a repetition rate around 107 MHz. A maximum output power of 238 mW was obtained at 2130 nm with a pulse duration of 66 ps.

An efficient continuous wave and passively mode-locked thulium-doped oxyorthosilicate Tm:LuYSiO5 laser is demonstrated. A maximum slope efficiency of 56.3% is obtained at 2057.4 nm in continuous wave operation regime. With an InGaAs quantum well SESAM, self-starting passively mode-locked Tm:LuYSiO5 laser is realized in the 1929 nm to 2065 nm spectral region. A maximum average output power of 130.2 mW with a pulse duration of 33.1 ps and a repetition rate of about 100 MHz is generated at 1984.1 nm. Pulses as short as 24.2 ps with an average output power of 100 mW are obtained with silicon prisms where used to manage the intracavity dispersion. The shortest pulse duration of about 19.6 ps is obtained with an average output power of 64.5 mW at 1944.3 nm.