Denoising time-resolved microscopy image sequences with singular value thresholding

Time-resolved imaging in microscopy is important for the direct observation of a range of dynamic processes in both the physical and life sciences. However, the image sequences are often corrupted by noise, either as a result of high frame rates or a need to limit the radiation dose received by the sample. Here we exploit both spatial and temporal correlations using low-rank matrix recovery methods to denoise microscopy image sequences. We also make use of an unbiased risk estimator to address the issue of how much thresholding to apply in a robust and automated manner. The performance of the technique is demonstrated using simulated image sequences, as well as experimental scanning transmission electron microscopy data, where surface adatom motion and nanoparticle structural dynamics are recovered at rates of up to 32 frames per second. •Correlations in space and time are harnessed to denoise microscopy image sequences.•A robust estimator provides automated selection of the denoising parameter.•Motion tracking and automated noise estimation provides a versatile algorithm.•Application to time-resolved STEM enables study of atomic and nanoparticle dynamics.