Unsupervised Structured Noise Removal with Variational Lossy Autoencoder

Most unsupervised denoising methods are based on the assumption that imaging noise is either pixel-independent, i.e., spatially uncorrelated, or signal-independent, i.e., purely additive. However, in practice many imaging setups, especially in microscopy, suffer from a combination of signal-dependent noise (e.g. Poisson shot noise) and axis-aligned correlated noise (e.g. stripe shaped scanning or readout artifacts). In this paper, we present the first unsupervised deep learning-based denoiser that can remove this type of noise without access to any clean images or a noise model. Unlike self-supervised techniques, our method does not rely on removing pixels by masking or subsampling so can utilize all available information. We implement a Variational Autoencoder (VAE) with a specially designed autoregressive decoder capable of modelling the noise component of an image but incapable of independently modelling the underlying clean signal component. As a consequence, our VAE's encoder learns to encode only underlying clean signal content and to discard imaging noise. We also propose an additional decoder for mapping the encoder's latent variables back into image space, thereby sampling denoised images. Experimental results demonstrate that our approach surpasses existing methods for self- and unsupervised image denoising while being robust with respect to the size of the autoregressive receptive field. Code for this project can be found at https://github.com/krulllab/DVLAE.