μSplit: efficient image decomposition for microscopy data

Light microscopy is routinely used to look at living cells and biological tissues at sub-cellular resolution. Components of the imaged cells can be highlighted using fluorescent labels, allowing biologists to investigate individual structures of interest. Given the complexity of biological processes, it is typically necessary to look at multiple structures simultaneously, typically via a temporal multiplexing scheme. Still, imaging more than 3 or 4 structures in this way is difficult for technical reasons and limits the rate of scientific progress in the life sciences. Hence, a computational method to split apart (decompose) superimposed biological structures acquired in a single image channel, i.e. without temporal multiplexing, would have tremendous impact. Here we present {\mu}Split, a dedicated approach for trained image decomposition. We find that best results using regular deep architectures is achieved when large image patches are used during training, making memory consumption the limiting factor to further improving performance. We therefore introduce lateral contextualization (LC), a memory efficient way to train deep networks that operate well on small input patches. In later layers, additional image context is fed at adequately lowered resolution. We integrate LC with Hierarchical Autoencoders and Hierarchical VAEs.For the latter, we also present a modified ELBO loss and show that it enables sound VAE training. We apply {\mu}Split to five decomposition tasks, one on a synthetic dataset, four others derived from two real microscopy datasets. LC consistently achieves SOTA results, while simultaneously requiring considerably less GPU memory than competing architectures not using LC. When introducing LC, results obtained with the above-mentioned vanilla architectures do on average improve by 2.36 dB (PSNR decibel), with individual improvements ranging from 0.9 to 3.4 dB.