PoSTcode: Probabilistic image-based spatial transcriptomics decoder

Milana Gataric, Jun Sung Park, Tong Li, Vasyl Vaskivskyi, Jessica Svedlund, Carina Strell, Kenny Roberts, Mats Nilsson, Lucy R. Yates, Omer Bayraktar, Moritz Gerstung

Abstract: h3>Abstract</h3> <p>Realising the full potential of novel image-based spatial transcriptomic (IST) technologies requires robust and accurate algorithms for decoding the hundreds of thousand fluorescent signals each derived from single molecules of mRNA. In this paper, we introduce PoSTcode, a probabilistic method for transcript decoding from cyclic multi-channel images, whose effectiveness is demonstrated on multiple large-scale datasets generated using different versions of the <i>in situ</i> sequencing protocols. PoSTcode is based on a re-parametrised matrix-variate Gaussian mixture model designed to account for correlated noise across fluorescence channels and imaging cycles. PoSTcode is shown to recover up to 50% more confidently decoded molecules while simultaneously decreasing transcript mislabeling when compared to existing decoding techniques. In addition, we demonstrate its increased stability to various types of noise and tuning parameters, which makes this new approach reliable and easy to use in practice. Lastly, we show that PoSTcode produces fewer doublet signals compared to a pixel-based decoding algorithm.</p>

External IDs:doi:10.1101/2021.10.12.464086