Journal article
M. Gataric, Jun Sung Park, Tong Li, Vasyl Vaskivskyi, J. Svedlund, C. Strell, Kenny Roberts, M. Nilsson, L. Yates, O. Bayraktar, M. Gerstung
bioRxiv, 2021
bioRxiv, 2021
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APA
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Gataric, M., Park, J. S., Li, T., Vaskivskyi, V., Svedlund, J., Strell, C., … Gerstung, M. (2021). PoSTcode: Probabilistic image-based spatial transcriptomics decoder. BioRxiv.
Chicago/Turabian
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Gataric, M., Jun Sung Park, Tong Li, Vasyl Vaskivskyi, J. Svedlund, C. Strell, Kenny Roberts, et al. “PoSTcode: Probabilistic Image-Based Spatial Transcriptomics Decoder.” bioRxiv (2021).
MLA
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Gataric, M., et al. “PoSTcode: Probabilistic Image-Based Spatial Transcriptomics Decoder.” BioRxiv, 2021.
BibTeX Click to copy
@article{m2021a,
title = {PoSTcode: Probabilistic image-based spatial transcriptomics decoder},
year = {2021},
journal = {bioRxiv},
author = {Gataric, M. and Park, Jun Sung and Li, Tong and Vaskivskyi, Vasyl and Svedlund, J. and Strell, C. and Roberts, Kenny and Nilsson, M. and Yates, L. and Bayraktar, O. and Gerstung, M.}
}
Abstract
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 in situ 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.
