NoButter: An R package for reducing transcript dis-persion in CosMx Spatial Molecular Imaging Data

O'Hora, B.; Laddach, R.; Nuamah, R.; Alberts, E.; Wall, I.; Bell, J.; Johnston, D. A.; James, S.; Norman, J.; Jones, M. G.; Chiappini, C.; Grigoriadis, A.; Quist, J.

doi:10.1101/2024.11.25.625243

bioRxiv · 10.1101/2024.11.25.625243

NoButter: An R package for reducing transcript dis-persion in CosMx Spatial Molecular Imaging Data

O'Hora, B.·Laddach, R.·Nuamah, R.·Alberts, E.·Wall, I.·Bell, J.·Johnston, D. A.·James, S.·Norman, J.·Jones, M. G.·Chiappini, C.·Grigoriadis, A.·Quist, J.

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Abstract

MotivationAdvances in spatial transcriptomics technologies at single-cell resolution have high-lighted the need for innovative quality assessment approaches and improved analytical tools. Imaging-based spatial transcriptomics technologies, such as the CosMx Spatial Molecular Imager (SMI), provide the location and abundance of transcripts through multifocal imaging. Optical sections (or Z-slices) form a Z-stack that represents the tissue depth. Transcript dispersion can be observed across these Z-slice and introduce considerable levels of technical noise to the data that can negatively impact downstream analysis. Package FunctionalityNoButter is an R package designed to evaluate transcript dispersion in CosMx SMI spatial transcriptomics data. Using the raw data, the transcript distribution is assessed for each Z-slice of a Z-stack across multiple fields of views (FOVs). To systematically identify transcript dispersion, the percentage of transcripts located outside cell boundaries is calculated. Z-slices exhibiting high levels of transcript dispersion can be excluded, while high-confidence transcripts are preserved. Usage ScenarioTo demonstrate the functionalities of NoButter, spatial transcriptomics data was generated using the CosMx SMI for lymph node tissue, a lung sample, and two triple-negative breast cancers (TNBCs). Use cases illustrate substantial transcript dispersion in optical planes closer to the glass slide. In these Z-slices, on average, an additional 10% of the transcripts were discarded using NoButter. Cleaning such Z-slices with high dispersion rates reduces technical noise and improves the overall quality of the spatial transcriptomics data. AvailabilityThe package can be accessed at https://github.com/cancerbioinformatics/NoButter.

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O'Hora, B., Laddach, R., Nuamah, R., Alberts, E., Wall, I., Bell, J., Johnston, D. A., James, S., Norman, J., Jones, M. G., Chiappini, C., Grigoriadis, A., Quist, J.. 2024-11-28. NoButter: An R package for reducing transcript dis-persion in CosMx Spatial Molecular Imaging Data. https://doi.org/10.1101/2024.11.25.625243

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