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bioRxiv · 10.1101/2021.11.12.468357

An end-to-end workflow for multiplexed image processing and analysis

Windhager, J.·Bodenmiller, B.·Eling, N.
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Abstract

Simultaneous profiling of the spatial distributions of multiple biological molecules at single-cell resolution has recently been enabled by the development of highly multiplexed imaging technologies. Extracting and analyzing biologically relevant information contained in complex imaging data requires the use of a diverse set of computational tools and algorithms. Here, we report the development of a user-friendly, customizable, and interoperable workflow for processing and analyzing data generated by highly multiplexed imaging technologies. The steinbock framework supports image pre-processing, segmentation, feature extraction, and standardized data export. Each step is performed in a reproducible fashion. The imcRtools R/Bioconductor package forms the bridge between image processing and single-cell analysis by directly importing data generated by steinbock. The package further supports spatial data analysis and integrates with tools developed within the Bio-conductor project. Together, the tools described in this workflow facilitate analyses of multiplexed imaging raw data at the single-cell and spatial level.

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Windhager, J., Bodenmiller, B., Eling, N.. 2021-11-13. An end-to-end workflow for multiplexed image processing and analysis. https://doi.org/10.1101/2021.11.12.468357

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