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bioRxiv · 10.1101/2024.06.28.601140

AURA: Automated Universal RNAscope Analysis for high-throughput applications

Descarpentrie, J.·Bernard, F.·Souleyreau, W.·Brisson, L.·Mathivet, T.·Pateras, I. S.·Martin, O. C.·Frisan, T.
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Abstract

In situ hybridization visualizes RNA in cells, but image analysis is complex. We present a protocol based on open-source software for automated high-content multiplex fluorescence in situ transcriptomics analysis. Steps include nuclei segmentation with a Fiji macro and quantification of up to 14 mRNA probes per image. We describe procedures for storing raw data, quality control images and the use of a Python app to summarize all the results in one spreadsheet detailing the number of single or co-positive cells.

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Descarpentrie, J., Bernard, F., Souleyreau, W., Brisson, L., Mathivet, T., Pateras, I. S., Martin, O. C., Frisan, T.. 2024-07-02. AURA: Automated Universal RNAscope Analysis for high-throughput applications. https://doi.org/10.1101/2024.06.28.601140

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