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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.

2024-07-02 cell biology
10.1101/2024.06.28.601140 bioRxiv
Show 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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