AI Article Synopsis
- In situ hybridization is a method used to visualize RNA in cells, but analyzing images can be complicated.
- The presented protocol utilizes open-source software for automating the analysis of multiple RNA probes (up to 14) in fluorescence in situ transcriptomics.
- Key steps involve segmenting cell nuclei, storing raw data, ensuring quality control, and using a Python app to compile results into a comprehensive spreadsheet that shows cell positivity.
Article 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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Source |
|---|---|
| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC11667704 | PMC |
| http://dx.doi.org/10.1016/j.xpro.2024.103508 | DOI Listing |
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