Protocol for open-source automated universal high-content multiplex fluorescence for RNA in situ analysisShow others and affiliations
2024 (English)In: STAR Protocols, E-ISSN 2666-1667, Vol. 5, no 4, article id 103508Article in journal (Refereed) Published
Abstract [en]
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.
Place, publisher, year, edition, pages
Elsevier, 2024. Vol. 5, no 4, article id 103508
Keywords [en]
cell biology, health sciences, in situ hybridization
National Category
Cell and Molecular Biology Medical Imaging
Identifiers
URN: urn:nbn:se:umu:diva-232964DOI: 10.1016/j.xpro.2024.103508ISI: 001375026800001PubMedID: 39644494Scopus ID: 2-s2.0-85211160702OAI: oai:DiVA.org:umu-232964DiVA, id: diva2:1924828
Funder
Swedish Research Council, 2021-00960Swedish Cancer Society, 23 2814 PjThe Kempe Foundations, 2021 JCK-3110Cancerforskningsfonden i Norrland, AMP20-993Lions Cancerforskningsfond i Norr, LP 22-2306Lions Cancerforskningsfond i Norr, LP 24-23572025-01-072025-01-072025-02-09Bibliographically approved