PUPAID: A R + ImageJ pipeline for thorough and semi-automated processing and analysis of multi-channel immunofluorescence data

Paul Régnier, Camille Montardi, Anna Maciejewski-Duval, Cindy Marques and David Saadoun

PLOS ONE, 2024, vol. 19, issue 9, 1-18

Abstract: PUPAID is a workflow written in R + ImageJ languages which is dedicated to the semi-automated processing and analysis of multi-channel immunofluorescence data. The workflow is designed to extract fluorescence signals within automatically-segmented cells, defined here as Areas of Interest (AOI), on whole multi-layer slides (or eventually cropped sections of them), defined here as Regions of Interest (ROI), in a simple and understandable yet thorough manner. The included (but facultative) R Shiny-based interactive application makes PUPAID also suitable for scientists who are not fluent with R programming. Furthermore, we show that PUPAID identifies significantly more cells, especially in high-density regions, as compared to already published state-of-the-art methods such as StarDist or Cellpose. For extended possibilities and downstream compatibility, single cell information is exported as FCS files (the standardized file format for single cell-based cytometry data) in order to be openable using any third-party cytometry analysis software or any analysis workflow which takes FCS files as input.

Date: 2024
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Persistent link: https://EconPapers.repec.org/RePEc:plo:pone00:0308970

DOI: 10.1371/journal.pone.0308970

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