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

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 Cellp

SUBMITTER: Regnier P 

PROVIDER: S-EPMC11412663 | biostudies-literature | 2024

REPOSITORIES: biostudies-literature