Get to know your neighbors with a SNAQ™: A framework for single cell spatial neighborhood analysis in immunohistochemical images
Year: 2024
Type: article
Abstract: uantification), which conducts a neighborhood analysis on immunofluorescent images without the need for extensive coding knowledge. As a demonstration, SNAQ™ was used to analyze images of pancreatic ductal adenocarcinoma. Samples stained for DAPI, PanCK, CD68, and PD-L1 were segmented and classified using QuPath. The resulting CSV files were exported into RStudio for further analysis and visualization using SNAQ™. Visualizations include plots revealing the cellular composition of neighborhoods around multiple cell types within a customizable radius. Additionally, the analysis includes measuring the distances between cells of certain types relative to others across multiple regions of interest. The R Markdown files that comprise the SNAQ™ algorithm and the input data from this paper are freely available on the web at https://github.com/AryehSilver1/SNAQ.
Authors: Aryeh Silver, Avirup Chakraborty, Avinash Pittu, Diana Feier, Miruna Anica, Illeana West, Matthew R. Sarkisian, Loic P. Deleyrolle
Language: English
Subfield: Biophysics
Domain: Life Sciences
Open Access status: gold
Estimated APC paid: $3,230
OpenAlex ID: W4404794047