RUNIMC: An R-based package for imaging mass cytometry data analysis and pipeline validation

BioRxiv : the Preprint Server for Biology
Luigi DolcettiT. Ng

Abstract

We propose a novel pipeline for the analysis of imaging mass cytometry data, comparing an unbiased approach, representing the actual gold standard, with a novel biased method. We made use of both synthetic/ controlled datasets as well as two datasets obtained from FFPE sections of follicular lymphoma, and head and neck patients, stained with a 14 and 29-markers panels respectively. The novel pipeline, denominated RUNIMC, has been completely developed in R and contained in a single package. The novelty resides in the ease with which multi-class random forest classifier can be used to classify image features, making the pathologist and expert classification pivotal, and the use of a random forest regression approach that permits a better detection of cell boundaries, and alleviates the necessity of relying on a perfect nuclear staining.

Methods Mentioned

BETA
fluorescence imaging
flowcytometry

Software Mentioned

R package philentropy
raster
Image
cellProfiler
Shiny
Shiny GUI
Fluidigm
deployFilters
IMC
R package

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