SABER-IMC_publication

List of Cellprofiler pipelines and R codes used for the analysis of the data used for the paper "DNA-barcoded signal amplification for imaging mass cytometry enables sensitive and highly multiplexed tissue imaging" (Hosogane et al.), about signal amplification for imaging mass cytometry.

Signal and background intensity quantification

thresholding_dev1.cppipe:

• Create signal and background region masks by thresholding using CellProfiler.

Single cell segmentation

calculate_intensity.cppipe:

• Quantification of mean signal and background intensities from region masks (Fig.3, Fig.S2, Fig.S3)

SABER_preprocessing script

SABER_preprocessing.Rmd :

• Conversion of single cell data from CellProfiler to SingleCellExperiment object.
• Data scaling and filtering

SABER_celltyping scripts

SABER_celltyping.Rmd :

• Single cell phenotyping and expression quantification (Fig.5,S5)
• Visualisation of cell populations and markers (Fig.5,S5)