EXAMPLE DATASETS

The companion data package CardinalWorkflows contains the following example datasets (saved as R data files):

• Human Renal Cell Carcinoma (RCC)
• Whole Pig Fetus Cross-Section
• Cardinal Oil Painting

• Mouse Brain (MALDI)*
• Mouse Brain (DESI)*

They are available as a separate download on the CardinalWorkflows releases page, and are included in the CardinalWorkflows package when downloaded from Bioconductor (see Installation instructions).

*Available only on the Github release of CardinalWorkflows.

OTHER PUBLIC DATASETS

The imzML website has several publicly available datasets in imzML format.

After downloading a dataset, start R and load Cardinal by typing:

library(Cardinal)

​
To load the dataset in Cardinal, type (for example):

data <- readMSIData("path/to/folder/file.imzML")

REPRODUCE

The following code should reproduce the first figure shown on the imzml.org “Example files” page, provided you have downloaded the PXD001283 mouse urinary bladder dataset from the PRIDE public data repository into your R working directory:

library(Cardinal)

options(Cardinal.dark=TRUE)

​mse <- readMSIData("HR2MSI mouse urinary bladder S096/HR2MSI mouse urinary bladder S096.imzML", mass.range=c(400, 1000), resolution=0.01, units="mz")

image(mse, mz=c(743.5483, 798.5419, 741.5307), superpose=TRUE, contrast.enhance="suppress", normalize.image="linear", col=c("red", "green", "blue"))