OMIP-088: Twenty-target imaging mass cytometry panel for major cell populations in mouse formalin fixed paraffin embedded liver

Here we provide the R markdown script to make all images in OMIP-088 Figure 1.  The folders contain the cell segmentation output from the steinbock framework:

https://bodenmillergroup.github.io/steinbock/v0.15.0/

as well as the raw data (TXT files from the Hyperion).

The OMIP_Figure_1.Rmd file can be run in RStudio using the contents of the steinbock folders.

OMIP-088 Abstract
The purpose of this 20-target imaging mass cytometry (IMC) panel is to identify
the main cell types in formalin fixed paraffin embedded (FFPE) mouse liver tissue
with the Hyperion™ mass cytometer from Standard BioTools (formerly Fluidigm).
The antibody panel includes markers to identify hepatocytes (E-cadherin, HNF4α
(hepatocyte nuclear factor 4 alpha), Arginase-1), liver sinusoidal endothelial cells
(LSECs; CD206), Kupffer cells (F4/80, CD206), neutrophils (Ly6G, CD11b), bone
marrow derived myeloid cells (BMDMs; CD11b), cholangiocytes (E-cadherin high),
endothelial cells (CD31, α-SMA), plasmacytoid dendritic cells (CD317), B cells
(CD19), T cells (CD3e, CD4, CD8a), NK cells (CD161) as well markers of cell activation
(CD44, CD74), proliferation (Ki-67) and to aid in cell segmentation (Pan-Actin,
E-cadherin, histone H3). The panel has been tested in other mouse tissues, namely
the spleen, colon and lung, and therefore is likely to work across various mouse
FFPE samples of interest. It has not been tested using human samples, frozen samples
or in suspension mass cytometry because FFPE treatment profoundly changes
epitope conformation. In summary, this panel is a powerful tool for pre-clinical
research to determine cellular abundance and spatial distribution within mouse tissues
and serves as a scaffold, to which more targets can be added for project specific
requirements.