Cell type labels for all clustering and normalization combinations compared for CODEX multiplexed imaging

We performed CODEX (co-detection by indexing) multiplexed imaging
on four sections of the human colon (ascending, transverse, descending,
and sigmoid) using a panel of 47 oligonucleotide-barcoded antibodies.
Subsequently images underwent standard CODEX image processing (tile
stitching, drift compensation, cycle concatenation, background
subtraction, deconvolution, and determination of best focal plane), and
single cell segmentation. Output of this process was a dataframe of nearly
130,000 cells with fluorescence values quantified from each marker. We
used this dataframe as input to 1 of the 5 normalization techniques of
which we compared z, double-log(z), min/max, and arcsinh normalizations to
the original unmodified dataset. We used these normalized dataframes as
inputs for 4 unsupervised clustering algorithms: k-means, leiden, X-shift
euclidian, and X-shift angular. From the clustering outputs, we then
labeled the clusters that resulted for cells observed in the data
producing 20 unique cell type labels. We also labeled cell types by
hiearchical hand-gating data within cellengine (cellengine.com). We also
created another gold standard for comparison by overclustering unormalized
data with X-shift angular clustering. Finally, we created one last label
as the major cell type call from each cell from all 21 cell type labels in
the dataset.  Consequently the dataset has individual cells
segmented out in each row. Then there are columns for the X, Y position in
pixels in the overall montage image of the dataset. There are also columns
to indicate which region the data came from (4 total). The rest are labels
generated by all the clustering and normalization techniques used in the
manuscript and what were compared to each other. These also were the data
that were used for neighborhood analysis for the last figure of the
manuscript. These are provided at all four levels of cell type level
granularity (from 7 cell types to 35 cell types).