Processed single cell data from CODEX multiplexed imaging of the human intestine

We performed CODEX (co-detection by indexing) multiplexed imaging on 64 sections of the human intestine (~16 mm2) from 8 donors (B004, B005, B006, B008, B009, B010, B011, and B012) using a panel of 57 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), single cell segmentation, and column marker z-normalization by tissue. The outputs of this process were data frames of 2.6 million cells with 57 antibody fluorescence values quantified from each marker. Each cell has its cell type, cellular neighborhood, community of neighborhooods, and tissue unit defined with x, y coordinates representing pixel location in the original image. This is from a total of 25 cell types, 20 multicellular neighborhoods, 10 communities of neighborhoods, and 3 tissue segments that could be used to understand the cellular interactio..., For a detailed description of each of the steps of protocols and processes to obtain this data see the detailed materials and methods in the associated manuscript. Briefly, intestine pieces from 8 different sites across the small intestine and colon were taken and frozen in OCT. These were assembled into an array of 4 tissues, cut into 7 um slices, and stained with a panel of 54 CODEX DNA-oligonucleotide barcoded antibodies. Tissues were imaged with a Keyence microscope at 20x objective and then processed using image stitching, drift compensation, deconvolution, and cycle concatenation. Processed data were then segmented using CellVisionSegmenter, a neural network R-CNN-based single-cell segmentation algorithm. Cell type analysis was completed on B004, 5, and 6 by z normalization of protein markers used for clustering and then overclustered using leiden-based clustering. The cell type labels were verified by looking back at the original image. Cell type labels were transferred to other ..., , # Processed single cell data from CODEX multiplexed imaging of the human intestine

[https://doi.org/10.5061/dryad.pk0p2ngrf](https://doi.org/10.5061/dryad.pk0p2ngrf)

We performed CODEX (co-detection by indexing) multiplexed imaging on 64 sections of the human intestine from 8 donors (B004, B005, B006, B008, B009, B010, B011, and B012) using a panel of 57 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), single cell segmentation, and column marker z-normalization by tissue. Output of this process were dataframe of 2.6 million cells with 57 antibody fluorescence values quantified from each marker.

### Methods

For detailed description of each of the steps of protocols and processes to obtain this data see the detailed materials and methods with the associated manuscript. Briefly, intestine pieces from 8...