Human intestine processed CODEX multiplexed images for donors B009-B012 (Part 2/2)

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). This data could be used to understand the cellular interactions, composition, and structure of the human intestine from the duodenum to the sigmoid colon and understand differences between different areas of the intestine. This data could be used as a healthy baseline to compare other single-cell datasets of the human intestine, particularly multiplexed imaging ones. The overall structure of the datasets is organized into 2 parts. This is the second part associated with this dataset are from donors B009, B010, B011, B012.
This data is complimentary and can ..., 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 57 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. , The overall structure of the datasets is organized into 2 parts. This second part associated with this dataset is from donors B009, B010, B011, and B012. Each donor has a total of 8 tissue imaging regions of the different areas of the intestine (except for B009, which includes 1 extra folder of 4 images that were used as \"test\" imaging data). Each donor was split into two folders of 4 regions each stained and imaged at the same time in a 4-tissue array. For B004 through B008, all small bowel (SB) or colon (CL) from the same donor were imaged together in the same array (hence the SB or CL designation in folder structure). For B009 through B012, each donor had 2 tissue regions from the small bowel and 2 tissue regions from the colon imaged together from the same array (hence the A or B designation in folder structure). These folder structure names will be useful to map back to the single cell CODEX dataframe (https://doi.org/10.5061/dryad.pk0p2ngrf) that connects each region back to its e...