Processed CODEX multiplexed imaging data of cellular microenvironment around T cell stimulating hydrogels

Our research used CODEX (Co-Detection by Indexing) multiplexed imaging to gain insights into the cellular microenvironment surrounding T cell stimulating hydrogels. These hydrogels were engineered with signals that could locally expand antigen-specific T cells for use in tumor immunotherapy. CODEX imaging involves an iterative process of annealing and stripping fluorophore-labeled oligonucleotide barcodes, complementing the barcodes attached to over 40 antibodies used for tissue staining. 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.
Our datasets comprise individual cells as rows, each characterized by 40+ antibody fluorescence values quantified from various markers evaluated for each study. These markers correspond to the antibodies targeting specific proteins with...,
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, murine injection sites were extracted from sacrificed mice at indicated timepoint post therapy and frozen in OCT. These were assembled into an array of 4-7 tissues, cut into 7 um slices, and stained with a panel of 40+ CODEX DNA-oligonucleotide barcoded antibodies. Tissues were imaged with a Phenocycler Fusion imaging system from Akoya Biosciences and processed using manufacturer’s v1.6.0 (e.g., background-subtracted, stitched, and shading correction).
Processed data were then segmented using CellVisionSegmenter, a neural network R-CNN-based single-cell segmentation algorithm. Cell type analysis was completed 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.
, , # Processed CODEX Multiplexed Imaging Data of Cellular Microenvironment Around T Cell Stimulating Hydrogels

Our research used CODEX (Co-Detection by Indexing) multiplexed imaging to gain insights into the microenvironment in and surrounding bioengineered hydrogels meant to stimulate antigen-specific T cell responses in situ. CODEX imaging involves an iterative process of annealing and stripping fluorophore-labeled oligonucleotide barcodes, complementing the barcodes attached to over 40 antibodies used for tissue staining. 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.

## Description of the data and file structure

Our datasets comprise individual cells as rows, each characterized by 40+ antibody fluorescence values quantified from various markers evaluated for ea...