Spatial dynamics of CD39⁺CD8⁺ exhausted T cells reveal tertiary lymphoid structures-mediated response to PD-1 blockade in esophageal cancer

Data related to the paper: "Spatial dynamics of CD39+CD8+ exhausted T cells reveal tertiary lymphoid structures-mediated response to PD-1 blockade in esophageal cancer,” Nature Communications (2024)

The repository data consists of two main folders: IMC_dataset and MC_normalized_dataset.

IMC_dataset includes:

1. IMC_denoised_dataset: This folder contains cell mask images and noise-reduced images for each sample.

2. IMC_raw_dataset: This folder contains raw, unprocessed data.

3. IMC_processed_data: This folder contains standardized single-cell information and spillover-corrected FCS files, along with the compensation matrix.

The MC_normalized dataset includes FCS files that have been sorted by barcode.

Please note that in the IMC dataset, the following mass channels are blank:

• Tumor-ROI: 80Ar, 127I, 131Xe, 145Nd, 146Nd, 149Sm, 160Gd, 171Yb, 174Yb, 176Yb, 190Os
• SLO-ROI: 80Ar, 127I, 131Xe, 145Nd, 146Nd, 149Sm, 160Gd, 176Yb, 190Os

The names attached to the file names are IDs.