Tumor-activated lymph node fibroblasts suppress T cell function in diffuse large B cell lymphoma

The following folders/files are part of this repository:

“List of samples” excel file: contains the list of samples used in this project

CD8_ANALYSIS:  contains two folders: CTRLs (control samples) and TMA (DLBCL TMA sample cores in duplicate).

Each subfolder contains the following excel files:

ImageNumber_legend_and_counts: excel file summarizing the image number associated to each sample, total number of CD8 and number of CD8 in contact with stroma

Info_CP_Pipeline: cell profile pipeline used for CD8 analysis

MyExpt_CD8_objects: raw data of all CD8

MyExpt_CD8_on_stroma: raw data of all CD8

ORIGINAL_IMAGES: it contains two folders:

exclusion_masks: masks used to exclude areas of the tissue from the analysis

Original_images:  spillover corrected TIFF images for each channel

STROMAL_CELL_ANALYSIS:

FRCs_Network_Shape: overlay TIFF images of the stromal network shape

PDL1_PDL2_Stromal_Masks: TIFF images of stromal cell masks for PD-L1 and PD-L2 checkpoints expression

Stromal_Cell_Masks: TIFF images of stromal cell masks for the three main stromal subpopulations of the lymph node (BECs, LECs, FRCs)