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

<p>The following folders/files are part of this repository:</p> <p>&nbsp;</p> <ul> <li>&ldquo;List of samples&rdquo; excel file: contains the list of samples used in this project</li> </ul> <p>&nbsp;</p> <ul> <li>CD8_ANALYSIS: &nbsp;contains two folders: CTRLs (control samples) and TMA&nbsp;(DLBCL TMA sample cores in duplicate).</li> </ul> <p>Each subfolder contains the following excel files:</p> <ul> <li>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</li> <li>Info_CP_Pipeline: cell profile pipeline used for CD8 analysis</li> <li>MyExpt_CD8_objects: raw data of all CD8</li> <li>MyExpt_CD8_on_stroma: raw data of all CD8</li> </ul> <p>&nbsp;</p> <ul> <li>ORIGINAL_IMAGES: it contains two folders: <ul> <li>exclusion_masks: masks used to exclude areas of the tissue from the analysis</li> <li>Original_images: &nbsp;spillover corrected TIFF&nbsp;images for each channel</li> </ul> </li> </ul> <p>&nbsp;</p> <ul> <li>STROMAL_CELL_ANALYSIS: <ul> <li>FRCs_Network_Shape: overlay TIFF images of the stromal network shape</li> <li>PDL1_PDL2_Stromal_Masks: TIFF images of stromal cell masks for PD-L1 and PD-L2 checkpoints expression</li> <li>Stromal_Cell_Masks: TIFF images of stromal cell masks for the three main stromal subpopulations of the lymph node (BECs, LECs, FRCs)</li> </ul> </li> </ul>