Multi-modal spatial analysis identifies a shared TLS niche in melanoma with pan-cancer prognostic significance

Folder structure: \TLS_VISIUM+---LN1| \---outs| | filtered_feature_bc_matrix.h5| | | +---raw_feature_bc_matrix| | barcodes.tsv.gz| | features.tsv.gz| | matrix.mtx.gz| | | \---spatial| aligned_fiducials.jpg| aligned_tissue_image.jpg| cytassist_image.tiff| detected_tissue_image.jpg| scalefactors_json.json| spatial_enrichment.csv| tissue_hires_image.png| tissue_lowres_image.png| tissue_positions.csv| +---LN2| \---outs| | filtered_feature_bc_matrix.h5| | | +---raw_feature_bc_matrix| | barcodes.tsv.gz| | features.tsv.gz| | matrix.mtx.gz| | | \---spatial| aligned_fiducials.jpg| aligned_tissue_image.jpg| cytassist_image.tiff| detected_tissue_image.jpg| scalefactors_json.json| spatial_enrichment.csv| tissue_hires_image.png| tissue_lowres_image.png| tissue_positions.csv| +---MADIBUG| \---outs| | filtered_feature_bc_matrix.h5| | | +---raw_feature_bc_matrix| | barcodes.tsv.gz| | features.tsv.gz| | matrix.mtx.gz| | | \---spatial| aligned_fiducials.jpg| aligned_tissue_image.jpg| cytassist_image.tiff| detected_tissue_image.jpg| scalefactors_json.json| spatial_enrichment.csv| tissue_hires_image.png| tissue_lowres_image.png| tissue_positions.csv| +---MAFIBAF| \---outs| | filtered_feature_bc_matrix.h5| | | +---raw_feature_bc_matrix| | barcodes.tsv.gz| | features.tsv.gz| | matrix.mtx.gz| | | \---spatial| aligned_fiducials.jpg| aligned_tissue_image.jpg| cytassist_image.tiff| detected_tissue_image.jpg| scalefactors_json.json| spatial_enrichment.csv| tissue_hires_image.png| tissue_lowres_image.png| tissue_positions.csv| +---MEVIXYV| \---outs| | filtered_feature_bc_matrix.h5| | | +---raw_feature_bc_matrix| | barcodes.tsv.gz| | features.tsv.gz| | matrix.mtx.gz| | | \---spatial| aligned_fiducials.jpg| aligned_tissue_image.jpg| cytassist_image.tiff| detected_tissue_image.jpg| scalefactors_json.json| spatial_enrichment.csv| tissue_hires_image.png| tissue_lowres_image.png| tissue_positions.csv| +---MIFOGIL_1_K| \---outs| | filtered_feature_bc_matrix.h5| | | +---raw_feature_bc_matrix| | barcodes.tsv.gz| | features.tsv.gz| | matrix.mtx.gz| | | \---spatial| aligned_fiducials.jpg| aligned_tissue_image.jpg| cytassist_image.tiff| detected_tissue_image.jpg| scalefactors_json.json| spatial_enrichment.csv| tissue_hires_image.png| tissue_lowres_image.png| tissue_positions.csv| +---MIFOGIL_2_K| \---outs| | filtered_feature_bc_matrix.h5| | | +---raw_feature_bc_matrix| | barcodes.tsv.gz| | features.tsv.gz| | matrix.mtx.gz| | | \---spatial| aligned_fiducials.jpg| aligned_tissue_image.jpg| cytassist_image.tiff| detected_tissue_image.jpg| scalefactors_json.json| spatial_enrichment.csv| tissue_hires_image.png| tissue_lowres_image.png| tissue_positions.csv| +---MIGEKUT| \---outs| | filtered_feature_bc_matrix.h5| | | +---raw_feature_bc_matrix| | barcodes.tsv.gz| | features.tsv.gz| | matrix.mtx.gz| | | \---spatial| aligned_fiducials.jpg| aligned_tissue_image.jpg| cytassist_image.tiff| detected_tissue_image.jpg| scalefactors_json.json| spatial_enrichment.csv| tissue_hires_image.png| tissue_lowres_image.png| tissue_positions.csv| +---MISYPUP| \---outs| | filtered_feature_bc_matrix.h5| | | +---raw_feature_bc_matrix| | barcodes.tsv.gz| | features.tsv.gz| | matrix.mtx.gz| | | \---spatial| aligned_fiducials.jpg| aligned_tissue_image.jpg| cytassist_image.tiff| detected_tissue_image.jpg| scalefactors_json.json| spatial_enrichment.csv| tissue_hires_image.png| tissue_lowres_image.png| tissue_positions.csv| +---MORUWUP| \---outs| | filtered_feature_bc_matrix.h5| | | +---raw_feature_bc_matrix| | barcodes.tsv.gz| | features.tsv.gz| | matrix.mtx.gz| | | \---spatial| aligned_fiducials.jpg| aligned_tissue_image.jpg| cytassist_image.tiff| detected_tissue_image.jpg| scalefactors_json.json| spatial_enrichment.csv| tissue_hires_image.png| tissue_lowres_image.png| tissue_positions.csv| +---MYGIFUD| \---outs| | filtered_feature_bc_matrix.h5| | | +---raw_feature_bc_matrix| | barcodes.tsv.gz| | features.tsv.gz| | matrix.mtx.gz| | | \---spatial| aligned_fiducials.jpg| aligned_tissue_image.jpg| cytassist_image.tiff| detected_tissue_image.jpg| scalefactors_json.json| spatial_enrichment.csv| tissue_hires_image.png| tissue_lowres_image.png| tissue_positions.csv| \---MYJUFAJ \---outs | filtered_feature_bc_matrix.h5 | +---raw_feature_bc_matrix | barcodes.tsv.gz | features.tsv.gz | matrix.mtx.gz | \---spatial aligned_fiducials.jpg aligned_tissue_image.jpg cytassist_image.tiff detected_tissue_image.jpg scalefactors_json.json spatial_enrichment.csv tissue_hires_image.png tissue_lowres_image.png tissue_positions.csv