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  "Title": "Detection and Spatial Analysis of Tertiary Lymphoid Structures",
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  "Description": "Fast, reproducible detection and quantitative analysis of\ntertiary lymphoid structures (TLS) in multiplexed tissue\nimaging. Implements Independent Component Analysis Trace (ICAT)\nindex, local Ripley's K scanning, automated K Nearest Neighbor\n(KNN)-based TLS detection, and T-cell clusters identification\nas described in Amiryousefi et al. (2025)\n<doi:10.1101/2025.09.21.677465>.",
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    {
      "page": "tlsR-package",
      "title": "tlsR: Detection and Spatial Analysis of Tertiary Lymphoid Structures",
      "topics": [
        "tlsR-package",
        "tlsR"
      ]
    },
    {
      "page": "calc_icat",
      "title": "Calculate ICAT (Independent Component Analysis Trace) Index for TLS",
      "topics": [
        "calc_icat"
      ]
    },
    {
      "page": "detect_tic",
      "title": "Detect T-cell Immune Clusters (TIC) on the Tissue",
      "topics": [
        "detect_tic"
      ]
    },
    {
      "page": "detect_TLS",
      "title": "Detect Tertiary Lymphoid Structures using a KNN-density approach",
      "topics": [
        "detect_TLS"
      ]
    },
    {
      "page": "plot_TLS",
      "title": "Plot Spatial Map of TLS and T-cell Clusters",
      "topics": [
        "plot_TLS"
      ]
    },
    {
      "page": "scan_clustering",
      "title": "Scan Tissue for Local Immune Cell Clustering (Ripley's L Heatmap)",
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        "scan_clustering"
      ]
    },
    {
      "page": "summarize_TLS",
      "title": "Summarize Detected TLS Across Samples",
      "topics": [
        "summarize_TLS"
      ]
    },
    {
      "page": "toy_ldata",
      "title": "Toy Multiplexed Imaging Data",
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      "source": "tlsR-workflow.Rmd",
      "filename": "tlsR-workflow.html",
      "title": "tlsR Workflow: From Raw Imaging Data to TLS Characterisation",
      "author": "Ali Amiryousefi",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Data Format",
        "Step 1 -- Detect TLS with detect_TLS()",
        "Quick base-R check plot",
        "Step 2 -- Local Ripley's L Map with scan_clustering()",
        "Single-phenotype map",
        "Side-by-side B and T cell panels",
        "Step 3 -- ICAT Score with calc_icat()",
        "How it works",
        "Step 4 -- Detect T-cell Clusters with detect_tic()",
        "Step 5 -- Summary Table with summarize_TLS()",
        "Step 6 -- Visualise with plot_TLS()",
        "Rendering improvements",
        "Multi-Sample Workflow",
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      "created": "2026-04-09 19:42:57",
      "modified": "2026-04-23 22:05:46",
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