Spatial transcriptomics — location and mixture
Combine tissue location, expression and morphology while retaining spot-level uncertainty. Mixed-cell capture areas require explicit deconvolution assumptions; proximity alone does not establish cell-to-cell signalling.
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{
"nodes": [
{ "id": "tis", "type": "rounded", "label": "Tissue section and orientation", "x": 40, "y": 200, "width": 150, "height": 104, "fill": "#ede9fe", "stroke": "#6d28d9" },
{ "id": "img", "type": "card", "label": "Histology image", "x": 215, "y": 40, "width": 150, "height": 104, "fill": "#ccfbf1", "stroke": "#0f766e" },
{ "id": "rna", "type": "card", "label": "Spatial expression counts", "x": 215, "y": 360, "width": 150, "height": 104, "fill": "#ccfbf1", "stroke": "#0f766e" },
{ "id": "align", "type": "rounded", "label": "Image–capture registration", "x": 390, "y": 200, "width": 150, "height": 104, "fill": "#fef3c7", "stroke": "#b45309" },
{ "id": "qc", "type": "octagon", "label": "Capture-area QC", "x": 565, "y": 200, "width": 150, "height": 104, "fill": "#e0f2fe", "stroke": "#0369a1" },
{ "id": "ref", "type": "card", "label": "Reference cell profiles", "x": 565, "y": 520, "width": 150, "height": 104, "fill": "#ccfbf1", "stroke": "#0f766e" },
{ "id": "mix", "type": "rounded", "label": "Cell-mixture estimation", "x": 740, "y": 200, "width": 150, "height": 104, "fill": "#fef3c7", "stroke": "#b45309" },
{ "id": "neigh", "type": "rounded", "label": "Spatial neighbourhood analysis", "x": 915, "y": 200, "width": 150, "height": 104, "fill": "#fef3c7", "stroke": "#b45309" },
{ "id": "lim", "type": "rounded", "label": "Proximity is not signalling proof", "x": 915, "y": 520, "width": 150, "height": 104, "fill": "#f1f5f9", "stroke": "#475569" }
],
"edges": [
{ "id": "e0", "source": "tis", "target": "img", "label": "image" },
{ "id": "e1", "source": "tis", "target": "rna", "label": "measure" },
{ "id": "e2", "source": "img", "target": "align", "label": "morphology" },
{ "id": "e3", "source": "rna", "target": "align", "label": "coordinates" },
{ "id": "e4", "source": "align", "target": "qc", "label": "inspect" },
{ "id": "e5", "source": "qc", "target": "mix", "label": "retain areas" },
{ "id": "e6", "source": "ref", "target": "mix", "label": "assumptions", "style": "dashed" },
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{ "id": "e8", "source": "neigh", "target": "lim", "label": "interpret" }
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}