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Add stories for Vallius-2025 (#122)
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thejohnhoffer authored Feb 12, 2025
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1 change: 1 addition & 0 deletions _data/config-vallius-2025/early_melanoma_cell_lineage_e24/MEL14-A3/exhibit.json
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{"Images": [{"Name": "i0", "Description": "Early Melanoma - Cell Lineage CyCIF Panel - MEL14-A3", "Path": "https://s3.amazonaws.com/www.cycif.org/vallius-2025/early_melanoma_cell_lineage_e24/MEL14-A3", "Width": 49781, "Height": 47976, "MaxLevel": 6}], "Header": "## Metadata \n\n### Demographics \n**Species:** Human \n**Sex:** M \n\n### Diagnosis \n**Age at Diagnosis:** 53 \n**Primary Diagnosis:** superficial spreading \n**Prior Melanoma:** N \n**Site of Resection or Biopsy:** right lower back \n**Tumor Grade:** III/IV \n**Stage (AJCC 8th Edition):** T2a \n**TIL Response:** present, brisk \n**Depth of invasion:** 1.10mm \n**Procedure:** excision \n\n### Imaging \n**Assay Type:** Cell Lineage CyCIF Panel \n**Fixative Type:** FFPE \n**Microscope:** Rarecyte HT14 \n**Objective:** 20\u00d7/0.75 NA objective with no pixel binning \n", "Rotation": 0, "Layout": {"Grid": [["i0"]]}, "Stories": [{"Name": "", "Description": "", "Waypoints": []}], "Channels": [{"Rendered": false, "Name": "DNA1", "Path": "DNA1_0__DNA1"}, {"Rendered": false, "Name": "SOX10", "Path": "SOX10-0_3__SOX10"}, {"Rendered": false, "Name": "CD3e", "Path": "CD3e_10__CD3e"}, {"Rendered": false, "Name": "panCK", "Path": "panCK_22__panCK"}, {"Rendered": false, "Name": "CD163", "Path": "CD163_6__CD163"}, {"Rendered": false, "Name": "CD8a", "Path": "CD8a_12__CD8a"}, {"Rendered": false, "Name": "CD4", "Path": "CD4_56__CD4"}, {"Rendered": false, "Name": "SOX10", "Path": "SOX10-0_3__SOX10"}, {"Rendered": false, "Name": "FOXP3", "Path": "FOXP3_20__FOXP3"}, {"Rendered": false, "Name": "CD20", "Path": "CD20_15__CD20"}, {"Rendered": false, "Name": "DNA1", "Path": "DNA1_0__DNA1"}, {"Rendered": false, "Name": "CD206", "Path": "CD206-0_25__CD206"}, {"Rendered": false, "Name": "DNA1", "Path": "DNA1_0__DNA1"}, {"Rendered": false, "Name": "CD68", "Path": "CD68_16__CD68"}, {"Rendered": false, "Name": "aSMA", "Path": "aSMA_13__aSMA"}, {"Rendered": false, "Name": "CD31", "Path": "CD31_26__CD31"}, {"Rendered": false, "Name": "KRT14", "Path": "KRT14_8__KRT14"}, {"Rendered": false, "Name": "Vim", "Path": "Vim_27__Vim"}, {"Rendered": false, "Name": "MART1", "Path": "MART1_1__MART1"}, {"Rendered": false, "Name": "MITF", "Path": "MITF_19__MITF"}, {"Rendered": false, "Name": "SOX9", "Path": "SOX9_35__SOX9"}, {"Rendered": false, "Name": "Ki67_2", "Path": "Ki67-2_57__Ki67-2"}, {"Rendered": false, "Name": "PCNA", "Path": "PCNA_37__PCNA"}, {"Rendered": false, "Name": "pH3", "Path": "pH3_42__pH3"}, {"Rendered": false, "Name": "CD11c", "Path": "CD11c-0_11__CD11c"}, {"Rendered": false, "Name": "CD1c", "Path": "CD1c_7__CD1c"}, {"Rendered": false, "Name": "CD16", "Path": "CD16_24__CD16"}, {"Rendered": false, "Name": "CD14", "Path": "CD14_39__CD14"}, {"Rendered": false, "Name": "PD1", "Path": "PD1_21__PD1"}, {"Rendered": false, "Name": "LAG3", "Path": "LAG3_30__LAG3"}, {"Rendered": false, "Name": "TIM3", "Path": "TIM3_50__TIM3"}, {"Rendered": false, "Name": "HLA-A/B", "Path": "HLA-AB_34__HLA-AB"}, {"Rendered": false, "Name": "HLA-DPB1", "Path": "HLA-DPB1_36__HLA-DPB1"}, {"Rendered": false, "Name": "CD11c", "Path": "CD11c-0_11__CD11c"}, {"Rendered": false, "Name": "CD206", "Path": "CD206-0_25__CD206"}], "Groups": [{"Name": "Overview", "Colors": ["0000FF", "FF0000", "00FF00", "FFFFFF", "FF00FF"], "Channels": ["DNA1", "SOX10", "CD3e", "panCK", "CD163"], "Descriptions": ["", "", "", "", ""]}, {"Name": "Lymphoid", "Colors": ["FF00FF", "00FF00", "FF0000", "FFFFFF", "00FFFF", "808080", "0000FF"], "Channels": ["CD8a", "CD4", "SOX10", "FOXP3", "CD20", "panCK", "DNA1"], "Descriptions": ["", "", "", "", "", "", ""]}, {"Name": "Myeloid-1", "Colors": ["FF00FF", "FF0000", "00FF00", "808080", "0000FF", "FFA500"], "Channels": ["CD163", "SOX10", "CD206", "panCK", "DNA1", "CD68"], "Descriptions": ["", "", "", "", "", ""]}, {"Name": "Structural", "Colors": ["0000FF", "FF0000", "808080", "00FF00", "FF00FF", "00FFFF", "FFA500"], "Channels": ["DNA1", "SOX10", "panCK", "aSMA", "CD31", "KRT14", "Vim"], "Descriptions": ["", "", "", "", "", "", ""]}, {"Name": "Tumor", "Colors": ["0000FF", "FF0000", "808080", "FFA500", "00FFFF", "00FF00"], "Channels": ["DNA1", "SOX10", "panCK", "MART1", "MITF", "SOX9"], "Descriptions": ["", "", "", "", "", ""]}, {"Name": "Proliferation", "Colors": ["0000FF", "FF0000", "808080", "FF00FF", "FFFF00", "00FFFF"], "Channels": ["DNA1", "SOX10", "panCK", "Ki67_2", "PCNA", "pH3"], "Descriptions": ["", "", "", "", "", ""]}, {"Name": "Myeloid-2", "Colors": ["0000FF", "FF0000", "808080", "00FF00", "FFFF00", "00FFFF", "FF00FF"], "Channels": ["DNA1", "SOX10", "panCK", "CD11c", "CD1c", "CD16", "CD14"], "Descriptions": ["", "", "", "", "", "", ""]}, {"Name": "Immune Checkpoint", "Colors": ["0000FF", "FF0000", "808080", "00FF00", "FF00FF", "00FFFF", "FFFF00"], "Channels": ["DNA1", "SOX10", "panCK", "PD1", "CD8a", "LAG3", "TIM3"], "Descriptions": ["", "", "", "", "", "", ""]}, {"Name": "Antigen Presentation", "Colors": ["0000FF", "FF0000", "808080", "00FFFF", "FFFF00", "FF00FF", "00FF00"], "Channels": ["DNA1", "SOX10", "panCK", "HLA-A/B", "HLA-DPB1", "CD11c", "CD206"], "Descriptions": ["", "", "", "", "", "", ""]}], "Masks": [{"Path": "histopath-roi", "Name": "histopath-roi", "Channels": ["Histopath Annotations"], "Colors": ["ffffff"]}, {"Path": "geomx-roi", "Name": "geomx-roi", "Channels": ["GeoMx Annotations"], "Colors": ["ffffff"]}], "PixelsPerMicron": 3.076923189783947}
1 change: 1 addition & 0 deletions _data/config-vallius-2025/early_melanoma_cell_lineage_e24/MEL16-A6/exhibit.json
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{"Images": [{"Name": "i0", "Description": "Early Melanoma - Cell Lineage CyCIF Panel - MEL16-A6", "Path": "https://s3.amazonaws.com/www.cycif.org/vallius-2025/early_melanoma_cell_lineage_e24/MEL16-A6", "Width": 49777, "Height": 33402, "MaxLevel": 6}], "Header": "## Metadata \n\n### Demographics \n**Species:** Human \n**Sex:** M \n\n### Diagnosis \n**Age at Diagnosis:** 77 \n**Primary Diagnosis:** superficial spreading \n**Prior Melanoma:** N \n**Site of Resection or Biopsy:** right upper neck \n**Tumor Grade:** IV \n**Stage (AJCC 8th Edition):** \n**TIL Response:** present, brisk \n**Depth of invasion:** 0.50mm \n**Procedure:** excision \n\n### Imaging \n**Assay Type:** Cell Lineage CyCIF Panel \n**Fixative Type:** FFPE \n**Microscope:** Rarecyte HT16 \n**Objective:** 20\u00d7/0.75 NA objective with no pixel binning \n", "Rotation": 0, "Layout": {"Grid": [["i0"]]}, "Stories": [{"Name": "", "Description": "", "Waypoints": []}], "Channels": [{"Rendered": false, "Name": "DNA1", "Path": 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"Path": "KRT14_8__KRT14"}, {"Rendered": false, "Name": "Vim", "Path": "Vim_27__Vim"}, {"Rendered": false, "Name": "MART1", "Path": "MART1_1__MART1"}, {"Rendered": false, "Name": "MITF", "Path": "MITF_19__MITF"}, {"Rendered": false, "Name": "SOX9", "Path": "SOX9_35__SOX9"}, {"Rendered": false, "Name": "Ki67_2", "Path": "Ki67-2_57__Ki67-2"}, {"Rendered": false, "Name": "PCNA", "Path": "PCNA_37__PCNA"}, {"Rendered": false, "Name": "pH3", "Path": "pH3_42__pH3"}, {"Rendered": false, "Name": "CD11c", "Path": "CD11c-0_11__CD11c"}, {"Rendered": false, "Name": "CD1c", "Path": "CD1c_7__CD1c"}, {"Rendered": false, "Name": "CD16", "Path": "CD16_24__CD16"}, {"Rendered": false, "Name": "CD14", "Path": "CD14_39__CD14"}, {"Rendered": false, "Name": "PD1", "Path": "PD1_21__PD1"}, {"Rendered": false, "Name": "LAG3", "Path": "LAG3_30__LAG3"}, {"Rendered": false, "Name": "TIM3", "Path": "TIM3_50__TIM3"}, {"Rendered": false, "Name": "HLA-A/B", "Path": "HLA-AB_34__HLA-AB"}, {"Rendered": false, "Name": "HLA-DPB1", "Path": "HLA-DPB1_36__HLA-DPB1"}, {"Rendered": false, "Name": "CD11c", "Path": "CD11c-0_11__CD11c"}, {"Rendered": false, "Name": "CD206", "Path": "CD206-0_25__CD206"}], "Groups": [{"Name": "Overview", "Colors": ["0000FF", "FF0000", "00FF00", "FFFFFF", "FF00FF"], "Channels": ["DNA1", "SOX10", "CD3e", "panCK", "CD163"], "Descriptions": ["", "", "", "", ""]}, {"Name": "Lymphoid", "Colors": ["FF00FF", "00FF00", "FF0000", "FFFFFF", "00FFFF", "808080", "0000FF"], "Channels": ["CD8a", "CD4", "SOX10", "FOXP3", "CD20", "panCK", "DNA1"], "Descriptions": ["", "", "", "", "", "", ""]}, {"Name": "Myeloid-1", "Colors": ["FF00FF", "FF0000", "00FF00", "808080", "0000FF", "FFA500"], "Channels": ["CD163", "SOX10", "CD206", "panCK", "DNA1", "CD68"], "Descriptions": ["", "", "", "", "", ""]}, {"Name": "Structural", "Colors": ["0000FF", "FF0000", "808080", "00FF00", "FF00FF", "00FFFF", "FFA500"], "Channels": ["DNA1", "SOX10", "panCK", "aSMA", "CD31", "KRT14", "Vim"], "Descriptions": ["", "", "", "", "", "", ""]}, {"Name": "Tumor", "Colors": ["0000FF", "FF0000", "808080", "FFA500", "00FFFF", "00FF00"], "Channels": ["DNA1", "SOX10", "panCK", "MART1", "MITF", "SOX9"], "Descriptions": ["", "", "", "", "", ""]}, {"Name": "Proliferation", "Colors": ["0000FF", "FF0000", "808080", "FF00FF", "FFFF00", "00FFFF"], "Channels": ["DNA1", "SOX10", "panCK", "Ki67_2", "PCNA", "pH3"], "Descriptions": ["", "", "", "", "", ""]}, {"Name": "Myeloid-2", "Colors": ["0000FF", "FF0000", "808080", "00FF00", "FFFF00", "00FFFF", "FF00FF"], "Channels": ["DNA1", "SOX10", "panCK", "CD11c", "CD1c", "CD16", "CD14"], "Descriptions": ["", "", "", "", "", "", ""]}, {"Name": "Immune Checkpoint", "Colors": ["0000FF", "FF0000", "808080", "00FF00", "FF00FF", "00FFFF", "FFFF00"], "Channels": ["DNA1", "SOX10", "panCK", "PD1", "CD8a", "LAG3", "TIM3"], "Descriptions": ["", "", "", "", "", "", ""]}, {"Name": "Antigen Presentation", "Colors": ["0000FF", "FF0000", "808080", "00FFFF", "FFFF00", "FF00FF", "00FF00"], "Channels": ["DNA1", "SOX10", "panCK", "HLA-A/B", "HLA-DPB1", "CD11c", "CD206"], "Descriptions": ["", "", "", "", "", "", ""]}], "Masks": [{"Path": "histopath-roi", "Name": "histopath-roi", "Channels": ["Histopath Annotations"], "Colors": ["ffffff"]}, {"Path": "geomx-roi", "Name": "geomx-roi", "Channels": ["GeoMx Annotations"], "Colors": ["ffffff"]}], "PixelsPerMicron": 3.076923189783947}
1 change: 1 addition & 0 deletions _data/config-vallius-2025/early_melanoma_cell_lineage_e24/MEL17-A1/exhibit.json
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{"Images": [{"Name": "i0", "Description": "Early Melanoma - Cell Lineage CyCIF Panel - MEL17-A1", "Path": "https://s3.amazonaws.com/www.cycif.org/vallius-2025/early_melanoma_cell_lineage_e24/MEL17-A1", "Width": 7533, "Height": 8407, "MaxLevel": 4}], "Header": "## Metadata \n\n### Demographics \n**Species:** Human \n**Sex:** F \n\n### Diagnosis \n**Age at Diagnosis:** 31 \n**Primary Diagnosis:** superficial spreading \n**Prior Melanoma:** Y \n**Site of Resection or Biopsy:** right lateral thigh \n**Tumor Grade:** III \n**Stage (AJCC 8th Edition):** T1a \n**TIL Response:** present, brisk \n**Depth of invasion:** 0.60mm \n**Procedure:** punch \n\n### Imaging \n**Assay Type:** Cell Lineage CyCIF Panel \n**Fixative Type:** FFPE \n**Microscope:** Rarecyte HT17 \n**Objective:** 20\u00d7/0.75 NA objective with no pixel binning \n", "Rotation": 0, "Layout": {"Grid": [["i0"]]}, "Stories": [{"Name": "", "Description": "", "Waypoints": []}], "Channels": [{"Rendered": false, "Name": "DNA1", "Path": "DNA1_0__DNA1"}, {"Rendered": false, "Name": "SOX10", "Path": "SOX10-0_3__SOX10"}, {"Rendered": false, "Name": "CD3e", "Path": "CD3e_10__CD3e"}, {"Rendered": false, "Name": "panCK", "Path": "panCK_22__panCK"}, {"Rendered": false, "Name": "CD163", "Path": "CD163_6__CD163"}, {"Rendered": false, "Name": "CD8a", "Path": "CD8a_12__CD8a"}, {"Rendered": false, "Name": "CD4", "Path": "CD4_56__CD4"}, {"Rendered": false, "Name": "SOX10", "Path": "SOX10-0_3__SOX10"}, {"Rendered": false, "Name": "FOXP3", "Path": "FOXP3_20__FOXP3"}, {"Rendered": false, "Name": "CD20", "Path": "CD20_15__CD20"}, {"Rendered": false, "Name": "DNA1", "Path": "DNA1_0__DNA1"}, {"Rendered": false, "Name": "CD206", "Path": "CD206-0_25__CD206"}, {"Rendered": false, "Name": "DNA1", "Path": "DNA1_0__DNA1"}, {"Rendered": false, "Name": "CD68", "Path": "CD68_16__CD68"}, {"Rendered": false, "Name": "aSMA", "Path": "aSMA_13__aSMA"}, {"Rendered": false, "Name": "CD31", "Path": "CD31_26__CD31"}, {"Rendered": false, "Name": "KRT14", "Path": "KRT14_8__KRT14"}, {"Rendered": false, "Name": "Vim", "Path": "Vim_27__Vim"}, {"Rendered": false, "Name": "MART1", "Path": "MART1_1__MART1"}, {"Rendered": false, "Name": "MITF", "Path": "MITF_19__MITF"}, {"Rendered": false, "Name": "SOX9", "Path": "SOX9_35__SOX9"}, {"Rendered": false, "Name": "Ki67_2", "Path": "Ki67-2_57__Ki67-2"}, {"Rendered": false, "Name": "PCNA", "Path": "PCNA_37__PCNA"}, {"Rendered": false, "Name": "pH3", "Path": "pH3_42__pH3"}, {"Rendered": false, "Name": "CD11c", "Path": "CD11c-0_11__CD11c"}, {"Rendered": false, "Name": "CD1c", "Path": "CD1c_7__CD1c"}, {"Rendered": false, "Name": "CD16", "Path": "CD16_24__CD16"}, {"Rendered": false, "Name": "CD14", "Path": "CD14_39__CD14"}, {"Rendered": false, "Name": "PD1", "Path": "PD1_21__PD1"}, {"Rendered": false, "Name": "LAG3", "Path": "LAG3_30__LAG3"}, {"Rendered": false, "Name": "TIM3", "Path": "TIM3_50__TIM3"}, {"Rendered": false, "Name": "HLA-A/B", "Path": "HLA-AB_34__HLA-AB"}, {"Rendered": false, "Name": "HLA-DPB1", "Path": "HLA-DPB1_36__HLA-DPB1"}, {"Rendered": false, "Name": "CD11c", "Path": "CD11c-0_11__CD11c"}, {"Rendered": false, "Name": "CD206", "Path": "CD206-0_25__CD206"}], "Groups": [{"Name": "Overview", "Colors": ["0000FF", "FF0000", "00FF00", "FFFFFF", "FF00FF"], "Channels": ["DNA1", "SOX10", "CD3e", "panCK", "CD163"], "Descriptions": ["", "", "", "", ""]}, {"Name": "Lymphoid", "Colors": ["FF00FF", "00FF00", "FF0000", "FFFFFF", "00FFFF", "808080", "0000FF"], "Channels": ["CD8a", "CD4", "SOX10", "FOXP3", "CD20", "panCK", "DNA1"], "Descriptions": ["", "", "", "", "", "", ""]}, {"Name": "Myeloid-1", "Colors": ["FF00FF", "FF0000", "00FF00", "808080", "0000FF", "FFA500"], "Channels": ["CD163", "SOX10", "CD206", "panCK", "DNA1", "CD68"], "Descriptions": ["", "", "", "", "", ""]}, {"Name": "Structural", "Colors": ["0000FF", "FF0000", "808080", "00FF00", "FF00FF", "00FFFF", "FFA500"], "Channels": ["DNA1", "SOX10", "panCK", "aSMA", "CD31", "KRT14", "Vim"], "Descriptions": ["", "", "", "", "", "", ""]}, {"Name": "Tumor", "Colors": ["0000FF", "FF0000", "808080", "FFA500", "00FFFF", "00FF00"], "Channels": ["DNA1", "SOX10", "panCK", "MART1", "MITF", "SOX9"], "Descriptions": ["", "", "", "", "", ""]}, {"Name": "Proliferation", "Colors": ["0000FF", "FF0000", "808080", "FF00FF", "FFFF00", "00FFFF"], "Channels": ["DNA1", "SOX10", "panCK", "Ki67_2", "PCNA", "pH3"], "Descriptions": ["", "", "", "", "", ""]}, {"Name": "Myeloid-2", "Colors": ["0000FF", "FF0000", "808080", "00FF00", "FFFF00", "00FFFF", "FF00FF"], "Channels": ["DNA1", "SOX10", "panCK", "CD11c", "CD1c", "CD16", "CD14"], "Descriptions": ["", "", "", "", "", "", ""]}, {"Name": "Immune Checkpoint", "Colors": ["0000FF", "FF0000", "808080", "00FF00", "FF00FF", "00FFFF", "FFFF00"], "Channels": ["DNA1", "SOX10", "panCK", "PD1", "CD8a", "LAG3", "TIM3"], "Descriptions": ["", "", "", "", "", "", ""]}, {"Name": "Antigen Presentation", "Colors": ["0000FF", "FF0000", "808080", "00FFFF", "FFFF00", "FF00FF", "00FF00"], "Channels": ["DNA1", "SOX10", "panCK", "HLA-A/B", "HLA-DPB1", "CD11c", "CD206"], "Descriptions": ["", "", "", "", "", "", ""]}], "Masks": [{"Path": "histopath-roi", "Name": "histopath-roi", "Channels": ["Histopath Annotations"], "Colors": ["ffffff"]}, {"Path": "geomx-roi", "Name": "geomx-roi", "Channels": ["GeoMx Annotations"], "Colors": ["ffffff"]}], "PixelsPerMicron": 3.076923189783947}
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