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exhibit.json
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{"PixelsPerMicron": 2.504, "Images": [{"Name": "i0", "Description": "", "Text": "Test", "Path": "images/lymph-roi-1", "Width": 32768, "Height": 49152, "MaxLevel": 6}], "Header": "", "Rotation": 0, "Layout": {"Grid": [["i0"]]},
"Appendix": "For more information on NanoString GeoMx technology visit [**our website**](https://www.nanostring.com/products/geomx-digital-spatial-profiler/geomx-dsp-overview/). \n\nDetails of the performance of WTA have been [**published**](https://doi.org/10.1101/2021.09.29.462442).\n\nMinerva is an open-source software package that was developed by Laboratory of Systems Pharmacology at Harvard University and is available [**here**](https://github.com/labsyspharm/minerva-story/wiki).\n\nWe would like to thank Jeremy Muhlich and John Thomas Hoffer for assistance in enabling Minerva features to support the Spatial Organ Atlas.\n\nSources:\n\nRashid R, Chen, YA, Hoffer J, Muhlich JL, Lin JR, Krueger R, Pfister H, Mitchell R, Santagata S, Sorger PK. (2021) Narrative online guides for the interpretation of digital-pathology images and tissue-atlas data. *Nature Biomedical Engineering*, p1-12 [https://doi.org/10.1038/s41551-021-00789-8](https://doi.org/10.1038/s41551-021-00789-8)\n\nHoffer J, Rashid R, Muhlich JL, Chen, YA, Russell D, Ruokonen J, Krueger R, Pfister H, Santagata S, Sorger PK. (2020). Minerva: a light-weight, narrative image browser for multiplexed tissue images. Journal of Open Source Software, 5(54), 2579, [https://doi.org/10.21105/joss.02579](https://doi.org/10.21105/joss.02579)\n\nFOR RESEARCH USE ONLY. Not for use in diagnostic procedures.",
"Stories": [{
"Name": "",
"Description": "Welcome to the [**Spatial Organ Atlas (SOA)**](https://www.nanostring.com/spatial-organ-atlas) Lymph Node Demonstration.\n\nThe SOA is a database for whole transcriptome spatial profiles of functional components of tissues from human and mouse generated with the GeoMx® Digital Spatial Profiler. All the data in the SOA is downloadable, including [**this lymph node sample (#001a)**](https://www.nanostring.com/products/geomx-digital-spatial-profiler/spatial-organ-atlas/human-lymph-node/).\n\nUsing [**Minerva**](https://github.com/labsyspharm/minerva-story/wiki), we will show you how the imaging and molecular data combine to give you a comprehensive profile of the tissue architecture and biology.\n\nClick around to explore on your own. \n\nHints:\n* Zoom and pan the image via the mouse/trackpad.\n* Open and close the left- and right-hand menus by clicking on < or >.\n* See results in the left-hand menu and click on the selectable regions to zoom to the featured area of the tissue.\n* Turn channels on and off with the right-hand menu.",
"Waypoints":
[{
"Name": "Gross Lymph Node Anatomy",
"Description": "There are hundreds of lymph nodes in the human body. They are oval-shaped organs that play a key role initiating immune responses to infection. Lymphatic fluid contains signaling molecules, cellular debris, and any other molecules that could inform the immune system. It drains from the tissues, enters the node via afferent vessels, and passes through an outer cortex and inner medulla before exiting via efferent vessels. Within the lymph node, immune cells are spatially organized to promote sampling of the lymphatic fluid and cell-cell interactions. The cortex contains B cell rich areas called follicles, which consist of an outer B cell rich zone called the mantle and an inner germinal center, which is the site of B cell activation and maturation. B cell maturation occurring within the germinal center depends on interactions with T cells, dendritic cells, and macrophages. Germinal center ROIs contain these cell types. The middle zone of the lymph node, called the paracortex, is enriched in T cells and dendritic cells, and the central medulla is the site of lymph drainage out of the node. Trabeculae, layers of fibrous tissue, encapsulate and provide structural support for the lymph node.\n\nThis lymph node is from tonsil and was sectioned so that only the cortex was profiled. It was visualized with antibodies to CD11c (dendritic cells and macrophages), CD20 (B cells), CD3 (T cells), and SYTO83 (nuclei). In parallel, the sample was molecularly profiled with the GeoMx Human Whole Transcriptome Atlas (WTA) assay.\n\nThe cartoon below illustrates the area covered in our sample. Due to the way this lymph node was sectioned, only cortex was available for profiling. If you select the cortex on the diagram, all the collected ROIs will be highlighted in the image to the right.",
"Footer": "Hints:\n* You can toggle the Regions of Interest (ROIs) that were molecularly profiled by clicking on the respective data layers (left-hand side of screen).\n* The “All data layers” category allows you to toggle between selecting all data layers and selecting no data layers. A single click can unselect all data layers, allowing easy selection of a single data layer (If any layers are unselected, the first click will select all layers, the second click will unselect all).\n* You can change the morphology markers being displayed by selecting channel groups - all markers or individual markers can be displayed. Switching to an individual marker can make it easier to see small or complex ROIs.",
"Arrows": [],
"Overlays": [],
"Group": "All markers",
"Masks": ["Germinal center", "Germinal center - CD11c+", "Germinal center - CD20+", "Germinal center - CD3+", "Mantle zone", "Paracortex zone"],
"ActiveMasks": ["Germinal center", "Germinal center - CD11c+", "Germinal center - CD20+", "Germinal center - CD3+", "Mantle zone", "Paracortex zone"],
"Zoom": 0.8230367332517142,
"Pan": [0.5, 0.5]
},
{
"Name": "Detailed Lymph Node Anatomy",
"Description": "With GeoMx DSP, Regions of Interest (ROIs) are selected by the user and then molecularly profiled. These ROIs can be either profiled in entirety (i.e., geometric profiling) or subdivided based on the visible morphology markers into compartments and profiled separately (i.e., segmented profiling).\n\nIn the cartoon below, the key features of the lymph nodes are highlighted with red outlines and shading. Selecting these features will show a typical ROI on the tissue image to the right.\n\n1. Germinal center: Geometric\n2. Germinal center dendritic cells + macrophages (CD11c+): Segmented\n3. Germinal center B cells (CD20+): Segmented\n4. Germinal center T cells (CD3+): Segmented\n5. Mantle zone: Geometric\n6. Paracortex zone: Geometric ",
"Footer": "Hints:\n* Toggle the different channels to see all ROIs.\n* The segmented regions (especially the T cell and dendritic cell regions) can be difficult to see. Switching to the Nuclei channel can enable localization. By toggling between the three germinal center segmented regions, you can see the degree of segmentation possible with the GeoMx DSP.",
"Arrows": [],
"Overlays": [],
"Group": "All markers",
"Masks": ["Germinal center", "Germinal center - CD11c+", "Germinal center - CD20+", "Germinal center - CD3+", "Mantle zone", "Paracortex zone"],
"ActiveMasks": ["Germinal center", "Germinal center - CD11c+", "Germinal center - CD20+", "Germinal center - CD3+", "Mantle zone", "Paracortex zone"],
"Zoom": 0.8230367332517142,
"Pan": [0.5, 0.5]
},
{
"Name": "Linking Molecular and Imaging Data",
"Description": "One of the key aspects of spatial biology is the ability to link molecular and spatial (image) data. In this figure, the average number of genes detected per ROI by structure is shown. Select a data point within the box plot to see its corresponding ROI. Unlike some other tissues in the SOA, the selected ROIs in lymph node all have relatively similar cell density. This leads to much more even distribution of number of genes seen, but the gene sets differ in content and expression level, as seen in the next few slides.",
"Footer": "Hints: \n* Select a single data point to be taken to that ROI.\n* If you hover your mouse over the boxplot, a summary of the distribution metrics for that ROI type will be displayed.",
"Arrows": [],
"Overlays": [],
"Group": "All markers",
"Masks": ["Germinal center", "Germinal center - CD11c+", "Germinal center - CD20+", "Germinal center - CD3+", "Mantle zone", "Paracortex zone"],
"ActiveMasks": ["Germinal center", "Germinal center - CD11c+", "Germinal center - CD20+", "Germinal center - CD3+", "Mantle zone", "Paracortex zone"],
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"Pan": [0.3333333333333332, 0.5191269561418047],
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"data": {"url": "data/WPT3_GenesDetected.json"},
"layer": [{
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"type": "boxplot",
"ticks": {"color": "white"},
"color": "white",
"size": 25
},
"encoding": {
"color": {
"legend": null,
"field": "type",
"scale": {
"domain": ["Germinal center", "Mantle zone", "Paracortex zone", "Germinal center - CD11c+", "Germinal center - CD3+", "Germinal center - CD20+"],
"range": ["#CC79A7", "#F0E442", "#484E4E", "#D55E00", "#DECAC2", "#E69F00"]
}
},
"x": {
"type": "nominal",
"field": "type",
"title": null,
"sort": ["Germinal center", "Germinal center - CD11c+", "Germinal center - CD20+", "Germinal center - CD3+", "Mantle zone", "Paracortex zone"]
},
"y": {
"type": "quantitative",
"field": "GenesDetected",
"title": "Genes Detected, # > LOQ"
}
}
},
{
"mark": {
"type": "point",
"color": "white",
"fill": "white",
"stroke": "red",
"strokeWidth": 1,
"size":50
},
"encoding": {
"x": {
"field": "x_axis",
"title":null,
"type": "quantitative",
"axis": {
"labels":false,
"ticks":false
}
},
"y": {
"field": "GenesDetected",
"type": "quantitative"
},
"tooltip": [
{"field": "GenesDetected", "type": "quantitative", "title": "Genes Detected"},
{"field": "type", "type": "nominal", "title": "Histological structure"}
]
}
}]
}},
{
"Name": "Cell Type Deconvolution",
"Description": "Here we are measuring the relative abundance of different cell types within each ROI using a [**cell type deconvolution algorithm**](https://www.nature.com/articles/s41467-022-28020-5). In this graph, each row is a single ROI, and each structure has a unique composition of cell types. For example, the mantle zone is enriched in naïve B cells. By segmenting the germinal center, we can see the CD20 segmented germinal centers are enriched in memory B cells. The CD3 segment of the germinal center was enriched in memory CD4 T cells and regulatory T cells, and the CD11c segment of germinal center was enriched in macrophages. Finally, the paracortex was enriched in T cells, consistent with the known cellularity of that region. The deconvolution matrix is in the R-package referenced in the paper [**Danaher P, Kim Y et al**](https://www.nature.com/articles/s41467-022-28020-5).",
"Footer": "Hint:\nSelect a single row of the figure to be taken to that ROI in the image.",
"Arrows": [],
"Overlays": [],
"Group": "All markers",
"Masks": ["Germinal center", "Germinal center - CD11c+", "Germinal center - CD20+", "Germinal center - CD3+", "Mantle zone", "Paracortex zone"],
"ActiveMasks": ["Germinal center", "Germinal center - CD11c+", "Germinal center - CD20+", "Germinal center - CD3+", "Mantle zone", "Paracortex zone"],
"Zoom": 0.6858639443764285,
"Pan": [0.3333333333333333, 0.5159945017860752],
"MaskAndPan": {"config": {"view": {"continuousWidth": 400, "continuousHeight": 300}, "background": null},
"$schema": "https://vega.github.io/schema/vega-lite/v5.json",
"layer": [{
"mark": "bar",
"data": {"url": "data\\decon_sorted.csv"},
"width": "container",
"encoding": {
"x": {
"field": "gene_value",
"type": "quantitative",
"stack": "normalize",
"title": "Proportion of Cell Type"
},
"y": {
"field": "ROI",
"type": "nominal",
"title": null,
"axis": {
"labels": false,
"ticks": false
}
},
"color": {
"field": "gene",
"type": "nominal",
"legend": {"orient": "bottom", "direction": "vertical", "offset": 900, "labelLimit": "200"},
"title": "Cell Type"
},
"tooltip": {
"field": "full_gene_name", "type":"nominal"
}
}
},
{
"data": {"url": "data/decon_sorted_annotation.csv"},
"mark": {"type": "bar", "xOffset": -7},
"width": 7,
"height": 900,
"encoding": {
"y": {
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"type": "quantitative",
"axis": {
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"ticks": false
},
"title": null
},
"x": {
"field": "bar",
"type": "nominal",
"title": null,
"axis": {
"labels": false,
"ticks": false
}
},
"color": {
"field": "name",
"type": "nominal",
"sort": null,
"legend": {"orient": "top", "direction": "vertical", "title": "Histological Structure"},
"scale": {"domain": ["Mantle zone", "GC - CD11c+", "GC - CD20+", "GC - CD3+", "Germinal center", "Paracortex zone"],
"range": ["#f0e442", "#d55e00", "#e69f00", "#decac2", "#cc79a7", "#484e4e"]}
},
"tooltip": {
"field": "type", "type": "nominal"
},
"order": {"field": "order"}
}
}],
"resolve": {"scale": {"color": "independent"}}
}},
{
"Name": "Spatial Mapping of Gene Pathways",
"Description": "Whole transcriptome profiling allows us to spatially map functional gene pathways and gene sets as well as individual genes. This heatmap of single sample gene set enrichment (ssGSEA) shows relative expression of various gene sets in different ROIs.\n\nFrom this plot, we can see that the germinal center is enriched in IgA genes associated with antibody production, and both the germinal center and mantle are enriched in the B cell receptor. The mantle is also enriched in genes associated with lymphocyte activation, including CD44 and members of the Immunoglobulin superfamily. In contrast, the paracortex is enriched in genes related to T cell presence, including TCR and CD8A/B, and T cell activation, including ICOSL. The mantle zone is enriched with genes associated with B cell receptor signaling and IgA antibody production.", "Footer": "Hint:\n* Click on a column to see the specific ROI the data applies to.",
"Arrows": [],
"Overlays": [],
"Group": "All markers",
"Masks": ["Germinal center", "Mantle zone", "Paracortex zone"],
"ActiveMasks": ["Germinal center", "Mantle zone", "Paracortex zone"],
"Zoom": 0.6858639443764285,
"Pan": [0.3333333333333335, 0.5122925102747581],
"MaskAndPan": {"config": {"axis": {"domain":false}, "view": {"continuousWidth": 400, "continuousHeight": 300}, "background": null}, "width": "container",
"$schema": "https://vega.github.io/schema/vega-lite/v5.json",
"layer": [{
"data": {"url": "data/WPT5_PathwayHeatmap.csv"},
"mark": "rect",
"encoding": {
"x": {
"field": "ROI_Name",
"type":"nominal",
"title": null,
"sort": null,
"axis":{
"labels": false,
"ticks": false
}
},
"y": {
"field": "PathwayName",
"type": "nominal",
"title": null,
"sort": null
},
"color": {
"field": "Pathway_Value",
"bin": {"binned": true},
"scale": {"range": ["#7D26CD", "#6B20AF", "#591B92", "#471575", "#351057", "#230A3A", "#11051D", "#000000", "#212100", "#434300", "#656500", "#888800", "#AAAA00", "#CBCB00", "#EEEE00"]},
"legend": {"orient": "top"}, "title": null
},
"tooltip": {
"field": "PathwayNameFull", "type":"nominal"
}
}
},
{
"data": {"url": "data/WPT5_PathwayHeatmap_annotations.csv"},
"mark": {
"type": "bar",
"yOffset": 560
},
"encoding": {
"x": {
"field": "percentage",
"type": "quantitative",
"axis": {
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"ticks": false
},
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},
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}
},
"color": {
"field": "type",
"type": "nominal",
"sort": null,
"legend": {"title": "Histological Structure", "offset": 580, "orient": "bottom"},
"scale": {"domain": ["Germinal center", "Paracortex zone", "Mantle zone"],
"range": ["#cc79a7", "#484e4e", "#f0e442"]}
},
"tooltip": {
"field": "type", "type": "nominal"
},
"order": {"field": "order"}
}
}],
"resolve": {"scale": {"y": "independent"}}
}},
{
"Name": "Differential Gene Expression",
"Description": "Spatially resolving whole transcriptome data allows us to understand how cells work within the context of their tissue environment. As expected, the marker genes (ITGAX, aka CD11c), and CD3 (CD3E/G) are enriched in their respective segments within the germinal center. CD3+ cells in the germinal center also showed enrichment for canonical T cell markers including CD8 (CD8A) and CD28, which provides co-stimulatory signals for T cell activation, and CTLA4, an inhibitor of T cell activation. Conversely, markers of the myeloid lineage (ITGAM, aka CD11b, CD68, LYZ) as well as signaling and activation (IL18, CCL18/19, TLR4/7) are enriched in CD11c+ staining segments.",
"Footer": "Hints:\n* Select the regions on the graph with the genes that are differentially expressed to see all the ROIs where they are more highly expressed.\n* Turning on only the nuclei channel may help you see smaller ROIs.",
"Arrows": [],
"Overlays": [],
"Group": "Nuclei",
"Masks": ["Germinal center - CD11c+", "Germinal center - CD3+"],
"ActiveMasks": ["Germinal center - CD11c+", "Germinal center - CD3+"],
"Zoom": 2.047978764084905,
"Pan": [0.32646398295399237, 0.7053196944477121],
"VisBarChart": {"config": {"view": {"continuousWidth": 400, "continuousHeight": 300}, "background": null}, "width": "container", "$schema": "https://vega.github.io/schema/vega-lite/v5.json",
"data":{"url": "data/WPT6_LymphDifferentialExpression.csv"},
"layer": [{
"mark": {"type": "point", "filled": true},
"encoding": {
"x": {
"field": "FC",
"type": "quantitative",
"title": "Enriched in CD11c+ Cells←log2(FC)→Enriched in CD3+ Cells",
"axis": {
"titleFontSize": 11
}
},
"y": {
"field": "Significance",
"type": "quantitative",
"title": "Significance, -log10(P)"
},
"color": {
"field": "Color",
"type": "nominal",
"scale": null
}
}
},
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"y2": {"datum": 13},
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},
"y": {
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"text": {
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}
}
},
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},
"text": {
"field": "GeneName2"
}
}
}]
}},
{
"Name": "Validating Gene Expression with Protein Expression 1",
"Description": "We explored the relationship between our data and the [**Human Protein Atlas**](https://www.proteinatlas.org/) to see if the gene expression patterns we observed would also be detected at the protein level. CD3 protein, which contains four distinct polypeptides (epsilon, gamma, delta, and zeta) is a defining feature of T cell lineage and is a T cell coreceptor. As seen in the immunohistochemistry image below from the Human Protein Atlas, the antibody to CD3 is specific for T cells, so it is localized to the paracortex and germinal centers. Molecular profiling of CD3E gene counts shows enrichment in the T cell zones and the CD3+ segments, reflecting the ability of GeoMx to enrich for cell types. The mantle zone and germinal center geometric regions have low T cell abundance and low CD3E counts. The paracortex has higher T cell abundance and proportionally higher counts.\n\n\n\n[*Image Credit: Human Protein Atlas*](https://images.proteinatlas.org/40957/159983_A_6_8.jpg)",
"Footer": "Hints: \n* Select a single data point to be taken to that ROI.\n* If you hover your mouse over the boxplot, a summary of the distribution metrics for that ROI type will be displayed.",
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"Overlays": [],
"Group": "All markers",
"Masks": ["Germinal center", "Germinal center - CD11c+", "Germinal center - CD20+", "Germinal center - CD3+", "Mantle zone", "Paracortex zone"],
"ActiveMasks": ["Germinal center", "Germinal center - CD11c+", "Germinal center - CD20+", "Germinal center - CD3+", "Mantle zone", "Paracortex zone"],
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"scale": {
"domain": ["Germinal center", "Mantle zone", "Paracortex zone", "Germinal center - CD11c+", "Germinal center - CD3+", "Germinal center - CD20+"],
"range": ["#CC79A7", "#F0E442", "#484E4E", "#D55E00", "#DECAC2", "#E69F00"]
}
},
"x": {
"type": "nominal",
"field": "type",
"title": null,
"sort": ["Germinal center", "Germinal center - CD11c+", "Germinal center - CD20+", "Germinal center - CD3+", "Mantle zone", "Paracortex zone"]
},
"y": {
"type": "quantitative",
"field": "CD3E",
"title": "CD3E Normalized Counts"
}
}
},
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"title":null,
"type": "quantitative",
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},
"y": {
"field": "CD3E",
"type": "quantitative"
},
"tooltip": [
{"field": "CD3E", "type": "quantitative", "format": ".0f", "title": "CD3E Expression"},
{"field": "type", "type": "nominal", "title": "Histological structure"}
]
}
}]
}},
{
"Name": "Validating Gene Expression with Protein Expression 2",
"Description": "Continuing to validate our data with the [**Human Protein Atlas**](https://www.proteinatlas.org/), we studied the relationship between expression of the *PDCD1* gene and the distribution of its protein product PDCD1 (programmed cell death protein 1), also known as PD-1. PD-1 is a cell surface receptor that functions as a T cell checkpoint and plays a central role in regulating T cell activation and exhaustion. It is expressed on T cells in the germinal center and not in surrounding tissue as seen in the immunohistochemistry image shown below and in the expression graph below. Higher *PDCD1* counts in the CD3+ segmented region as compared to the unsegmented ROIs of the germinal center show the power of using segmentation to enrich the genomic signal.\n\n\n\n[*Image Credit: Human Protein Atlas*](https://images.proteinatlas.org/76386/160142_A_8_8.jpg)",
"Footer": "Hints: \n* Select a single data point to be taken to that ROI.\n* If you hover your mouse over the boxplot, a summary of the distribution metrics for that ROI type will be displayed.",
"Arrows": [],
"Overlays": [],
"Group": "All markers",
"Masks": ["Germinal center", "Germinal center - CD11c+", "Germinal center - CD20+", "Germinal center - CD3+", "Mantle zone", "Paracortex zone"],
"ActiveMasks": ["Germinal center", "Germinal center - CD11c+", "Germinal center - CD20+", "Germinal center - CD3+", "Mantle zone", "Paracortex zone"],
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"field": "type",
"scale": {
"domain": ["Germinal center", "Mantle zone", "Paracortex zone", "Germinal center - CD11c+", "Germinal center - CD3+", "Germinal center - CD20+"],
"range": ["#CC79A7", "#F0E442", "#484E4E", "#D55E00", "#DECAC2", "#E69F00"]
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"x": {
"type": "nominal",
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"title": null,
"sort": ["Germinal center", "Germinal center - CD11c+", "Germinal center - CD20+", "Germinal center - CD3+", "Mantle zone", "Paracortex zone"]
},
"y": {
"type": "quantitative",
"field": "PDCD1",
"title": "PDCD1 Normalized Counts"
}
}
},
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},
"y": {
"field": "PDCD1",
"type": "quantitative"
},
"tooltip": [
{"field": "PDCD1", "type": "quantitative", "format": ".0f", "title": "PDCD1 Expression"},
{"field": "type", "type": "nominal", "title": "Histological structure"}
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}
}]
}},
{
"Name": "Validating Gene Expression with Protein Expression 3",
"Description": "Finally, we compared protein expression of CD11c from the [**Human Protein Atlas**](https://www.proteinatlas.org/) with its corresponding gene *ITGAX* from the GeoMx WTA data. CD11c is expressed on dendritic cells as well as macrophages throughout the lymph node, as seen in the immunohistochemistry data. GeoMx expression data for *ITGAX* reflects the same distribution. We also see higher counts of *ITGAX* expression from the CD11c+ segment in the germinal centers compared to geometric germinal center ROIs, reflecting enrichment of the expressing cell population.\n\n\n\n[*Image Credit: Human Protein Atlas*](https://images.proteinatlas.org/4458/14042_A_7_8.jpg)",
"Footer": "Hints: \n* Select a single data point to be taken to that ROI.\n* If you hover your mouse over the boxplot, a summary of the distribution metrics for that ROI type will be displayed.",
"Arrows": [],
"Overlays": [],
"Group": "All markers",
"Masks": ["Germinal center", "Germinal center - CD11c+", "Germinal center - CD20+", "Germinal center - CD3+", "Mantle zone", "Paracortex zone"],
"ActiveMasks": ["Germinal center", "Germinal center - CD11c+", "Germinal center - CD20+", "Germinal center - CD3+", "Mantle zone", "Paracortex zone"],
"Zoom": 0.8230367332517142,
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"scale": {
"domain": ["Germinal center", "Mantle zone", "Paracortex zone", "Germinal center - CD11c+", "Germinal center - CD3+", "Germinal center - CD20+"],
"range": ["#CC79A7", "#F0E442", "#484E4E", "#D55E00", "#DECAC2", "#E69F00"]
}
},
"x": {
"type": "nominal",
"field": "type",
"title": null,
"sort": ["Germinal center", "Germinal center - CD11c+", "Germinal center - CD20+", "Germinal center - CD3+", "Mantle zone", "Paracortex zone"]
},
"y": {
"type": "quantitative",
"field": "ITGAX",
"title": "ITGAX Normalized Counts"
}
}
},
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"type": "quantitative",
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},
"y": {
"field": "ITGAX",
"type": "quantitative"
},
"tooltip": [
{"field": "ITGAX", "type": "quantitative", "format": ".0f", "title": "ITGAX Expression"},
{"field": "type", "type": "nominal", "title": "Histological structure"}
]
}
}]
}}
]}],
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{"Path": "Germinal-center", "Name": "Germinal center", "Colors": ["cc79a7"], "Channels": ["Germinal center"]},
{"Path": "CD11c", "Name": "Germinal center - CD11c+", "Colors": ["d55e00"], "Channels": ["Germinal center - CD11c+"]},
{"Path": "CD20", "Name": "Germinal center - CD20+", "Colors": ["e69f00"], "Channels": ["Germinal center - CD20+"]},
{"Path": "CD3", "Name": "Germinal center - CD3+", "Colors": ["decac2"], "Channels": ["Germinal center - CD3+"]},
{"Path": "Mantle-zone", "Name": "Mantle zone", "Colors": ["f0e442"], "Channels": ["Mantle zone"]},
{"Path": "Paracortex-zone", "Name": "Paracortex zone", "Colors": ["484e4e"], "Channels": ["Paracortex zone"]}
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"Groups": [
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{"Name": "CD11c", "Path": "CD11c_0__CD11c", "Colors": ["00ffff"], "Channels": ["CD11c"]},
{"Name": "CD20", "Path": "CD20_2__CD20", "Colors": ["00ff00"], "Channels": ["CD20"]},
{"Name": "CD3", "Path": "CD3_3__CD3", "Colors": ["ff0054"], "Channels": ["CD3"]}
]}