04 Annotanted ADF

Annotated ADF

Here, we give an example of an ADF annotated with comments to understand the structure better.

[
  {
    "scenario": "Mitochondria Analysis",  // an analysis scenario is a high level research question. Here you the name is specified. 
    "datasets": ["mouse_3"],  // which data sets are used
    "scenario_subtasks": [ // A scenario subtask is a specific analysis step towards an analysis scenario. 
                           // A analysis scenario can be compromised of many scenario subtasks
      {
        "name": "Task 1: synapses", // specify the name of the scenario subtask
        "target_type": "mitochondria", // the target type specifies the structure type around which the neighborhood is centered
        "low_cardinality_vis": { // the low cardinality visualization is used for comparing a low number of neighborhoods
          "id": 0,
          "name": "distance-tree", // for details refer to the available visualization section of the Barrio wiki
          "params": "surrounding-synapses",
          "comment": "related-synapses" // comments are not considered but helpful to preserve context
        },
        "medium_cardinality_vis": { // medium cardinality visualizations are used for comparing a medium number of neighborhoods
          "id": 1,
          "name": "grouped-bar-chart",  // for details refer to the available visualization section of the Barrio wiki
          "params": "surrounding-synapses",
          "comment": "related-synapses"
        },
        "high_cardinality_vis": { // high cardinality visualization are used for comparing a large number of spatial neighborhoods. 
          "id": 2,
          "name": "distance-matrix",  // for details refer to the available visualization section of the Barrio wiki
          "params": "surrounding-synapses",
          "comment": "related-synapses"

        }
      },
      {
        "name": "ST2: mito placement",  // define a second scenario subtask
        "target_type": "mitochondria",
        "low_cardinality_vis": {
          "id": 3,
          "name": "cumulative-histogram",  // for details refer to the available visualization section of the Barrio wiki
          "bins": "distance-to-cell-membrane",
          "normalized": true,
          "params": "adjustable"
        },
        "medium_cardinality_vis": {
          "id": 4,
          "name": "violin-plot",  // for details refer to the available visualization section of the Barrio wiki
          "bins": "distance-to-cell-membrane",
          "normalized": true
        },
        "high_cardinality_vis": {
          "id": 5,
          "name": "scatter-plot",   // for details refer to the available visualization section of the Barrio wiki
          "x-axis": {
            "label": "% of mito closer than 50 nm to cell membrane",
            "attribute": "surf-percentage",
            "threshold": 0.05
          },
          "y-axis": {
            "label": "mitochondria volume in cubic microns",
            "attribute": "mito-volume"
          }
        }
      },
      {
        "name": "ST3: spine coverage",  //define a third scenario subtask
        "target_type": "mitochondria",
        "low_cardinality_vis": {
          "id": 6,
          "name": "dendrite-abstraction-1"  // for details refer to the available visualization section of the Barrio wiki
        },
        "medium_cardinality_vis": {
          "id": 7,
          "name": "dendrite-abstraction-2"  // for details refer to the available visualization section of the Barrio wiki
        },
        "high_cardinality_vis": {
          "id": 8,
          "name": "scatter-plot",   // for details refer to the available visualization section of the Barrio wiki
          "x-axis": {
            "label": "number of spines covered by mitochondrion",
            "attribute": "mito-spine-coverage"
          },
          "y-axis": {
            "label": "mitochondria volume in cubic microns",
            "attribute": "mito-volume"
          }
        }
      }
    ]
  }
]