03 Available Visualizations
Here we summarize the visualizations that are currently available. The table lists each visualization method, its comparison cardinality (low, medium, high), and a short description. An example of how these visualization can be combined to an analysis definition file can be found here.
| Visualization | Cardinality | Description | Preview |
|---|---|---|---|
| Distance Tree | Low | The distance tree visualization is used for showing distances between hierarchically organized structures. |  |
| Dendrite Abstraction 1 | Low | The dendrite abstraction level 1 shows a detailed visual abstraction of a dendrite, its mitochondria, and its spines. |  |
| Histogram | Low | A histogram is suited for the detailed visualization of distributions. |  |
| (Grouped) Bar Chart | Medium | A grouped bar chart is an efficient way to compare many objects with a single quantitative value organized into groups. |  |
| Viloin Plot | Medium | A set of juxtaposed violin plots provides detailed and space-efficient visualization and comparison of distributions. |  |
| Dendrite Abstraction 2 | Medium | The dendrite abstraction level 2 shows a compact abstraction of dendrites, their mitochondria, and spines. It is especially well suited for comparing dendrites. |  |
| Scatterplot | High | Scatterplots are a scalable method to visualize two quantitative values of many objects. |  |
| Distance Matrix | High | The distance matrix helps to quickly compare a quantitative value of many objects in relation to two properties (x, y position in the matrix). |  |
- Best use: Visualizing and comparing a low number of hierarchically ordered objects and their distances.
- Comparison use: For low cardinality comparison (comparing a low number of structures).
- Required data: A hierarchal structure and quantitative values describing the hierarchy.
{
"name": "distance-tree",
"header": "add header name here",
"x-axis": {
"label": "add label here",
"attribute": ["mito-synapse-distance"]
},
"params": ["related-synapses", "surrounding-synapses"]
}- mito-synapse-distance: maps distances between a mitochondrion and synapses onto the distance tree visualization. The related-synapses and the surrounding-synapses parameters determine which synapses are taken into account.
- related-synapses: displays only synapses that belong to the mitochondrion cells.
- surrounding-synapses: synapses that not belong to the mitochondrions cell are also taken into account. The threshold distance is adjustable using a slider.
- Best use: Visualizing and comparing a low number of dendrites and the relation of mitochondria with their dendritic spines.
- Comparison use: For low cardinality comparison (comparing a low number of structures).
- Required data: Segmented dendritic spines and quantitative information about the dendrites, mitochondria and spines. An example can be found here.
{
"name": "dendrite-abstraction-1",
}
- Best use: Visualizing and comparing a low number of distance distributions.
- Comparison use: For low cardinality comparison (comparing a low number of structures).
- Required data: A distribution of values (e.g. distances).
{
"name": "cummulative-histogram",
"header": "add header name here",
"x-axis": {
"label": "add a label name here",
"attribute": ["mito-cell-distance"]
},
"params": ["fixed", "adjustable"]
}- mito-cell-distance: The distances between the mitochondrions surface and the cell membrane are mapped to the histogram visualization.
- fixed: The number of bins in the histogram is fixed.
- adjustable: The number of bins in the histogram can be adjusted through a slider in the UI.
- Best use: Visualizing and comparing a low number of distance distributions.
- Comparison use: For medium cardinality comparison (comparing a medium number of structures).
- Required data: A distribution of values (e.g. distances).
{
"name": "grouped-bar-chart",
"header": "add header name here",
"y-axis": {
"label": "add a label here",
"attribute": ["mito-synapse-distance"]
},
"params": ["fixed", "adjustable"]
}- mito-synapse-distance: map the distances between mitochondria and surrounding synapses to the bar chart.
- fixed: displays only synapses that belong to the mitochondrion cell
- adjustable: synapses that not belong to the mitochondrions cell are also taken into account. The threshold distance is adjustable using a slider.
- Best use: Visualizing and comparing a medium number of distance distributions. More space efficient that the histogram.
- Comparison use: For medium cardinality comparison (comparing a medium number of structures).
- Required data: A distribution of values (e.g. distances).
{
"name": "violin-plot",
"bins": "distance-to-cell-membrane",
"normalized": [true, false]
}- normalized: If true the area of all juxtaposed violins is the same, if false then the area of the violin scales with the size of the structure (e.g., the mitochondrion).
- Best use: Visualizing and comparing a medium number of dendrites, their mitochondria and spines.
- Comparison use: For medium cardinality comparison (comparing a medium number of structures).
- Required data: Segmented dendritic spines and quantitative information about the dendrites, mitochondria and spines. An example can be found here.
{
"name": "dendrite-abstraction-2",
}
- Best use: Visualizing and comparing a high number of neighborhoods characterized through two quantitative attributes.
- Comparison use: For high cardinality comparison (comparing a high number of structures).
- Required data: At least two quantitative attributes per neighborhood and a optional third one to map to the dot color.
{
"name": "scatter-plot",
"header": "add header name here",
"x-axis": {
"label": "add a label here",
"attribute": [ "mito-min-distance-to-cell", "syn-volume", "syn-surface-area", "mito-volume", "mito-surface-area", "syn-close-mitos",
"mito-spine-coverage", "mito-surface-closer-than-threshold"]
},
"y-axis": {
"label": "add a label here",
"attribute": [ "mito-min-distance-to-cell", "syn-volume", "syn-surface-area", "mito-volume", "mito-surface-area", "syn-close-mitos",
"mito-spine-coverage", "mito-surface-closer-than-threshold"]
}
}- mito-min-distance-to-cell: Minimal distance of mitochondrion to cell membrane.
- syn-volume: Volume of the synaptic cleft.
- syn-surface-area: Surface area of the pre- and postsynaptic axon / dendritic parts.
- mito-volume: Volume of a mitochondrion.
- mito-surface-area: Surface area of a mitochondrion.
- syn-close-mitos: Number of close mitochondria to a specific synapse. Needs additional threshold as parameter. See example here.
- mito-spine-coverage: Number of spines covered by a specific mitochondrion.
- mito-surface-closer-than-threshold: The percentage of a mitochondrions surface that is closer than a specific threhold to the cell membrane. Needs additional threshold as parameter. See example here.
- Best use: Visualizing and comparing a high number of neighborhoods characterized through a single quantitative attributes and two categorical values.
- Comparison use: For high cardinality comparison (comparing a high number of structures).
- Required data: At least a quantitative value per neighborhood and two categorical values (e.g. synapse name and mitochondrion name).
{
"name": "distance-matrix",
"header": "add header name here",
"x-axis": {
"label": "add a label here",
"attribute": ["mito-synapse-distance"]
},
"params": ["fixed", "adjustable"]
}- mito-synapse-distance: map the distance between a synapse and a mitochondrion on the cells of the distance matrix.
- fixed: displays only synapses that belong to the mitochondrion cell.
- adjustable: synapses that not belong to the mitochondrions cell are also taken into account. A threshold distance is adjustable using a slider.