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docs/usage/connectivity.md
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# Connectivity matrix
# Exploring connectivity
One of the new features from the Interactive Viewer's [version 2.1.0](https://interactive-viewer-user-documentation.apps.hbp.eu/releases/v2.1.0/) is to explore connectivity data, based on the parcellation area (region). Source of connectivity data is specific dataset(s) from HBP Knowledge Graph.
The interactive atlas viewer allows the exploration of connectivity of parcellation regions, based on datasets curated in HBP Knowledge Graph.
For now, connectivity data is explorable for parcellation: "JuBrain Cytoarchitectonic Atlas" which is available on "MNI Colin 27" and "ICBM 2009c Nonlinear Asymmetric" template spaces.
Currently, connectivity data is explorable for the parcellation `JuBrain Cytoarchitectonic Atlas`, which is available in template spaces `MNI Colin 27` and `ICBM 2009c Nonlinear Asymmetric`.
## Explore area connectivity
Select parcellation "JuBrain Cytoarchitectonic Atlas" and click on a region to bring up a context-specific menu
## Getting started
[![](images/region_menu_with_connectivity.png)](images/region_menu_with_connectivity.png)
- Select parcellation `JuBrain Cytoarchitectonic Atlas` and click on a region to bring up a context-specific menu
By clicking on the "Connectivity" button, available datasets for connectivity will be displayed
[![](images/region_menu_with_connectivity.png)](images/region_menu_with_connectivity.png)
[![](images/connectivity_dataset_menu.png)](images/connectivity_dataset_menu.png)
- Click the `Connectivity` button, available datasets for connectivity will be displayed
From the picture above, connectivity is available from the dataset "1000 Brain Study". Click on a dataset name to explore connectivity data and color visualization on the parcellation.
After selecting the desired dataset you can mention several changes:
[![](images/connectivity_dataset_menu.png)](images/connectivity_dataset_menu.png)
1. Color map for parcellation regions will be changed by connectivity data. (The selected area is marked on the image below)
- Color map before selecting connectivity
[![](images/connectivity_color_before.png)](images/connectivity_color_before.png)
- Color map after selecting connectivity
- Click on a dataset (e.g. `1000 Brain Study - DTI connectivity`) to explore the connectivity data associated with it.
## Working with connectivity data
Upon selecting a preview dataset, several aspects of the UI will change:
- the color map of the parcellation will be replaced by a heat map, derived from the magnitutde of connectivity.
| Regular color map | Connectivity heat map |
| --- | --- |
| [![](images/connectivity_color_before.png)](images/connectivity_color_before.png) | [![](images/connectivity_color_after.png)](images/connectivity_color_after.png) |
[![](images/connectivity_color_after.png)](images/connectivity_color_after.png)
2. A Side panel will be opened (If it is closed) and connectivity data will be displayed
- a side panel will be opened, showing the tabulated data of the connectivity.
[![](images/connectivity_data_main.png)](images/connectivity_data_main.png)
## Work with connectivity data
In the connectivity panel, under selected dataset, you can find the source region
[![](images/connectivity_source_region.png)](images/connectivity_source_region.png)
### Tabulated side panel
In the tabulated view, the selected dataset can be reviewed and changed.
[![](images/see_dataset_connectivity.png)](images/see_dataset_connectivity.png)
[![](images/connectivity_dataset_description.png)](images/connectivity_dataset_description.png)
### Explore/change dataset
From connectivity panel, you can change dataset or explore the description of the current dataset
The source region is displayed in the tabulated view.
[![](images/see_dataset_connectivity.png)](images/see_dataset_connectivity.png)
Hover on (i) info icon to display dataset description
[![](images/connectivity_source_region.png)](images/connectivity_source_region.png)
[![](images/connectivity_dataset_description.png)](images/connectivity_dataset_description.png)
### Connected regions view
At the top of the connectivity diagram, you can see two checkboxes: "Log10" and "All results"
1. "Log10" checkbox is to see a diagram with logarithmic data. (Log10 checkbox is checked by default)
| Diagram with logarithmic data | Diagram without logarithmic data |
|-------------------------------|----------------------------------|
| [![](images/con_diagram_log.png)](images/con_diagram_log.png) | [![](images/con_diagram_no_log.png)](images/con_diagram_no_log.png) |
The magnitude of the connectivity can either be displayed linearly or logarithmically by toggling the `Log10` checkbox.
2. To see a number of connections on each connected region, the cursor should hover the desired area.
"All results" checkbox, displays connection number of all connected areas at once (Checkbox is unchecked by default)
| Diagram with disabled "All results" | Diagram with enabled "All results" |
|-------------------------------|----------------------------------|
| [![](images/conn_disabled_all.png)](images/conn_disabled_all.png) | [![](images/conn_enabled_all.png)](images/conn_enabled_all.png) |
| Connectivity plotted logarithmically `default` | Connectivity plotted linearly |
| --- | --- |
| [![](images/con_diagram_log.png)](images/con_diagram_log.png) | [![](images/con_diagram_no_log.png)](images/con_diagram_no_log.png) |
By clicking the connected region, special panel will be expanded.
The display of magnitude of the connectivity can also be toggled with `All results` checkbox.
[![](images/conn_expanded_area.png)](images/conn_expanded_area.png)
At the panel you can find a full name of the connected area and two buttons:
"Navigate" - to change template navigation and move to region.
"Connectivity" - to set region as source region and explore connectivity of it.
| Hiding magnitude `default` | Showing magnitude |
| --- | --- |
| [![](images/conn_disabled_all.png)](images/conn_disabled_all.png) | [![](images/conn_enabled_all.png)](images/conn_enabled_all.png) |
Clicking on any of the connected region will reveal a region context menu. In addition to the full name of the region, two buttons are present:
- `Navigate` - navigate to the region of interest.
- `Connectivity` - to the region of interest as the source, and explore its connectivity with other parcellation regions.
## Export connectivity data
At the end of the connectivity panel, you can find export buttons.
[![](images/conn_expanded_area.png)](images/conn_expanded_area.png)
[![](images/conn_export.png)](images/conn_export.png)
### Export
At the bottom of the side panel, `export` buttons can be found. The data can either be exported as a CSV or PNG.
You can export connectivity data with two options
[![](images/conn_export.png)](images/conn_export.png)
1. Export data as a CSV file
2. Export data as "png" format image
## Exit
## Close Connectivity
You can close connectivity from a close button on the top right side of the connectivity section at the right-side panel.
To exit the connectivity mode, click the close button located at the top right side of the side panel.
[![](images/close_connectivity.png)](images/close_connectivity.png)
[![](images/close_connectivity.png)](images/close_connectivity.png)
Exiting the connectivity mode will:
1. After clicking the close button, the standard parcellation region color map will be returned to the viewer.
2. Connectivity data will be disappeared from a side panel
\ No newline at end of file
- restore the colour map of the parcellation
- remove the connectivity side panel
mkdocs.yml
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......@@ -21,7 +21,7 @@ pages:
- Selecting: 'usage/selecting.md'
- Navigating: 'usage/navigating.md'
- Searching: 'usage/search.md'
- Connectivity: 'usage/connectivity.md'
- Exploring connectivity: 'usage/connectivity.md'
- Advanced usage:
- Keyboard shortcuts: 'advanced/keyboard.md'
- URL parsing: 'advanced/url.md'
......
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