Merge pull request #73 from FZJ-INM1-BDA/dev_connectivity_manual

Add connectivity manual

docs/usage/connectivity.md

+# Exploring connectivity
+
+Powered by <https://github.com/FZJ-INM1-BDA/HBP-connectivity-component>, the interactive atlas viewer allows the exploration of connectivity of parcellation regions, based on datasets curated in HBP Knowledge Graph.
+
+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`.
+
+## Getting started
+
+- Select parcellation `JuBrain Cytoarchitectonic Atlas` and click on a region to bring up a context-specific menu
+
+   [![](images/region_menu_with_connectivity.png)](images/region_menu_with_connectivity.png)
+
+- Click the `Connectivity` button, available datasets for connectivity will be displayed
+
+   [![](images/connectivity_dataset_menu.png)](images/connectivity_dataset_menu.png)
+
+- 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) |
+    
+
+- a side panel will be opened, showing the tabulated data of the connectivity.
+
+   [![](images/connectivity_data_main.png)](images/connectivity_data_main.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)
+
+The source region is displayed in the tabulated view.
+
+[![](images/connectivity_source_region.png)](images/connectivity_source_region.png)
+
+The magnitude of the connectivity can either be displayed linearly or logarithmically by toggling the `Log10` checkbox.
+
+| 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) |
+
+The display of magnitude of the connectivity can also be toggled with `All results` checkbox.
+
+| 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.
+
+[![](images/conn_expanded_area.png)](images/conn_expanded_area.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.
+
+[![](images/conn_export.png)](images/conn_export.png)
+
+## Exit
+
+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)
+
+Exiting the connectivity mode will:
+
+- restore the colour map of the parcellation 
+- remove the connectivity side panel 

mkdocs.yml

@@ -21,6 +21,7 @@ pages:
     - Selecting: 'usage/selecting.md'
     - Navigating: 'usage/navigating.md'
     - Searching: 'usage/search.md'
+    - Exploring connectivity: 'usage/connectivity.md'
   - Advanced usage:
     - Keyboard shortcuts: 'advanced/keyboard.md'
     - URL parsing: 'advanced/url.md'