Update connectivity.md

docs/usage/connectivity.md

 # Exploring a connectivity matrix for the selected brain parcellation
 
-Via the <https://github.com/FZJ-INM1-BDA/HBP-connectivity-component>, the interactive atlas viewer allows interactive exploration of a connectivity matrix, that is defined for the currently selected brain parcellation and available from the HBP Knowledge Graph.
-
-As of now, this function is only available for the `JuBrain Cytoarchitectonic Atlas.
+Via the <https://github.com/FZJ-INM1-BDA/HBP-connectivity-component>, the interactive atlas viewer allows interactive exploration of a connectivity matrix, that is defined for the currently selected brain parcellation and available from the HBP Knowledge Graph. As of now, this function is only available for the `JuBrain Cytoarchitectonic Atlas.
 
 ## Launching the connectivity browser
 
@@ -13,49 +11,51 @@ As of now, this function is only available for the `JuBrain Cytoarchitectonic At
 - Select `Connectivity` to select one of the available connecitivty matrices. Note that this list will be growing in the near future, to inlude connectivity information from different sources.
 
    [![](images/connectivity_dataset_menu.png)](images/connectivity_dataset_menu.png)
+   
+- This will load the connectivity browser with the source region for connection strengths set to the initially selected brain region.
 
 
 ## 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.
+- the color map of the parcellation will be replaced by a heat map of the connection strengths to the source region, effectively visualizing the corresponding row of the connectivity matrix:
 
    | 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.
+- a side panel will be opened, showing the same connections strenghts as a horizontal bar plot. The source reion
 
    [![](images/connectivity_data_main.png)](images/connectivity_data_main.png)
 
 
-### Tabulated side panel
+### Interactive exploration of connectivity using the tabulated view
 
-In the tabulated view, the selected dataset can be reviewed and changed.
+In the side panel, the selected connectivity matrix can be changed if applicable. 
 
 [![](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.
+It also provides information about the selected source region.
 
 [![](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.
+Display of connection strengths can be set to logarithmic scale using 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.
+Selecting the `All results` checkbox will make the bar plot display the floating point numbers for each connection strength:
 
 | 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:
+By clicking any of the bars, a context menu of the corersponding brain region will be brought up, providing information about the region and allowing to center the 3D view at this region, or select it as the new source region. The latter effectively selects a new row from the connectivity matrix.
 
 - `Navigate` - navigate to the region of interest.
 - `Connectivity` - to the region of interest as the source, and explore its connectivity with other parcellation regions.
@@ -64,17 +64,14 @@ Clicking on any of the connected region will reveal a region context menu. In ad
 
 ### Export
 
-At the bottom of the side panel, `export` buttons can be found. The data can either be exported as a CSV or PNG.
+Using the `export` buttons, the connectivity matrix can be exported as a CSV or PNG file.
 
 [![](images/conn_export.png)](images/conn_export.png)
 
-## Exit
+## Closing the connectivity browser
 
 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 
+This will restore the colour map of the parcellation and close the side panel.