some restructuring of documentation elements

common/helpOnePager.md

@@ -11,7 +11,5 @@
 | Multiple region select | `<ctrl>` + `[click]` on region | - |
 | Context menu | `[right click]` | - |
 
----
+You can enable touch interface by `[Portrait]` > `Settings` > `Enable Mobile UI`
 
-
-You can enable touch interface by `[Portrait]` > `Settings` > `Enable Mobile UI`
\ No newline at end of file

docs/basic_functionalities/selecting_parcellation_maps.md

-# Selecting Parcellation Maps
-
-On the bottom left of the viewer, you find selectors for choosing the species, reference space, and parcellation map. The latter two are shown only if more than one option is available.
-
-![](https://data-proxy.ebrains.eu/api/v1/buckets/reference-atlas-data/static/siibra-explorer-chips.png){ style="width:700px"}
-
-When selecting a species, a default reference space and parcellation will be automatically preselected.
-If you switch to a different reference space, `siibra-explorer` will first check if a map of the currently selected parcellation is available for the chosen space. If it is not, you will be asked to select a different parcellation.
-Vice versa, when selecting a parcellation which is not available as a map in the currently selected reference space, you will be asked to select a different space.
-

docs/basic_functionalities/exploring_3d_parcellation_maps.md → docs/basics/exploring_3d_parcellation_maps.md

 # Exploring 3D Parcellation Maps
 
+On the bottom left of the viewer, you find selectors for choosing the species, reference space, and parcellation map. The latter two are shown only if more than one option is available.
+
+![](https://data-proxy.ebrains.eu/api/v1/buckets/reference-atlas-data/static/siibra-explorer-chips.png){ style="width:700px"}
+
+When selecting a species, a default reference space and parcellation will be automatically preselected.
+If you switch to a different reference space, `siibra-explorer` will first check if a map of the currently selected parcellation is available for the chosen space. If it is not, you will be asked to select a different parcellation.
+Vice versa, when selecting a parcellation which is not available as a map in the currently selected reference space, you will be asked to select a different space.
+
+
 In the case of a volumetric template, siibra-explorer combines a rotatable 3D surface view of a brain volume with three planar views of orthogonal image planes (coronal, sagittal, horizontal). It can visualize very large brain volumes in the Terabyte range.
 
 ![](https://data-proxy.ebrains.eu/api/v1/buckets/reference-atlas-data/static/julichbrain_bigbrain_4panel.png){: style="width:700px" }

docs/basic_functionalities/storing_and_sharing_3d_views.md → docs/basics/storing_and_sharing_3d_views.md

@@ -2,21 +2,19 @@
 
 ## Bookmarks
 
-Any views in siibra-explorer can be shared via their URLs. You can use any native share functionality offered by your browser, or manually copy the URL.
+Any views in `siibra-explorer` can be shared via their URLs. You can use any native share functionality offered by your browser, or manually copy the URL.
 
 !!! info
     Automatic markdown renderer such as rocketchat can interfere with the rendering of the URL. To circumvent the issue, it is recommended that you generate a sane URL, or use a `code` block to escape markup
 
-## sane URL
+## Creating short URLs ("saneURL")
 
-Whilst sharing views with URLs are convenient, full URLs are lengthy, fail to be recitable or memorable. While you can use any URL shortener, siibra-explorer provide a URL shortener. To access this service, expand navigation panel, click share icon and click `Create custom URL`.
+Whilst sharing views with URLs are convenient, full URLs are lengthy, fail to be recitable or memorable. While you can use any URL shortener, `siibra-explorer` provide a URL shortener. To access this service, expand navigation panel, click share icon and click `Create custom URL`.
 
 !!! warning
     Links generated by unauthenticated users will expire automatically after 72 hours. To circumvent the expiry, ensure you are logged in using an ebrains user account. Links generated by an authenticated user does not expire.
 
 ## Taking Screenshots
 
-Whilst you can use any browser level or OS level screenshot tool, siibra-explorer also offers a screenshot tool. To access the screenshot tool, click `Plugin`, then select `Screenshot`.
+Whilst you can use any browser level or OS level screenshot tool, `siibra-explorer` also offers a dedicated screenshot tool which generates a clean and exact image of the current 3D view which automatically hides other user interface elements. To access the screenshot tool, click `Plugin`, then select `Screenshot`.
 
-!!! info
-    Screenshot taken by the built in screenshot tool hides all UIs. 

docs/basic_functionalities/overview_of_ui.md → docs/ui/main_elements.md

-# Organisation of the user interface
+# Main elements of the user interface
 
-At its core, the viewer presents a 3D view of a brain. 
+**3D view.** At its core, the viewer presents a 3D view of a brain. 
 The precise layout of the 3D view depends on the select reference space. 
-
 For volumetric reference spaces, it presents 2D views of three orthogonal planes in the reference template, combined with a rotatable 3D overview of the brain surface indicating the location of these planes.
 The planes default to the coronal, sagittal and axial plane, and can be freely adjusted in position and orientation to select arbitrary oblique views. 
 
-![](https://data-proxy.ebrains.eu/api/v1/buckets/reference-atlas-data/static/siibra-explorer-waxholm.png){ style="width:300px"}
+![](https://data-proxy.ebrains.eu/api/v1/buckets/reference-atlas-data/static/siibra-explorer-waxholm.png){ style="width:600px"}
 
 The volumetric views support ultrahigh-resolution data, and can be zoomed in if the underlying image data allows. Each of the 3 planar views can be maximized using the "[ ]" icon in each view.
 
-![](https://data-proxy.ebrains.eu/api/v1/buckets/reference-atlas-data/static/siibra-explorer-v1border.png){ style="width:300px"}
+![](https://data-proxy.ebrains.eu/api/v1/buckets/reference-atlas-data/static/siibra-explorer-v1border.png){ style="width:600px"}
 
 For pure surface spaces, such as the fsaverage space, the viewer shows only a 3D view.
 
-![](https://data-proxy.ebrains.eu/api/v1/buckets/reference-atlas-data/static/siibra-explorer-surfaceview.png){ style="width:300px"}
+![](https://data-proxy.ebrains.eu/api/v1/buckets/reference-atlas-data/static/siibra-explorer-surfaceview.png){ style="width:600px"}
+
+
+**Navigation panel.** At the top left of the user interface, `siibra-explorer` displays the 3D coordinate of the currently selected center of view. When you click it with the mouse pointer, a navigation panel opens, which allows to enter a different coordinates, and create a shareable link to the current view (see ["Storing and sharing 3D views"](../basics/storing_and_sharing_3d_views.md)).
 
-At the bottom of the window, you find buttons to switch between different species, different reference templates, and different parcellation maps. Note that buttons may be hidden in case that only one option is available.
+**Parcellation map selectors.** At the bottom of the window, you find buttons to switch between different species, different reference templates, and different parcellation maps (see ["Exploring parcellation maps"](../basics/exploring_3d_parcellation_maps.md)). Note that buttons may be hidden in case that only one option is available.
 
 ![](https://data-proxy.ebrains.eu/api/v1/buckets/reference-atlas-data/static/siibra-explorer-chips.png){ style="width:700px"}
 
-At the top right of the viewer, there are several icons guiding you to additional functionalites.
+**Additional tools.** At the top right of the viewer, there are several icons guiding you to additional functionalites.
 
 ![](https://data-proxy.ebrains.eu/api/v1/buckets/reference-atlas-data/static/siibra-explorer-tools.png){ style="width:250px"}
 
@@ -28,6 +30,6 @@ From left to right you find
 
 - The help button. Here you find information about keyboard shortcuts and terms of use. You can also launch the interactive quick tour, which is launched automatically when you use `siibra-explorer` for the first time.
 - The download button, which will download the reference template and parcellation map currently displayed in the viewer
-- The plugin menu, which allows you to launch interactive plugins (see “Advanced functionalities” below)
+- The plugin menu, which allows you to launch interactive plugins (see “Advanced functionalities”)
 - The login menu, which allows you to login with an EBRAINS account to access some custom functionalities for sharing.
 

mkdocs.yml

@@ -22,19 +22,19 @@ nav:
   - Home: 'index.md'
   - Getting Started: 'getting_started.md'
   - Key concepts: 'concepts.md'
+  - User interface:
+    - Main elements: 'ui/main_elements.md'
+    - Keyboard shortcuts: 'basics/helperOnePager.md'
   - Basic Functionalities:
-    - Organisation of user interface: 'basic_functionalities/overview_of_ui.md'
-    - Selecting parcellation maps: 'basic_functionalities/selecting_parcellation_maps.md'
-    - Exploring 3D parcellation maps: 'basic_functionalities/exploring_3d_parcellation_maps.md'
-    - Keyboard shortcuts: 'basic_functionalities/helperOnePager.md'
-    - Storing and sharing 3D views: 'basic_functionalities/storing_and_sharing_3d_views.md'
-    - Selecting brain regions: 'basic_functionalities/selecting_brain_regions.md'
-    - Looking up coordinates in reference space: 'basic_functionalities/looking_up_coordinates.md'
-    - Finding multimodal data: 'basic_functionalities/finding_multimodal_data.md'
+    - Exploring parcellation maps: 'basics/exploring_3d_parcellation_maps.md'
+    - Storing and sharing 3D views: 'basics/storing_and_sharing_3d_views.md'
+    - Selecting brain regions: 'basics/selecting_brain_regions.md'
+    - Looking up coordinates in reference space: 'basics/looking_up_coordinates.md'
+    - Finding multimodal data: 'basics/finding_multimodal_data.md'
   - Advanced functionalities:
-    - Annotating structures in the brain: "advanced_functionalities/annotating_structures.md"
-    - Differential gene expression analysis: "advanced_functionalities/differential_gene_expression_analysis.md"
-    - Superimposing local files: "advanced_functionalities/superimposing_local_files.md"
+    - Annotating structures in the brain: "advanced/annotating_structures.md"
+    - Differential gene expression analysis: "advanced/differential_gene_expression_analysis.md"
+    - Superimposing local files: "advanced/superimposing_local_files.md"
 
   - Release notes:
     - v2.14.0: 'releases/v2.14.0.md'