Neuroglancer Contour Annotations Documentation

Volume session

• To draw/edit polygons of a volume (structure) user needs to start a session selecting the corresponding volume.
• User will have the option of drawing/editing polygons ONLY belonging to the volume that is selected in the session.
• More details about volume session can be found in this design document here.

Start a new volume

• To start a new volume left click on the VOL shape icon in the toolbar of annotations tab.
• The user must select a landmark and a color for the volume and finally do a left click on Start a new volume.

Edit an existing volume

• To edit an existing volume, user needs to first select the volume. To select the volume, left click on the volume in the list of annotations displayed and make sure its pinned. (tge structure will be highlighted in a mauve color)
• Once the volume is selected, left click on the VOL shape icon in the toolbar of annotations tab and finally do a left click on Edit selected volume.

Close volume session

• Once the user is done with drawing/editing the polygons of the volume currently active in the session, user can close the volume session by doing a left click on the VOL shape icon in the toolbar of annotations tab and finally do a left click on Close current active session.

Polygon modes

• Once a volume session is active, user can switch between different modes, each mode has its own set of functionalities to draw/edit polygons of the volume. User can see the mode they are currently in the top right corner of the neuroglancer window.

Controls to switch between modes

• If the user is currently in view mode or edit mode, pressing control+z takes them to draw mode.
• If the user is currently in view mode, pressing control+z takes them to draw mode.
• If the user is currently in view mode or draw mode, pressing control+x takes them to edit mode.
• If the user is currently in edit mode, pressing control+x takes them to view mode.

Draw mode

• Draw Polygon [left click]
  • To start drawing a polygon, user can do simply do a left click to insert vertices on the section.
• Close Polygon [right click]
  • After user has drawn all the vertices, user can close the polygon by simply doing a right click.

• Undo [key z]
  • To undo last drawn vertex, user can press 'z' on the keyboard to delete the last vertex on the section.

Edit mode

• Edit polygon vertices [left click]
  • To edit position of a polygon vertex, simply do a left click on the vertex and drag the mouse to move the vertex around in the section.

**NOTE: To edit vertices make sure that the vertices are big enough (have good amount of size and border width), these parameters can be adjusted in the Rendering Tab in the top right corner.

• Add a vertex to polygon [control+alt+left click]
  • To add a vertex to the polygon, press control+alt+left click anywhere on the line segment of the polygon, a vertex will be added to the polygon at that position.
• Delete a vertex of polygon [control+alt+right click]
  • To delete a vertex to the polygon, press control+alt+right click on the vertex of the polygon.
• Translate Polygon [shift+left click]
  • To translate the polygon in the section, press shift+left click on any line segment of the polygon and drag the mouse with left click pressed.
• Clone Polygon [control+c]
  • To clone a polygon, the polygon needs to be selected first using control+right click on the polygon or doing a left click on the polygon in the annotations tab.
  • Once the polygon is selected user can press control+c to clone the polygon.
• Rotate Polygon [key r, key e]
  • To rotate the polygon, the polygon needs to be selected first using control+right click on the polygon or doing a left click on the polygon in the annotations tab.
  • Once the polygon is selected user can press r/e to rotate the polygon.
• Scale Polygon [control+'+', control+'-']
  • To scale the polygon, the polygon needs to be selected first using control+right click on the polygon or doing a left click on the polygon in the annotations tab.
  • Once the polygon is selected, user can press control+'-'/control+'+' to shrink/enlarge the polygon.
• Polygon configuration
  • User can click on the △ icon in the top right corner of the neuroglancer to open the polygon configuration.
  • Clone section offset value denotes the offset between current section and cloned section. For example: if the current section is x and offset value is y, the polygon will be cloned to x+y section.
  • Scale factor value denotes the percentage change in the polygon size with the scaling operation.
  • Rotate factor value denotes the number of degrees the polygon rotates with rotate operation.

No op mode

• Currently in draw/edit mode user DOES NOT have the ability to move around the section by dragging the mouse, in view mode user has the ability to move around the section by dragging the mouse.
• Insert view mode gif15

Control sheet

Function	Key	mode
draw polygon vertex	left mouse click	draw mode
close polygon	right mouse click	draw mode
undo last vertex	key z	draw mode
edit polygon vertex	left mouse click	edit mode
add vertex to polygon	control+alt+left mouse click	edit mode
delete vertex of polygon	control+alt+right mouse click	edit mode
select polygon	control+right mouse click	draw/edit/view mode
translate polygon	shift+left mouse click	edit mode
clone polygon	control+c (polygon needs to be selected first)	draw/edit mode
rotate polygon	key r / key e (polygon needs to be selected first)	edit mode
scale polygon	control+'+' / control+'-' (polygon needs to be selected first)	edit mode
switch edit/view -> draw mode	control+z	edit/view mode
switch draw/view -> edit mode	control+x	draw/view mode
switch draw -> view mode	control+z	draw mode
switch edit -> view mode	control+x	edit mode