Membrane Surface Viewer

The Membrane Surface Viewer displays a membrane variable as a 3D rendered surface that can be rotated, zoomed and panned. Hovering the mouse pointer over a point on the surface displays the variable's value. The rendered display is initialized with the color scaling and data values for the current membrane variable name and time point.

• Rotate (mouse) - The view may be rotated arbitrarily using a "trackball" interface by dragging the mouse with the left mouse button (leftMB) pressed. The view rotates as if the mouse were attached to a sphere containing the surfaces. The amount of possible rotation depends on where the mouse is when the leftMB is first pressed and the direction of drag.
• Pan (mouse)- The view may also be moved side to side and up or down by dragging the mouse with the right mouse button (rightMB) pressed.
• Zoom (mouse)- The view can also be zoomed closer or farther away by dragging the mouse with the left and right mouse buttons (leftMB-rightMB) pressed.
• Point Info (mouse)- Hover the mouse pointer over a point on the surface and the data value and centroid location will appear below the render display.
• Reset View (button) - Resets the rotation, pan and zoom (mouse) to the default orientation to center the surface in the display area.
• Bounding Box (check-box)- The bounding box outlining the entire simulation data volume can be turned on/off using the check box at the bottom of the viewer panel.

The Surface Table contains information and controls to adjust the display of the rendered membrane surface. Each row represents an individual surface with the following column information:

• Name - Membrane surface identifier.
• Size - Surface area given in square microns.
• Visible - Check-box allows the user to turn on and of the viewing of surfaces. Making a particular surface invisible allows for viewing interior surfaces that would otherwise be ob- scured.
• Wire-frame - Check-box allows the user to produce an outline of each simulation mesh volume element. The resulting outline is only a gross approximation of the actual computational surface used to generate the simulation data.
• Transparent - Menu button contains settings to make a surface less opaque. The larger the number selected, the more any underlying surfaces will show through on the display.

Statistics button Starts calculation of minimum, maximum and mean statistics on the currently define ROI.

• Add User cntrl-click on a surface will add membrane elements to the ROI.
• Remove User cntrl-click on a surface will remove membrane elements from the ROI.
• Clear Resets the ROI. All membrane elements are removed from the ROI.
• Area(manual) User cntrl-click on surface will add/remove membrane elements to the ROI around the click point. The size of the area affected is set with the 'radius' menu-button.
• Area(range) Enter minimum and maximum membrane data values to add/remove from ROI then click 'Apply'.
• Area(region) Select whole pre-defined membrane surface to add/remove from ROI then click 'Apply'
• Area(analytic function of x,y,z) Enter an expression as a function of the simulation spatial domain that will add/remove from the ROi wherever the function evaluates to 'true' then click 'Apply'. (e.g. 'x>5 && x<10' will affect all membrane elements that lie within that spatial range)

Make Movie... button Shows dialog with options create a 'QuickTime' formatted movie sequence over selected timepoints using all the settings for the current surface view

• Movie format - Select type of movie file to create.
• Movie width/height - Displays the size of each movie frame. These values are taken from the surface render display panel and can be changed by making the main surface viewer window larger or smaller.
• Frames per second - Sets the playback speed for the finished movie.
• Begin/End/Skip Time - Select which timepoints from the simulation data are used to create the movie frames.
• Total Frames/Movie Duration - Displays information about the final movie based on the other settings in the dialog.