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Rendering Options

Various rendering options are available which control the display in both the 2D and 3D windows. These settings are strictly for visualization purposes only, and therefore have no effect on the structure of the model, spines, etc. Most of these options can be set through the top level Render menu of the main window.

Shape Schemes

You can choose the shape of rendered objects such as model vertices, connections (edges), and spines from the Render menu of the main window. See 2D examples below.

Model Shape Option 1 Model Shape Option 2 Model Shape Option 3 Model Shape Option 4
Model vertices shaped as solid ellipses. Model vertices shaped as hollow ellipses. Model edges shaped as solid lines. Model edges shaped as solid frustums.

Color Selection

You can set various colors of the rendered elements by selecting the menu item View >> Colors.... This will bring up a window that contains a list of the elements, controls for RGB (red green blue) and HSV (hue, saturation, value) colorspaces, etc. The use of this window is fairly simple. Worth mentioning however are the Apply and Default buttons. The Apply button will re-render the displays with the new selected colors so that you can preview how it will look. The Default button resets the color of the selected element to a programmed default. Note also that hitting the Cancel button will undo any changes you made to the colors.

Color Schemes

In addition to the shape of rendered elements, you can control the coloring scheme from the Render menu of the main window. See 2D examples below.

Model Color Option 1 Model Color Option 2 Model Color Option 3 Model Color Option 4
Model vertices with a single color. Model vertices colored by type. Model edges with a single color. Model edges colored by section.

Line and Point Size

You can set the size in pixels of lines and points that are rendered in 2D and 3D. See the menu item View >> Line/Point Size for a list of available sizes.


Another topic worth mentioning is synchronizing the display of the 2D and 3D windows. The menu item Render >> Flicker Free is checked by default. If this item is not checked, then either of the display windows may "skip" a frame if the other display is currently drawing or internal structures are being updated. This will sometimes cause the display to flicker, which may be visually unappealing. Of course ensuring that this doesnt happen may cause some operations to slow down.

TIP: If viewing the display is not important to you for long operations such as tracing or running spine detection on a large cell, you may turn off rendering completely to possibly gain an increase in speed. See the Render menu for shape options that are labeled as Off.

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