Tracing Neurons in Aivia

There are two methods of tracing neurons in Aivia: an automated recipe and a manual neuron editing tool.

The first tool is one of the recipes included in Aivia, called the 3D Neuron Analysis recipe. This has presets for soma detection and dendrite detection as well as more precise parameters for soma diameter, dendrite diameter, minimum branch length, intensity threshold, intensity offset, and the ability to enable or disable dendritic spine detection. Measurements for the soma diameter, dendrite diameter, and branch length parameters can be taken using the Annotation tool in a normal 2D view then input into the Recipe Console. Switch the the 3D View (or even VR!) using the View Controls at the top of the screen and the recipe will automatically detect and trace all of the neurons in the image.

If there are any errors with the first method, Aivia also features a manual editing suite when in 3D view. To use the manual tools, select the Neuron Editor tab above the recipe console. This has tools to add soma, trace dendrites using the Dendrite Pencil, connect or delete existing neuron elements, and add spines. Select the tool you wish to use and the apply the edits in the 3D view with your cursor.

Pro tip: In images with higher levels of background fluorescence or lots of dendrites, it may be hard to rotate the image to correctly while using the Dendrite Pencil. Using the (d) hotkey on your keyboard allows you to quickly and easily switch in and out of the Dendrite Pencil mode to manipulate your image and get the best view for tracing!