Guide to Playing Mozak

Creating Axon and Dendrite Traces

• Introduction
• Getting to Know the Project
• Getting to Know a Neuron
• Getting to Know an Image Stack
• Noise vs. Signal
• Types of Neurons — Spiny/Aspiny
• Tracing Faint Branches
• Creating a Fully Connected Structure
• Creating Axon and Dendrite Traces

One of the challenges of creating a high quality reconstruction is correctly identifying whether a branch is an axon and dendrite.

A couple of things to pay attention to when identifying axons are thinness, direction, and initial location of the neurite.

Thinness

Axons tend to be thinner than dendrites, which is another reason they can be more difficult to track down. If you are unsure whether or not you are looking at an axon, look at the thickness of the other neurites around it to compare. An axon should almost always be thinner.

Direction

Axons tend to be more erratic in their direction. While dendrites consistently move away from the soma, axons can double back on themselves, coming back toward the soma and moving away as they please.

Initial Location

Axons will either come from the soma or from the base of a dendrite very near the soma.

Viewing in disconnected mode

The axon and dendrite view can be combined with the disconnected view, which will results in up to four different colors being visible. The axon will be colored pink if not connected to the soma and light blue if it is. The overall goal remains the same, getting as much of the reddish traces to turn blue. However, you will generally want to try to connect the axon fragments with other axon and the dendrites with dendrites.