Guide to Playing Mozak

Tracing Faint Branches

• 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

Accurately tracing faint branch is one of the most challenging parts of creating a complete reconstruction. Here are some tips that can help!

Remember to use the brightness slider to find the faintest signal. Inverting the images can also be useful (your eyes may prefer black signal on white background). The images below show the same location with the brightness adjusted. Can you find more branches in the image on the right?

Rotating the image can be a useful way to find and follow a neurite. This is especially true if the neurite is moving directly towards or away from you. Turning the image stack 90 degrees, so the narrow side is facing you, can allow you to see when neurites are truncated at the surface of the slice.

Capturing a faint axon ends up being like a game of connect-the-dots. Axon labeling can be discontinuous. It is helpful to go into connect the dots mode and scroll through planes with your mouse wheel, looking for dots that travel in a consistent direction. Here is an example to show you what intermittent labeling looks like, and how to trace it: