Mastering Ctrax: The Ultimate Guide to Behavioral Video Tracking

Ctrax is a free, open-source video tracking software used by scientists to track the movements of multiple insects, like fruit flies, while keeping track of each individual identity over time.

When analyzing a video, tracking errors will naturally happen due to flies walking too close together, crossing paths, or standing completely still. To solve these issues instantly, Ctrax provides a companion tool called the FixErrors MATLAB GUI. This tool automatically flags “suspicious” data segments and lets you repair mistakes quickly. 🛠️ Common Ctrax Errors & How to Fix Them Instantly

The following steps cover how to troubleshoot the most frequent tracking bugs using Ctrax and the FixErrors program. 1. Swapped Identities or Split Tracks

The Problem: Two flies walk past each other, and the software accidentally swaps their IDs, or one fly’s track completely breaks into two separate files.

Instant Fix: Use the Connect Tracks tool inside the FixErrors MATLAB GUI. Scroll to the frame where the tracking broke. Select the first fly and click First Fly.

Scroll to the frame where the track continues, select the fly, and click Do It. This bridges the gap instantly. 2. The Video Won’t Load

The Problem: You try to upload your video file, but Ctrax displays an error or only loads a tiny fraction of the total frames.

Instant Fix: Ctrax works best with uncompressed AVI files or FlyMovieFormat (.fmf or .ufmf) files. If your video fails to load, download the free any2ufmf tool provided by the Ctrax FAQ page to convert your video into a highly compressed, tracker-friendly format. 3. Stationary Flies Disappear From the Tracker

The Problem: A fly stops moving for a long time, and the program suddenly stops tracking it entirely.

Instant Fix: The background model thinks the resting fly is part of the floor. Go to Ctrax Settings -> Background Model. Use the “Fixing Background” interpolation tool to manually draw a region over the sleeping fly, telling the software to ignore that spot when building the background. 4. “Isnan” Matlab Crash Errors