What is RodentFlow?
RodentFlow is an iPhone app for rodent behavior experiments. It covers the path from a recorded session to a group comparison:
- Track a top-down video of one animal and convert its position to centimeters inside a calibrated arena or maze.
- Score the session. Zone times, entries, distance, latencies, freezing and other assay-specific metrics are computed from the positions.
- Collect one result per animal and session. Results can also come from values scored by hand or from a table exported by another program.
- Compare groups. The app picks a test that fits the design, draws a figure with every animal shown, and exports the figure, the statistics and the data.
Everything runs on the phone. There is no account, no server and no upload. See the privacy policy.
RodentFlow is open source under the MIT License. The app's source code and this manual are public at github.com/seesaw-earth/RodentFlow; see Open source & building.
Two tabs
| Tab | What you do there |
|---|---|
| Experiment | Start a new experiment: pick the assay, then analyze a video, enter values or import a table. The Results card lists everything saved so far. |
| Groups | Choose an assay and a measure, set the design, and read the statistics and figure for all saved results of that assay. |
Three ways to get data in
| Source | Use it when | Assays |
|---|---|---|
| Video tracking | You have a top-down recording of a single animal | Open field, elevated plus maze, light–dark box, Y-maze, T-maze, novel object recognition, Morris water maze, Barnes maze, fear conditioning, conditioned place preference |
| Manual entry | You scored the session by hand (stopwatch, counts, weights) | All 15 assays |
| Table import | Values come from a spreadsheet or another tracker (ANY-maze, EthoVision, DeepLabCut post-processing …) | All 15 assays, plus any custom table |
All three produce the same kind of result. Video, manual and imported results of the same assay can be analyzed together in the Groups tab.
What the tracker measures, and what it does not
RodentFlow uses a classic, transparent tracker: background subtraction followed by the centroid of the animal's body. Tracking explains every step. This choice has consequences that are worth knowing before you start.
- One animal per arena. Each analysis follows one animal inside the calibrated arena. Several arenas filmed side by side can be analyzed one after the other, with one calibration each.
- Body center, not nose. The tracking point is the center of the body. Assays that are usually scored by nose position, namely novel object exploration and Barnes hole pokes, use a zone around the object or hole that is large enough for the body center. The assay pages explain how to set it.
- Top-down view. Positions are converted to centimeters on the floor plane, which assumes the camera looks down on the arena.
- No pose or behavior classification. Rearing, grooming or sniffing are not detected. Freezing is measured from frame-to-frame pixel change, which is the standard automated approach for freezing.
If you need body-part tracking or several interacting animals, deep-learning pose estimators are the right tool; Further reading lists recent ones. Their per-animal output can then be imported into RodentFlow for statistics.
Requirements
- iPhone with iOS 17 or later.
- English or Simplified Chinese. The app follows the iPhone language. To choose a different language for RodentFlow only, tap Aa › Language / 语言, which opens the app's page in Settings.
- Text size: Aa offers Small to Largest, or "Same as iPhone".
How this manual is organized
- Getting started — a five-minute walkthrough and recording advice.
- Using the app — each screen in order: video analysis, manual entry and import, results, group analysis.
- Assays — what to set and how every metric is defined, assay by assay.
- How it works — tracking, metrics, statistics and validation against ground-truth videos.
- Reference — files, FAQ, further reading and release notes.