— Automation for Mouse Behavioural Research

The Problem

Manual scoring is the
silent bottleneck

Hours of video review per experiment — before the science has even begun.

Behavioural neuroscience runs on video data. The analysis hasn't kept up.

Researchers spend hours reviewing footage, hand-timing behavioural events, and transcribing observations into spreadsheets. This process introduces inter-rater variability, accumulates fatigue-related scoring errors, and consumes time that should belong to experimental design and interpretation.

Existing commercial solutions are expensive, require dedicated workstations or cloud upload, and often demand coding knowledge to configure. The result: many laboratories continue to score manually — not by choice, but by default.

MouseScope

A free, open-source desktop application that replaces manual scoring entirely. Configure once, run hundreds of videos overnight. No subscription, no cloud upload, no Python installation required.

Supported Paradigms

Five canonical paradigms.
One unified interface.

The same five-step workflow applies across all paradigms, minimising onboarding time for new lab members.

Open Field Test

OFT

Anxiety assessment, locomotor activity, drug-induced hyper/hypoactivity

Key Metrics

Total distance Time in centre Mean velocity

Tail Suspension Test

TST

Antidepressant screening; despair-like behaviour quantification

Key Metrics

Immobility time Struggle latency Bout count

Novel Object Recognition

NOR

Hippocampal memory; cognitive decline and neurodegeneration models

Key Metrics

Discrimination index Exploration time

Elevated Plus Maze

EPM

Anxiety phenotyping; anxiolytic drug efficacy screening

Key Metrics

Open-arm time % Arm entries Centre dwell

Y-Maze

Y-MAZE

Spatial working memory; neurodegeneration and ageing models

Key Metrics

Spontaneous alternation % Total arm entries

Workflow

Five steps.
Every paradigm.

The same structured workflow across all supported tests means a new lab member can run their first analysis in under 15 minutes.

01

Select module & import videos

Choose your paradigm from the module selector. Drag and drop video files — MP4, AVI, and other common laboratory formats are supported. Batch-import an entire session folder in one step.

02

Draw ROIs on the first frame

Use the drag-and-drop ROI tool to define zones on a still frame — centre zone for OFT, arms for EPM, object locations for NOR. No coordinate entry, no scripting.

03

Preview tracking on a short clip

Run a 30-second preview to verify tracking quality. Adjust contrast threshold if needed to accommodate your specific video conditions before committing to the full batch.

04

Launch batch analysis

Set the full batch running in the background. MouseScope processes all imported videos sequentially using frame-by-frame computer vision — no manual attention required. Run overnight for large datasets.

05

Export results in one click

A single export action produces structured CSV data, an annotated tracking video, spatial heatmaps, and a parameter config file — all organised in a structured output folder ready for statistical analysis.

Validation

Research-grade accuracy.
Validated against human scorers.

Our automated tracking reliably replicates expert manual scoring, maintaining high correlation across experimental sessions.

📈

High Correlation

MouseScope outputs show robust correlation with expert human scoring, confirming reliability without fatigue or inter-rater drift.

⏱️

Ethogram Precision

Chronological breakdown of identified behaviours illustrates precise temporal matching against manual ethograms.

Output Files

Every analysis session
produces four files.

Formatted for direct import into GraphPad Prism, SPSS, R, or Python. No reformatting required.

📊

data_results.csv

Behavioural metrics table

All computed metrics in a single flat table, one row per animal per session. Ready for direct import into any statistical software.

🎬

annotated_output.mp4

Tracking overlay video

Original footage with tracking markers, zone labels, and real-time metric overlays. Enables manual audit of automated results and supports methods documentation.

🗺️

heatmap.png · trackmap.png

Spatial distribution figures

Publication-quality spatial occupancy heatmaps and trajectory maps, generated automatically. Export-ready at print resolution.

⚙️

params_config.json

Parameter record

Complete analysis parameter set saved alongside results. Enables full methodological reproducibility — share the config file with collaborators or reviewers to replicate any analysis exactly.

🖥️

Fully local processing

All computation happens on your lab workstation. Video data never leaves your network, protecting unpublished experimental results.

📋

Reproducible by design

Every analysis is paired with a .json parameter record. Rerun any analysis identically — months later, on a different machine, by a different researcher.

🔓

Open-source & extensible

GPL-3.0 license. Free to use, modify, and distribute. Researchers with Python experience can extend the modular codebase via GitHub.

Platform	Windows 10 / 11 · Standalone .exe, no Python installation required
Video formats	MP4, AVI, and other common laboratory recording formats
Hardware	Standard lab workstation · No GPU required for most analyses
Privacy	All processing is local — no data is transmitted externally
License	GPL-3.0 open-source — free to use, modify, and distribute
Support	GitHub Issues · Feature requests and bug reports welcome
Current scope	Optimised for single-animal paradigms · Multi-animal social tracking on development roadmap

Other Projects

Part of a three-tool
research pipeline

MouseScope handles classical single-animal paradigms. For colony-scale behaviour and chronic stress modelling, we've built — or partnered on — two complementary tools.

Commercial Flagship

TruMouse Pro

Multi-animal behavioural tracking system. 144-channel RFID + video fusion tracks up to 20 individually identified mice continuously, in their home environment. 41 metrics output per session.

RFID × Video × DeepLabCut Explore TruMouse Pro → Partner Product

BlueBox

Automated chronic stress platform for depression and anxiety modelling. Supports CUMS and CRS protocols with programmable, unattended stress delivery.

CUMS & CRS · Programmable Explore BlueBox →

Stop scoring
videos by hand.

Manual scoring is the
silent bottleneck

Behavioural neuroscience runs on video data. The analysis hasn't kept up.