https://github.com/rulen111/animaltracker
Desktop application for automated tracking and trajectory analysis of rodents in behavioral research
https://github.com/rulen111/animaltracker
behavior-analysis tracking
Last synced: 10 months ago
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Desktop application for automated tracking and trajectory analysis of rodents in behavioral research
- Host: GitHub
- URL: https://github.com/rulen111/animaltracker
- Owner: rulen111
- License: mit
- Created: 2024-04-16T19:08:45.000Z (about 2 years ago)
- Default Branch: main
- Last Pushed: 2024-08-01T11:04:47.000Z (almost 2 years ago)
- Last Synced: 2024-12-28T13:27:51.626Z (over 1 year ago)
- Topics: behavior-analysis, tracking
- Language: Python
- Homepage:
- Size: 78.1 KB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# Animal Tracker
## About
Desktop application for automated tracking and trajectory analysis of rodents in behavioral research.
## Prerequisites
`opencv-python>=4.5.5.64
PyForms-GUI>=5
tqdm>=4.66.2`
## Features
### Preprocessing
Adjust frame preprocessing parameters. Currently, Preprocessing module supports following features:
- **Define tracking interval.** Specify starting and last frames to include in tracking. Interactive player helps you find a specific frame and its number;
- **Resize.** Select a down scaling factor from 1% to 100%;
- **Preview.** Look at the picture of a frame with all preprocessing rules applied for validation.
### Tracking
Tracking module parameters. Supports following features:
- **Background reference computation.** Create and preview a background reference image for specified video file;
- **Adjustable threshold.** Specify threshold value for the segmentation filter.
### Validation
User validation module. Check generated trajectory, make changes and save it to a file. Supports following features:
- **Interactive track editing.** Choose multiple points and change their position by click;
- **Save to file.** Save both starting and result versions of a track to csv.
### ROI
Specify Regions Of Interest. Supports following features:
- **Draw custom region.** Add points by clicking to form a polygon on top of a frame;
- **Include in analysis.** Run separate analysis for specific regions of interest.
### Analysis
Analyse rodent trajectory. Supports following features:
- Movement characteristics. Calculate average speed, total time and path;
- Spatial characteristics. Count number of times subject entered a certain ROI, total time spent in ROI.
## How ot run
1. Install prerequisites:
`pip install -r requirements.txt`
2. Start application:
`python run_app.py`