Welcome to ByoTrack’s documentation!
ByoTrack is a Python library that enables tracking of biological object in videos. Many bioimage informatics tools already implement their own tracking tools (Icy, ImageJ, TrackMate…) but most of them are implemented in Java which makes it difficult for non-Java developers to experiment with the code. It is also difficult to integrate deep learning algorithms (mainly developed in Python) into these software.
We provide a unified python API for tracking that can be easily extended with new (and old) algorithms. We also provide implementations of well-known algorithms following our API.
Note
This project and documentation is under active development.
Contents
Getting started
- ByoTrack fundamental features
- Loading a video
- Detections on a video: Example of WaveletDetector
- Link detections: Example of IcyEMHTLinker
- Tracks refinement: Example of Cleaner, followed by EMC2 Stitcher
- End-to-end tracking: Example of MultiStepTracker
- Postprocessing: Fill NaN with interpolated values
- Load or save tracks to files
- Detectors
API
- Video
- Video
- Video Reader
MetaVideoReaderVideoReaderVideoReader.supported_extensionsVideoReader.pathVideoReader.releasedVideoReader.fpsVideoReader.shapeVideoReader.channelsVideoReader.lengthVideoReader.frame_idVideoReader.release()VideoReader.grab()VideoReader.retrieve()VideoReader.read()VideoReader.seek()VideoReader.tell()VideoReader.open()VideoReader.ensure_3d()
OpenCVVideoReaderTiffVideoReader
- Video transforms
- Detections
- Tracks
- Tracker
- Detector
- Linker
- Refiner
- Parameters
API implementations
Icy support
Visualization