trackpy
0.3.0
Tutorial
Site
Introduction to Trackpy
Installing Trackpy
Updating Your Installation
API reference
What’s new in the package
Walkthrough
Prediction: Beyond Simple Random Walks
Feature finding in 3D confocal images
Subpixel Accuracy and Uncertainty Estimation
Advanced Linking: Subnetworks and
search_range
Adaptive Search: Changing
search_range
on the Fly
Streaming: Processing Unlimited Frames On-Disk
Making trackpy fast(er)
Obtaining Diagnostic Information from Linking
Parallelized Feature Location using IPython Parallel
Custom Feature Detection: Bubble tracking in 2D foams
Page
Trackpy tutorial
Basic Usage
Processing Large Data Sets
Extending & Customizing Trackpy
Trackpy tutorial
¶
Basic Usage
¶
Walkthrough
Scientific IPython Setup
Step 1: Read the Data
Step 2: Locate Features
Step 3: Link features into particle trajectories
Step 4: Analyze trajectories
Preview of Advanced Features
Streaming
Optional High Performance Component: Numba
Parellelization
Prediction: Beyond Simple Random Walks
Prescribed predictors
Dynamic predictors
Feature finding in 3D confocal images
Setup IPython, pims, trackpy
Import 3D images
Feature finding
Batch processing
Linking
Mean squared displacement
About this work
Subpixel Accuracy and Uncertainty Estimation
How is subpixel resolution possible?
Demonstration of trackpy’s uncertainty estimation on noisy images
The effect of
diameter
on precision
How tracking errors can qualitatively affect physical interpretation
Advanced Linking: Subnetworks and
search_range
Introduction
Techniques for limiting subnetwork size
Adaptive Search: Changing
search_range
on the Fly
How it works
How to use it
Example
Obtaining Diagnostic Information from Linking
How to use it
Example
Processing Large Data Sets
¶
Streaming: Processing Unlimited Frames On-Disk
Install PyTables
Locate Features, Streaming Results into an HDF5 File
Link Trajectories, Streaming From and Updating the HDF5 File
Framewise Data Interfaces
Making trackpy fast(er)
General advice
Using numba for acceleration
Advanced topics
Parallelized Feature Location using IPython Parallel
Intsall ipyparallel
Extending & Customizing Trackpy
¶
Custom Feature Detection: Bubble tracking in 2D foams
Scientific libraries
Image preprocessing
Custom feature detection
Bubble tracking
Velocity field
About this work
References