Tracker

Tracker is a particle tracking trajectory connector tool that generates trajectories by tracking swarms of interacting particles through a sequence of video frames. Tracker formulates optimal trajectory connection problems as instances of the linear assignment problem (LAP), and uses the a sparse-matrix implementation of the Jonker-Volgenant Algorithm to solve the LAP problems.

Tracker provides C++ and Matlab object-oriented interfaces. tracker::LAPTrack
Tracker is designed for cross-platform compilation to Linux and Windows 64-bit targets.

Trajectory connection problem

In single particle tracking applications, a set of likely particles are localized for each frame of a video capture. The goal of trajectory connection is to partition the localizations from all the frames into a set of trajectories. Each trajectory is a sequence of localizations which are likely to be from the same object (point emitter).

The Tracker library implements a two-phase strategy to trajectory connection. First a frame-to-frame algorithm sequentially builds a set of trajectories connecting localizations in adjacent frames, next a gap-closing phase connects shorter trajectories across several frames as particles are often not localized in every frame for various reasons including experimental and photo-chemical effects.

Figure 1: The frame-to-frame trajectory connection problem

Documentation

The Tracker Doxygen documentation can be build with the OPT_DOC CMake option and is also available on online:

Installing

Tracker uses the CMake build system. The script build.sh sets the project-specific CMake options to sensible values and builds the project under ./_build/Release and installs it to the ./_install prefix, which can be set with the INSTALL_PREFIX environment variable.

INSTALL_PREFIX="..." ./build.sh <additional cmake args...>

Edit build.sh to customize or alternatively use the CMake gui directly:

cmake -B $BUILD_DIR -DCMAKE_INSTALL_PREFIX=$INSTALL_DIR
cmake-gui $BUILD_DIR
cmake --build $BUILD_DIR --target install

Dependencies

Armadillo - A high-performance array library for C++.
- [Ubuntu: libarmadillo-dev] [Gentoo: sci-libs/armadillo]

External Projects

These packages are specialized CMake projects. If they are not installed on the development system, the add_external_dependency() function will automatically download, configure, build and install them to CMAKE_INSTALL_PREFIX.

BacktraceException - A library to provide debugging output on exception calls. Important for Matlab debugging.
MexIFace - MexIFace provides an object-oriented C++/Matlab interface and provides cross-compilation support to build for Matlab target environments on Linux and Windows 64-bit targets.

CMake options

The following CMake options control the build.

BUILD_SHARED_LIBS - Build shared libraries
BUILD_STATIC_LIBS - Build static libraries
BUILD_TESTING - Build testing framework
OPT_DOC - Build documentation
OPT_INSTALL_TESTING - Install testing executables in install-tree.
OPT_EXPORT_BUILD_TREE - Export the package from the build-tree and place in the CMake user package registry.
OPT_MATLAB - Enable matlab module building with MexIFace.

Building for matlab

See:

Using tracker

Using Tracker in C++ applications

Tracker exports a CMake config-file, allowing it to be found easily with CMake build systtems

    find_package(Tracker)
    target_link_libraries(${MY_TARGET} Tracker::Tracker)

In the C++ source

#include <Tracker/LAPTrack.h>
tracker::LAPTrack tracker(params);

Using Tracker in Matlab applications

LICENSE

Author: Mark J. Olah
Email: (mjo@cs.unm DOT edu)
LICENSE: Apache 2.0. See LICENSE file.

markjolah/Tracker