Welcome to EllipTrack’s documentation!

System Requirement

Hardware
A modern computer, at least 8GB RAM.
Software

MATLAB (Mathworks), R2017a or later.

Required toolboxes: System Identification Toolbox, Image Processing Toolbox, Computer Vision Toolbox, Statistics and Machine Learning Toolbox, Parallel Computing Toolbox, and MATLAB Distributed Computing Server.

A C++ compiler in MATLAB with C++11 support. Install a free minGW compiler by following the instruction here.

Installation

Download

Download the latest version from the Github repository. Click “Clone or Download” button, and then click “Download ZIP”. Extract files to the destination folder.

Compile generate_tracks.cpp

generate_tracks.cpp is implemented in C++ for speed consideration. Compilation of this file is required before execution. Instruction:

  • Execute mex -setup to check whether a C++ compiler has been installed in MATLAB. Install a free minGW compiler (instruction here) if not.

  • Navigate MATLAB to the functions/track_linking folder.

  • Execute the following command in the command window.

    mex -largeArrayDims generate_tracks.cpp

  • Compilation succeeds if the following message appears

MEX completed successfully.

and file generate_tracks.mexXXX appears. Here, XXX refers to the operating system (e.g. w64 for 64-bit Windows, maci64 for 64-bit Mac OS X, and a64 for 64-bit Linux).

Install BioformatsImage

Required for analyzing Nikon ND2 files. Follow the instruction here for installation. Courtesy of Jian Wei Tay.

Overview of Files

  • mainfile.m. Main script of EllipTrack.
  • parameters.m. Parameters.
  • functions. Customized scripts. Scripts are organized by their functions.
  • GUI. Parameter Generator GUI and Training Data GUI.
  • third_party_functions. Scripts downloaded from Zafari et al. 2015 and MATLAB central.

MIT License

Copyright (c) 2020 Chengzhe Tian, Chen Yang, Sabrina Leigh Spencer

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the “Software”), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.