TomSeg

TomSeg is an efficient cross-platorm software tool to segment (electron) tomograms, allowing to:

• import RAW tomogram data (i.e., stacks of tomogram slices);
• align the data using reference markers, or global signals;
• view and navigate across the slices;
• test a new 3D segmentation procedure, based on region growing techniques;
• export the results as a stack of individual images, or as a 3D volume in MRC files.

Characteristics

• This software includes a new efficient algorithmic approach to segment 3D volumes;
• It supports multi-threaded parallelism, using OpenMP;
• OpenCV is used to perform basic operations such as image loading and represent the images as matrices;
• Both GUI and CLI are available:
  • The GUI depends on QT,
  • The CLI depends on boost_program_options;
• This software is capable of persist and resume the work at any time;
• Was developed to allow easy integration of new features and alternatives;
• Supports CUDA;
• It is open-source!

Installation

Command Line Interface

With OpenCV and boost_program_options installed:

$ git clone https://github.com/prsousa/TomSeg.git
$ cd TomSeg
$ mkdir build
$ cd build
$ cmake ..
$ make
$ ./TomSeg --help

Graphical User Interface

Clone and open the project with Qt Creator, or:

$ git clone https://github.com/prsousa/TomSeg.git
$ cd TomSeg
$ mkdir build
$ cd build
$ qmake ..
$ make
$ ./TomSeg

License

GNU General Public License v3.0