Introduction

Introduction

The ASTRA Toolbox is a MATLAB toolbox of high-performance GPU primitives
for 2D and 3D tomography, from 2009-2014 developed by iMinds-VisionLab from the University of Antwerp and since 2014 jointly developed by iMinds-VisionLab, UAntwerpen and CWI, Amsterdam.

We support 2D parallel and fan beam geometries, and 3D parallel and cone beam.
All of them have highly flexible source/detector positioning.

A large number of 2D and 3D algorithms are available, including FBP, SIRT,
SART, CGLS.

The basic forward and backward projection operations are GPU-accelerated,
and directly callable from MATLAB to enable building new algorithms.

references

• W. Van Aarle, W J. Palenstijn, J. Cant, E. Janssens, F. Bleichrodt, A. Dabravolski, J. De Beenhouwer, K. J. Batenburg, and J. Sijbers, "Fast and Flexible X-ray Tomography Using the ASTRA Toolbox", Optics Express, vol. 24, no. 22, pp. 25129-25147, 2016
• W. Van Aarle, W J. Palenstijn, J. De Beenhouwer, T. Altantzis, S. Bals, K. J. Batenburg, and J. Sijbers, "The ASTRA Toolbox: a platform for advanced algorithm development in electron tomography", Ultramicroscopy, vol. 157, pp. 35–47, 2015
• W. J. Palenstijn, K J. Batenburg, and J. Sijbers, "Performance improvements for iterative electron tomography reconstruction using graphics processing units (GPUs)", Journal of Structural Biology, vol. 176, issue 2, pp. 250-253, (2011)

Toolbox concepts

Geometry

Most of the operations supported by the ASTRA Toolbox require
you to specify what the geometry of the (real or virtual) experimental
setup you have used or want to simulate is.

This has two parts: a volume geometry, and a projection geometry.
The volume geometry specifies where in 2D or 3D space the sample or phantom
is located. It takes the form of a 2D rectangle or 3D box, and is
usually centered around the origin.

The projection geometry specifies the location and trajectory of the
ray source and detector. The available types of projection geometries are
2D parallel beam, 2D fan beam, 3D parallel beam and 3D cone beam.

Data

Toolbox objects are stored in memory separate from Matlab, and have to
be explicitly transferred from/to Matlab matrices.

They come in four varieties: 2D/3D volume data, and 2D/3D projection data.

Data objects are manipulated with the [astra_mex_data2d] and [astra_mex_data3d]
commands. The usage of these commands is illustrated in the available sample
scripts.

Algorithms

To operate on data objects, the ASTRA Toolbox defines a number of algorithms.
These include the basic forward and backward projection operations, and also
various reconstruction algorithms.

To create algorithm objects, use the [astra_mex_algorithm] command. The usage
of this command is illustrated in the available sample scripts.

How to acknowledge?

If you the ASTRA toolbox in your research, we would appreciate it if you would refer to the following papers:

• W. Van Aarle, W J. Palenstijn, J. Cant, E. Janssens, F. Bleichrodt, A. Dabravolski, J. De Beenhouwer, K. J. Batenburg, and J. Sijbers, "Fast and Flexible X-ray Tomography Using the ASTRA Toolbox", Optics Express, vol. 24, no. 22, pp. 25129-25147, 2016
• W. Van Aarle, W J. Palenstijn, J. De Beenhouwer, T. Altantzis, S. Bals, K. J. Batenburg, and J. Sijbers, "The ASTRA Toolbox: a platform for advanced algorithm development in electron tomography", Ultramicroscopy, vol. 157, pp. 35–47, (2015)
• W. J. Palenstijn, K J. Batenburg, and J. Sijbers, "Performance improvements for iterative electron tomography reconstruction using graphics processing units (GPUs)", Journal of Structural Biology, vol. 176, issue 2, pp. 250-253, (2011)