Assessment of freeware programs for the reconstruction of tomography datasets obtained with a monochromatic synchrotron-based X-ray source

Abstract

Synchrotron-based in-line phase-contrast computed tomography (PC-CT) allows soft tissue to be imaged with sub-gross resolution and has potential to be used as a diagnostic tool. The reconstruction and processing of in-line PC-CT datasets is a computationally demanding task; thus, an efficient and user-friendly software program is desirable. Four freeware programs (NRecon, PITRE, H-PITRE and Athabasca Recon) were compared for the availability of features such as dark-and flat-field calibration, beam power normalization, ring artifact removal, and alignment tools for optimizing image quality. An in-line PC-CT projection dataset (3751 projections, 180 rotation, 10.13 mm  0.54 mm) was collected from a formalin-fixed canine prostate at the Biomedical Imaging and Therapy Bending Magnet (BMIT-BM) beamline of the Canadian Light Source. This dataset was processed with each of the four software programs and usability of the program was evaluated. Efficiency was assessed by how each program maximized computer processing power during computation. Athabasca Recon had the least-efficient memory usage, least user-friendly interface, and lacked a ring artifact removal feature. NRecon, PITRE and H-PITRE produced similar quality images, but the Athabasca Recon reconstruction suffered from the lack of a native ring remover algorithm. The 64-bit version of NRecon uses GPU (graphics processor unit) memory for accelerated processing and is userfriendly, but does not provide necessary parameters for in-line PC-CT data, such as dark-field and flat-field correction and beam power normalization. PITRE has many helpful features and tools, but lacks a comprehensive user manual and help section. H-PITRE is a condensed version of PITRE and maximizes computer memory for efficiency. To conclude, NRecon has fewer imaging processing tools than PITRE and H-PITRE, but is ideal for less experienced users due to a simple user interface. Based on the quality of reconstructed images, efficient use of computer memory and parameter availability, H-PITRE was the preferred of the four programs compared.

Self-assembled micro-computed tomography for dental education

“…An additional US$2,500 was needed for additional items, namely a high-precision rotation stage (approximately US$1,500), optical breadboards (approximately US$400), an XYX axis, and an XY axis precision fine-tuning table (approximately US$600). Free software such as NRecon, PITRE, H-PITRE, and Athabasca Recon are available to conduct back projection on 2D projection images for image reconstruction [18]. Many open access image reconstruction codes in Matlab or C are available online.…”

X-ray tomography of the aerospace products

“…The INKCT software package (TPU) collects shadow projections. The NRecon software package (Skyscan) performs the 3D reconstruction ( Figure. 3.a) by filtered back projection [5,6]. Finally, the CTvox software package (Skyscan) implements further volumetric visualization of the reconstructed slices ( Figure. Computed tomography, reconstruction, segmentation and visualisation are performed to study the object in detail.…”

Analytical formula for two-dimensional ring artefact suppression

“…Basically methods from these two groups are similar. A detailed description of some of these methods and their comparison for various data sets can be found in (Sijbers & Postnov, 2004;Prell et al, 2009;Münch et al, 2009;Titarenko et al, 2010b;Sadi et al, 2010;Titarenko et al, 2010c;Rashid et al, 2012;Brun et al, 2013;Wei et al, 2013;Altunbas et al, 2014;Miqueles et al, 2014;Paleo & Mirone, 2015;Wolkowski et al, 2015;Baek et al, 2015).…”