Brun et al. Adv Struct Chem Imag (2017) 3:4 DOI 10.1186/s40679-016-0036-8 RESEARCH SYRMEP Tomo Project: a graphical user interface for customizing CT reconstruction workfows Francesco Brun 1,2,3* , Lorenzo Massimi 1 , Michela Fratini 1,4 , Diego Dreossi 3 , Fulvio Billé 3 , Agostino Accardo 2 , Roberto Pugliese 3 and Alessia Cedola 1 Abstract When considering the acquisition of experimental synchrotron radiation (SR) X-ray CT data, the reconstruction work- flow cannot be limited to the essential computational steps of flat fielding and filtered back projection (FBP). More refined image processing is often required, usually to compensate artifacts and enhance the quality of the recon- structed images. In principle, it would be desirable to optimize the reconstruction workflow at the facility during the experiment (beamtime). However, several practical factors affect the image reconstruction part of the experiment and users are likely to conclude the beamtime with sub-optimal reconstructed images. Through an example of applica- tion, this article presents SYRMEP Tomo Project (STP), an open-source software tool conceived to let users design custom CT reconstruction workflows. STP has been designed for post-beamtime (off-line use) and for a new recon- struction of past archived data at user’s home institution where simple computing resources are available. Releases of the software can be downloaded at the Elettra Scientific Computing group GitHub repository https://github.com/ ElettraSciComp/STP-Gui. Keywords: Phase-contrast computed tomography, Tomographic reconstruction, Image processing, Phase retrieval, Artifacts compensation © The Author(s) 2017. This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. Background Synchrotron radiation (SR) X-ray Computed micro- Tomography ( μ -CT) in its simplest form deals with the inversion of the Radon transform of acquired paral- lel beam projection data. In this case, the application of an implementation of the fltered back projection (FBP) algorithm after the so-called flat fielding of the projec- tion data is often proposed as a solution for the tomo- graphic problem. Tis approach is formally correct and, in general, easy to apply since most of the computing software tools used by scientists (e.g., MATLAB ® , Math- ematica ® , IDL ® ) ofer an implementation of the inverse Radon transform. However, this approach is based on the traditional way to extract contrast in X-ray radiography, i.e., the consideration of the diferent attenuation proper- ties of the elements composing the imaged object. Such properties are related to β, the complex part of the index of refraction n = 1 - δ + iβ. Tanks to the coherence of SR, quantities other than absorption, like the electron density, related to δ might be exploited leading to phase- contrast imaging [1]. Among the phase-contrast modalities, single-distance propagation-based imaging (PBI) is one of the most exploited in SR μ -CT experiments as it is based only on the relative distance between the rotating sample and the detector. According to this modality, neither hardware elements (e.g., crystals or gratings) nor multiple acquisi- tions are required to derive information about the phase shifts induced by the imaged object. In this case, rather than performing the conventional reconstruction of the attenuation coefcient (that would result in the so-called edge enhanced image), a phase retrieval algorithm is typically applied to the (fat-corrected) projection data Open Access *Correspondence: francesco.brun@nanotec.cnr.it 1 National Research Council-Institute of Nanotechnology (CNR-Nanotec), c/o University La Sapienza, P.le Aldo Moro, 5, 00185 Rome, Italy Full list of author information is available at the end of the article