Core Imaging Library - Part I: a versatile Python framework for tomographic imaging

Unsupervised Denoising in Spectral CT: Multi-Dimensional U-Net for Energy Channel Regularisation

Spectral Computed Tomography (CT) is a versatile imaging technique widely utilized in industry, medicine, and scientific research. This technique allows us to observe the energy-dependent X-ray attenuation throughout an object by using Photon Counting Detector (PCD) technology. However, a major drawback of spectral CT is the increase in noise due to a lower achievable photon count when using more energy channels. This challenge often complicates quantitative material identification, which is a major application of the technology. In this study, we investigate the Noise2Inverse image denoising approach for noise removal in spectral computed tomography. Our unsupervised deep learning-based model uses a multi-dimensional U-Net paired with a block-based training approach modified for additional energy-channel regularization. We conducted experiments using two simulated spectral CT phantoms, each with a unique shape and material composition, and a real scan of a biological sample containing a characteristic K-edge. Measuring the peak signal-to-noise ratio (PSNR) and structural similarity index (SSIM) for the simulated data and the contrast-to-noise ratio (CNR) for the real-world data, our approach not only outperforms previously used methods-namely the unsupervised Low2High method and the total variation-constrained iterative reconstruction method-but also does not require complex parameter tuning.

Open-source magnetic resonance imaging: Improving access, science, and education through global collaboration

Open-source practices and resources in magnetic resonance imaging (MRI) have increased substantially in recent years. This trend started with software and data being published open-source and, more recently, open-source hardware designs have become increasingly available. These developments towards a culture of sharing and establishing nonexclusive global collaborations have already improved the reproducibility and reusability of code and designs, while providing a more inclusive approach, especially for low-income settings. Community-driven standardization and documentation efforts are further strengthening and expanding these milestones. The future of open-source MRI is bright and we have just started to discover its full collaborative potential. In this review we will give an overview of open-source software and open-source hardware projects in human MRI research.

tomoCAM: fast model-based iterative reconstruction via GPU acceleration and non-uniform fast Fourier transforms

X-ray-based computed tomography is a well established technique for determining the three-dimensional structure of an object from its two-dimensional projections. In the past few decades, there have been significant advancements in the brightness and detector technology of tomography instruments at synchrotron sources. These advancements have led to the emergence of new observations and discoveries, with improved capabilities such as faster frame rates, larger fields of view, higher resolution and higher dimensionality. These advancements have enabled the material science community to expand the scope of tomographic measurements towards increasingly in situ and in operando measurements. In these new experiments, samples can be rapidly evolving, have complex geometries and restrictions on the field of view, limiting the number of projections that can be collected. In such cases, standard filtered back-projection often results in poor quality reconstructions. Iterative reconstruction algorithms, such as model-based iterative reconstructions (MBIR), have demonstrated considerable success in producing high-quality reconstructions under such restrictions, but typically require high-performance computing resources with hundreds of compute nodes to solve the problem in a reasonable time. Here, tomoCAM, is introduced, a new GPU-accelerated implementation of model-based iterative reconstruction that leverages non-uniform fast Fourier transforms to efficiently compute Radon and back-projection operators and asynchronous memory transfers to maximize the throughput to the GPU memory. The resulting code is significantly faster than traditional MBIR codes and delivers the reconstructive improvement offered by MBIR with affordable computing time and resources. tomoCAM has a Python front-end, allowing access from Jupyter-based frameworks, providing straightforward integration into existing workflows at synchrotron facilities.

Shot noise reduction in radiographic and tomographic multi-channel imaging with self-supervised deep learning

Shot noise is a critical issue in radiographic and tomographic imaging, especially when additional constraints lead to a significant reduction of the signal-to-noise ratio. This paper presents a method for improving the quality of noisy multi-channel imaging datasets, such as data from time or energy-resolved imaging, by exploiting structural similarities between channels. To achieve that, we broaden the application domain of the Noise2Noise self-supervised denoising approach. The method draws pairs of samples from a data distribution with identical signals but uncorrelated noise. It is applicable to multi-channel datasets if adjacent channels provide images with similar enough information but independent noise. We demonstrate the applicability and performance of the method via three case studies, namely spectroscopic X-ray tomography, energy-dispersive neutron tomography, and in vivo X-ray cine-radiography.

Simulation of X-ray projections on GPU: Benchmarking gVirtualXray with clinically realistic phantoms

BACKGROUND AND OBJECTIVES

This study provides a quantitative comparison of images created using gVirtualXray (gVXR) to both Monte Carlo (MC) and real images of clinically realistic phantoms. gVirtualXray is an open-source framework that relies on the Beer-Lambert law to simulate X-ray images in realtime on a graphics processor unit (GPU) using triangular meshes.

METHODS

Images are generated with gVirtualXray and compared with a corresponding ground truth image of an anthropomorphic phantom: (i) an X-ray projection generated using a Monte Carlo simulation code, (ii) real digitally reconstructed radiographs (DRRs), (iii) computed tomography (CT) slices, and (iv) a real radiograph acquired with a clinical X-ray imaging system. When real images are involved, the simulations are used in an image registration framework so that the two images are aligned.

RESULTS

The mean absolute percentage error (MAPE) between the images simulated with gVirtualXray and MC is 3.12%, the zero-mean normalised cross-correlation (ZNCC) is 99.96% and the structural similarity index (SSIM) is 0.99. The run-time is 10 days for MC and 23 ms with gVirtualXray. Images simulated using surface models segmented from a CT scan of the Lungman chest phantom were similar to (i) DRRs computed from the CT volume and (ii) an actual digital radiograph. CT slices reconstructed from images simulated with gVirtualXray were comparable to the corresponding slices of the original CT volume.

CONCLUSIONS

When scattering can be ignored, accurate images that would take days using MC can be generated in milliseconds with gVirtualXray. This speed of execution enables the use of repetitive simulations with varying parameters, e.g. to generate training data for a deep-learning algorithm, and to minimise the objective function of an optimisation problem in image registration. The use of surface models enables the combination of X-ray simulation with real-time soft-tissue deformation and character animation, which can be deployed in virtual reality applications.

Quantifying multiple stain distributions in bioimaging by hyperspectral X-ray tomography

Chemical staining of biological specimens is commonly utilised to boost contrast in soft tissue structures, but unambiguous identification of staining location and distribution is difficult without confirmation of the elemental signature, especially for chemicals of similar density contrast. Hyperspectral X-ray computed tomography (XCT) enables the non-destructive identification, segmentation and mapping of elemental composition within a sample. With the availability of hundreds of narrow, high resolution (~ 1 keV) energy channels, the technique allows the simultaneous detection of multiple contrast agents across different tissue structures. Here we describe a hyperspectral imaging routine for distinguishing multiple chemical agents, regardless of contrast similarity. Using a set of elemental calibration phantoms, we perform a first instance of direct stain concentration measurement using spectral absorption edge markers. Applied to a set of double- and triple-stained biological specimens, the study analyses the extent of stain overlap and uptake regions for commonly used contrast markers. An improved understanding of stain concentration as a function of position, and the interaction between multiple stains, would help inform future studies on multi-staining procedures, as well as enable future exploration of heavy metal uptake across medical, agricultural and ecological fields.

TIGRE-VarianCBCT for on-board cone-beam computed tomography, an open-source toolkit for imaging, dosimetry and clinical research

We presented TIGRE-VarianCBCT, an open-source toolkit Matlab-GPU for Varian on-board cone-beam CT with particular emphasis to address challenges in raw data preprocessing, artifacts correction, tomographic reconstruction and image post-processing. The aim of this project is to provide not only a tool to bridge the gap between clinical usage of CBCT scan data and research algorithms but also a framework that breaks down the imaging chain into individual processes so that research effort can be focused on a specific part. The entire imaging chain, module-based architecture, data flow and techniques used in the creation of the toolkit are presented. Raw scan data are first decoded to extract X-ray fluoro image series and set up the imaging geometry. Data conditioning operations including scatter correction, normalization, beam-hardening correction, ring removal are performed sequentially. Reconstruction is supported by TIGRE with FDK as well as a variety of iterative algorithms. Pixel-to-HU mapping is calibrated by a Catphan^TM 504 phantom. Imaging dose in CTDIw is calculated in an empirical formula. The performance was validated on real patient scans with good agreement with respect to vendor-designed program. Case studies in scan protocol optimization, low dose imaging and iterative algorithm comparison demonstrated its substantial potential in performing scan data based clinical studies. The toolkit is released under the BSD license, imposing minimal restrictions on its use and distribution. The toolkit is accessible as a module at https://github.com/CERN/TIGRE.

Development of two-dimensional beam hardening correction for X-ray micro-CT

BACKGROUND

Beam-hardening in tomography with polychromatic X-ray sources results from the nonlinear relationship between the amount of substance in the X-ray beam and attenuation. Simple linearisation curves can be derived with the use of an appropriate step wedge, however, this does not yield good results when different materials are present whose relationships between X-ray attenuation and energy are very different.

OBJECTIVE

To develop a more accurate method of beam-hardening correction for two-phase samples, particularly immersed or embedded biological hard tissue.

METHODS

Use of a two-dimensional step wedge is proposed in this study. This is not created physically but is derived from published X-ray attenuation coefficients in conjunction with a modelled X-ray spectrum, optimised from X-ray attenuation measurements of a calibration carousel. To test this method, a hydroxyapatite disk was scanned twice; first dry, and then immersed in 70% ethanol solution (commonly used to preserve biological specimens).

RESULTS

With simple linearisation the immersed disk reconstruction exhibited considerable residual beam hardening, with edges appearing approximately 10% more attenuating. With 2-dimensional correction, the attenuation coefficient showed only around 0.5% deviation from the dry case.

CONCLUSION

Two-dimensional beam-hardening correction yielded accurate results and does not require segmentation of the two phases individually.

Tomosipo: fast, flexible, and convenient 3D tomography for complex scanning geometries in Python

Tomography is a powerful tool for reconstructing the interior of an object from a series of projection images. Typically, the source and detector traverse a standard path (e.g., circular, helical). Recently, various techniques have emerged that use more complex acquisition geometries. Current software packages require significant handwork, or lack the flexibility to handle such geometries. Therefore, software is needed that can concisely represent, visualize, and compute reconstructions of complex acquisition geometries. We present tomosipo, a Python package that provides these capabilities in a concise and intuitive way. Case studies demonstrate the power and flexibility of tomosipo.

Enhanced hyperspectral tomography for bioimaging by spatiospectral reconstruction

Here we apply hyperspectral bright field imaging to collect computed tomographic images with excellent energy resolution (~ 1 keV), applying it for the first time to map the distribution of stain in a fixed biological sample through its characteristic K-edge. Conventionally, because the photons detected at each pixel are distributed across as many as 200 energy channels, energy-selective images are characterised by low count-rates and poor signal-to-noise ratio. This means high X-ray exposures, long scan times and high doses are required to image unique spectral markers. Here, we achieve high quality energy-dispersive tomograms from low dose, noisy datasets using a dedicated iterative reconstruction algorithm. This exploits the spatial smoothness and inter-channel structural correlation in the spectral domain using two carefully chosen regularisation terms. For a multi-phase phantom, a reduction in scan time of 36 times is demonstrated. Spectral analysis methods including K-edge subtraction and absorption step-size fitting are evaluated for an ex vivo, single (iodine)-stained biological sample, where low chemical concentration and inhomogeneous distribution can affect soft tissue segmentation and visualisation. The reconstruction algorithms are available through the open-source Core Imaging Library. Taken together, these tools offer new capabilities for visualisation and elemental mapping, with promising applications for multiply-stained biological specimens.

Synergistic tomographic image reconstruction: part 2

This special issue is the second part of a themed issue that focuses on synergistic tomographic image reconstruction and includes a range of contributions in multiple disciplines and application areas. The primary subject of study lies within inverse problems which are tackled with various methods including statistical and computational approaches. This volume covers algorithms and methods for a wide range of imaging techniques such as spectral X-ray computed tomography (CT), positron emission tomography combined with CT or magnetic resonance imaging, bioluminescence imaging and fluorescence-mediated imaging as well as diffuse optical tomography combined with ultrasound. Some of the articles demonstrate their utility on real-world challenges, either medical applications (e.g. motion compensation for imaging patients) or applications in material sciences (e.g. material decomposition and characterization). One of the desired outcomes of the special issues is to bring together different scientific communities which do not usually interact as they do not share the same platforms such as journals and conferences. This article is part of the theme issue 'Synergistic tomographic image reconstruction: part 2'.

Core Imaging Library - Part II: multichannel reconstruction for dynamic and spectral tomography

The newly developed core imaging library (CIL) is a flexible plug and play library for tomographic imaging with a specific focus on iterative reconstruction. CIL provides building blocks for tailored regularized reconstruction algorithms and explicitly supports multichannel tomographic data. In the first part of this two-part publication, we introduced the fundamentals of CIL. This paper focuses on applications of CIL for multichannel data, e.g. dynamic and spectral. We formalize different optimization problems for colour processing, dynamic and hyperspectral tomography and demonstrate CIL's capabilities for designing state-of-the-art reconstruction methods through case studies and code snapshots. This article is part of the theme issue 'Synergistic tomographic image reconstruction: part 2'.

Motion estimation and correction for simultaneous PET/MR using SIRF and CIL

SIRF is a powerful PET/MR image reconstruction research tool for processing data and developing new algorithms. In this research, new developments to SIRF are presented, with focus on motion estimation and correction. SIRF's recent inclusion of the adjoint of the resampling operator allows gradient propagation through resampling, enabling the MCIR technique. Another enhancement enabled registering and resampling of complex images, suitable for MRI. Furthermore, SIRF's integration with the optimization library CIL enables the use of novel algorithms. Finally, SPM is now supported, in addition to NiftyReg, for registration. Results of MR and PET MCIR reconstructions are presented, using FISTA and PDHG, respectively. These demonstrate the advantages of incorporating motion correction and variational and structural priors. This article is part of the theme issue 'Synergistic tomographic image reconstruction: part 2'.