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

We present the Core Imaging Library (CIL), an open-source Python framework for tomographic imaging with particular emphasis on reconstruction of challenging datasets. Conventional filtered back-projection reconstruction tends to be insufficient for highly noisy, incomplete, non-standard or multi-channel data arising for example in dynamic, spectral and in situ tomography. CIL provides an extensive modular optimization framework for prototyping reconstruction methods including sparsity and total variation regularization, as well as tools for loading, preprocessing and visualizing tomographic data. The capabilities of CIL are demonstrated on a synchrotron example dataset and three challenging cases spanning golden-ratio neutron tomography, cone-beam X-ray laminography and positron emission tomography. This article is part of the theme issue 'Synergistic tomographic image reconstruction: part 2'.

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'.

Early individualized positive end-expiratory pressure guided by electrical impedance tomography in acute respiratory distress syndrome: a randomized controlled clinical trial.

BACKGROUND: Individualized positive end-expiratory pressure (PEEP) by electrical impedance tomography (EIT) has potential interest in the optimization of ventilation distribution in acute respiratory distress syndrome (ARDS). The aim of the study was to determine whether early individualized titration of PEEP with EIT improved outcomes in patients with ARDS. METHODS: A total of 117 ARDS patients receiving mechanical ventilation were randomly assigned to EIT group (n = 61, PEEP adjusted based on ventilation distribution) or control group (n = 56, low PEEP/FiO2 table). The primary outcome was 28-day mortality. Secondary and exploratory outcomes were ventilator-free days, length of ICU stay, incidence of pneumothorax and barotrauma, and difference in Sequential Organ Failure Assessment (SOFA) score at day 1 (ΔD1-SOFA) and day 2 (ΔD2-SOFA) compared with baseline. MEASUREMENTS AND MAIN RESULTS: There was no statistical difference in the value of PEEP between the EIT group and control group, but the combination of PEEP and FiO2 was different between groups. In the control group, a significantly positive correlation was found between the PEEP value and the corresponding FiO2 (r = 0.47, p < 0.00001) since a given matched table was used for PEEP settings. Diverse combinations of PEEP and FiO2 were found in the EIT group (r = 0.05, p = 0.68). There was no significant difference in mortality rate (21% vs. 27%, EIT vs. control, p = 0.63), ICU length of stay (13.0 (7.0, 25.0) vs 10.0 (7.0, 14.8), median (25th-75th percentile); p = 0.17), and ventilator-free days at day 28 (14.0 (2.0, 23.0) vs 19.0 (0.0, 24.0), p = 0.55) between the two groups. The incidence of new barotrauma was zero. Compared with control group, significantly lower ΔD1-SOFA and ΔD2-SOFA were found in the EIT group (p < 0.001) in a post hoc comparison. Moreover, the EIT group exhibited a significant decrease of SOFA at day 2 compared with baseline (paired t-test, difference by - 1 (- 3.5, 0), p = 0.001). However, the control group did show a similar decrease (difference by 1 (- 2, 2), p = 0.131). CONCLUSION: Our study showed a 6% absolute decrease in mortality in the EIT group: a statistically non-significant, but clinically non-negligible result. This result along with the showed improvement in organ function might justify further reserach to validate the beneficial effect of individualized EIT-guided PEEP setting on clinical outcomes of patients with ARDS. TRIAL REGISTRATION: ClinicalTrials, NCT02361398. Registered 11 February 2015-prospectively registered, https://clinicaltrials.gov/show/NCT02361398 .

Fusing electrical and elasticity imaging.

Electrical and elasticity imaging are promising modalities for a suite of different applications, including medical tomography, non-destructive testing and structural health monitoring. These emerging modalities are capable of providing remote, non-invasive and low-cost opportunities. Unfortunately, both modalities are severely ill-posed nonlinear inverse problems, susceptive to noise and modelling errors. Nevertheless, the ability to incorporate complimentary datasets obtained simultaneously offers mutually beneficial information. By fusing electrical and elastic modalities as a joint problem, we are afforded the possibility to stabilize the inversion process via the utilization of auxiliary information from both modalities as well as joint structural operators. In this study, we will discuss a possible approach to combine electrical and elasticity imaging in a joint reconstruction problem giving rise to novel multi-modality applications for use in both medical and structural engineering. This article is part of the theme issue 'Synergistic tomographic image reconstruction: part 1'.

Synergistic tomographic image reconstruction: part 1.

This special issue focuses on synergistic tomographic image reconstruction in a range of contributions in multiple disciplines and various application areas. The topic of image reconstruction covers substantial inverse problems (Mathematics) which are tackled with various methods including statistical approaches (e.g. Bayesian methods, Monte Carlo) and computational approaches (e.g. machine learning, computational modelling, simulations). The issue is separated in two volumes. This volume focuses mainly on algorithms and methods. Some of the articles will demonstrate their utility on real-world challenges, either medical applications (e.g. cardiovascular diseases, proton therapy planning) or applications in material sciences (e.g. material decomposition and characterization). One of the desired outcomes of the special issue 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 1'.

Arteriovenous Fistula Surveillance Using Tomographic 3D Ultrasound.

OBJECTIVE: A well functioning arteriovenous fistula (AVF) is essential for haemodialysis. Despite regular duplex ultrasound (DUS) a significant number of AVFs fail. Tomographic 3D ultrasound (tUS) creates a 3D image of the AVF that can be interpreted by the clinician. DUS, tUS, and fistulograms were compared for the identification and measurement of flow limiting stenosis. METHODS: Patients with AVF dysfunction on routine Transonic surveillance, defined as (1) > 15% reduction in flow on two consecutive occasions, (2) > 30% reduction in flow on one occasion, (3) flow of < 600 mL/sec, (4) presence of recirculation, underwent DUS. AVF tUS imaging was performed prior to fistulography. All fistulograms were reported by the same consultant radiologist and tUS images by the same vascular scientist blinded to the fistulogram results. Maximum diameter reduction in all stenoses were measured using all three imaging techniques. RESULTS: In 97 patients with 101 stenoses, the mean (± standard deviation [SD]) severity of stenosis was 63.0 ± 13.9%, 65.0 ± 11.6%, and 64.8 ± 11.7% for the fistulograms, DUS, and tUS respectively. The mean (± SD) time between ultrasound and fistulography imaging was 15.0 ± 14.5 days. Assuming the fistulogram as the "gold standard", Bland-Altman agreement for DUS was -1.9 ± 15.5% (limit of agreement [LOA] -32.2 - 28.4) compared with -1.7 ± 15.4% (LOA -31.9 - 28.4) for tUS. Median (± interquartile range) time to complete the investigation was 09:00 ± 03:19 minutes for DUS and 03:13 ± 01:56 minutes for tUS (p < .001). CONCLUSION: DUS and tUS were equally accurate at detecting AVF complications but tUS investigation requires less skill and was significantly quicker than DUS.

Electrical Impedance Tomography-Based Abdominal Subcutaneous Fat Estimation Method Using Deep Learning.

This paper proposes a deep learning method based on electrical impedance tomography (EIT) to estimate the thickness of abdominal subcutaneous fat. EIT for evaluating the thickness of abdominal subcutaneous fat is an absolute imaging problem that aims at reconstructing conductivity distributions from current-to-voltage data. Existing reconstruction methods based on EIT have difficulty handling the inherent drawbacks of strong nonlinearity and severe ill-posedness of EIT; hence, absolute imaging may not be possible using linearized methods. To handle nonlinearity and ill-posedness, we propose a deep learning method that finds useful solutions within a restricted admissible set by accounting for prior information regarding abdominal anatomy. We determined that a specially designed training dataset used during the deep learning process significantly reduces ill-posedness in the absolute EIT problem. In the preprocessing stage, we normalize current-voltage data to alleviate the effects of electrodeposition and body geometry by exploiting knowledge regarding electrode positions and body geometry. The performance of the proposed method is demonstrated through numerical simulations and phantom experiments using a 10 channel EIT system and a human-like domain.

[Effect of implementation of a trauma leader on process parameters for polytrauma treatment in the shock room of a tertiary care hospital]. / Auswirkung der Implementierung eines Schockraumkoordinators auf Prozessparameter der Polytraumaversorgung im Schockraum eines Maximalversorgers.

BACKGROUND: In patients up to the age of 40 years old severe trauma is the most frequent cause of death in Germany. According to the current S3 guidelines on treatment of polytrauma and the severely injured, since 2011 the presence of a shock room coordinator should be considered, who can improve the survival of patients by optimized treatment quality and times. The aim of the present study was to analyze various parameters of shock room treatment for polytraumatized patients before and after implementation of a shock room coordinator for treatment of polytrauma. MATERIAL AND METHODS: To ensure an adequate period of time between the implementation of the shock room coordinator in 2011, data from 2009 and 2012 were included for comparative purposes. All scanned protocols of shock room treatment in the period from 1 January 2009 to 31 December 2009 and from 1 January 2012 to 31 December 2012 were inspected and evaluated. RESULTS: In total 213 shock room treatments from 2009 and 420 from 2012 were included. The mean number of shock room treatments in 2009 was 17.8 per month and in 2012 the mean number was 35 per month. The mean number of shock room treatments was nearly doubled in comparison (p < 0.001). The mean time for shock room treatment in 2009 was 74.8 min and in 2012 the mean time was 69 min and was therefore reduced by 5.8 min (p = 0.56). CONCLUSION: The treatment of polytraumatized patients in the presence of a shock room coordinator and after implementation of the standard operating procedure (SOP) was neither statistically nor clinically relevantly shortened.

Thoracic electrical impedance tomography in Chinese hospitals: a review of clinical research and daily applications.

Chinese scientists and researchers have a long history with electrical impedance tomography (EIT), which can be dated back to the 1980s. No commercial EIT devices for chest imaging were available until the year 2014 when the first device received its approval from the China Food and Drug Administration. Ever since then, clinical research and daily applications have taken place in Chinese hospitals. Up to this date (2019.11) 47 hospitals have been equipped with 50 EIT devices. Twenty-three SCI publications are recorded and a further 21 clinical trials are registered. Thoracic EIT is mainly used in patients before or after surgery, or in intensive care units (ICU). Application fields include the development of strategies for protective lung ventilation (e.g. tidal volume and positive end-expiratory pressure (PEEP) titration, recruitment, choice of ventilation mode and weaning from ventilator), regional lung perfusion monitoring, perioperative monitoring, and potential feedback for rehabilitation. The main challenges for promoting clinical use of EIT are the financial cost and the education of personnel. In this review, the past, present and future of EIT in China are introduced and discussed.

Quantitative 3D structural analysis of the cellular microstructure of sea urchin spines (I): Methodology.

The mineralized skeletons of echinoderms are characterized by their complex, open-cell porous microstructure (also known as stereom), which exhibits vast variations in pore sizes, branch morphology, and three-dimensional (3D) organization patterns among different species. Quantitative description and analysis of these cellular structures in 3D are needed in order to understand their mechanical properties and underlying design strategies. In this paper series, we present a framework for analyzing such structures based on high-resolution 3D tomography data and utilize this framework to investigate the structural designs of stereom by using the spines from the sea urchin Heterocentrotus mamillatus as a model system. The first paper here reports the proposed cellular network analysis framework, which consists of five major steps: synchrotron-based tomography and hierarchical convolutional neural network-based reconstruction, machine learning-based segmentation, cellular network registration, feature extraction, and data representation and analysis. This framework enables the characterization of the porous stereom structures at the individual node and branch level (~10 µm), the local cellular level (~100 µm), and the global network level (~1 mm). We define and quantify multiple structural descriptors at each level, such as node connectivity, branch length and orientation, branch profile, ring structure, etc., which allows us to investigate the cellular network construction of H. mamillatus spines quantitatively. The methodology reported here could be tailored to analyze other natural or engineering open-cell porous materials for a comprehensive multiscale network representation and mechanical analysis. STATEMENT OF SIGNIFICANCE: The mechanical robustness of the biomineralized porous structures in sea urchin spines has long been recognized. However, quantitative cellular network representation and analysis of this class of natural cellular solids are still limited in the literature. This constrains our capability to fully understand the mechanical properties and design strategies in sea urchin spines and other similar echinoderms' porous skeletal structures. Combining high-resolution tomography and computer vision-based analysis, this work presents a multiscale 3D network analysis framework, which allows for extraction, registration, and quantification of sea urchin spines' complex porous structure from the individual branch and node level to the global network level. This 3D structural analysis is relevant to a diversity of research fields, such as biomineralization, skeletal biology, biomimetics, material science, etc.

Performance of Different Imaging Techniques for Detection of Para-Aortic Lymph Node Metastasis from Gynecological Malignancies: A Systematic Review and Meta-Analysis.

OBJECT: The purpose of this review is to assess the diagnostic performance of different imaging techniques for the detection of para-aortic lymph node (PALN) metastasis from gynecological malignancies. METHODS: Six databases, from the earliest available date of indexing through July 22, 2018, were systematically searched. In addition, the reference lists of relevant articles were searched by hand. Study allocation, data extraction, and quality assessment were independently performed by 2 reviewers. The size effect, sensitivity (SEN), specificity (SPE), positive likelihood ratio, negative likelihood ratio, diagnostic OR, and 95% CIs were used in the meta-analysis. The area under the curve (AUC) and Q* were calculated to reflect the synthesized diagnostic accuracy. Statistical calculations of this meta-analysis were conducted using STATA version 14.0 software. RESULTS: Across 41 eligible studies (1,615 participants), pooled SEN, SPE, and AUC of magnetic resonance imaging (MRI), computed tomography (CT), positron emission tomography (PET), PET-CT, and lymphangiography analyses were 25%, 93%, 0.7675; 60%, 94%, 0.9050; 83%, 96%, 0.9422; 66%, 97%, 0.9501; 77%, 75%, 0.8332, respectively. Analysis of combined summary receiver operating characteristic curves indicated that PET and PET-CT were superior to other imaging modalities. CONCLUSION: The present meta-analysis demonstrated that PET and PET-CT should be the first choice for detecting PALN metastasis in gynecological malignancies. CT was also suitable for confirmation. MRI was not recommended. Further studies are needed for PALN assessment.

What is a significant defect of the anal sphincter on translabial ultrasound?

OBJECTIVE: The anal sphincter is commonly evaluated with endoanal ultrasound. Recently, translabial ultrasound imaging has been proposed for sphincter imaging, with moderate to good correlation between the methods. An endosonographic defect is defined as one with a radial extension of > 30° in at least two-thirds of the length of the anal sphincter. This is equivalent to defining significant anal sphincter trauma on translabial tomographic ultrasound imaging (TUI) as a defect in at least four of six slices, a definition which has been validated. This study was designed to validate a residual defect angle of > 30° for the definition of significant anal sphincter trauma on translabial ultrasound. METHODS: This was a retrospective study involving 399 women attending a tertiary urogynecology unit in 2014. All underwent a standardized interview, including determination of St Mark's fecal incontinence score (SMIS), clinical examination and 3D/4D translabial ultrasound examination with the woman at rest and on pelvic floor muscle contraction (PFMC). External (EAS) and internal (IAS) anal sphincter defect angles were measured in individual TUI slices and associations with anal incontinence symptoms, bother score and SMIS were analyzed. RESULTS: There were weak but significant correlations of anal incontinence symptoms, bother score and SMIS with EAS and IAS defect angle, measured on images acquired with the woman at rest and on PFMC. The predictive value of single-slice defect angle on TUI was low, and areas under the receiver-operating-characteristics curves were too low to determine a distinct cut-off value for defect angle. CONCLUSIONS: Anal sphincter residual defects on single translabial TUI slices are weakly associated with measures of anal incontinence. Single-slice defect angle is too poor a predictor to allow validation of the 30° defect angle cut-off used in endoanal ultrasound. Larger studies in populations with a higher prevalence of anal incontinence are needed before we can disregard anal sphincter defects smaller than 30° on translabial ultrasound. Copyright © 2019 ISUOG. Published by John Wiley & Sons Ltd.

Accuracy and reliability of noninvasive stroke volume monitoring via ECG-gated 3D electrical impedance tomography in healthy volunteers.

Cardiac output (CO) and stroke volume (SV) are parameters of key clinical interest. Many techniques exist to measure CO and SV, but are either invasive or insufficiently accurate in clinical settings. Electrical impedance tomography (EIT) has been suggested as a noninvasive measure of SV, but inconsistent results have been reported. Our goal is to determine the accuracy and reliability of EIT-based SV measurements, and whether advanced image reconstruction approaches can help to improve the estimates. Data were collected on ten healthy volunteers undergoing postural changes and exercise. To overcome the sensitivity to heart displacement and thorax morphology reported in previous work, we used a 3D EIT configuration with 2 planes of 16 electrodes and subject-specific reconstruction models. Various EIT-derived SV estimates were compared to reference measurements derived from the oxygen uptake. Results revealed a dramatic impact of posture on the EIT images. Therefore, the analysis was restricted to measurements in supine position under controlled conditions (low noise and stable heart and lung regions). In these measurements, amplitudes of impedance changes in the heart and lung regions could successfully be derived from EIT using ECG gating. However, despite a subject-specific calibration the heart-related estimates showed an error of 0.0 ± 15.2 mL for absolute SV estimation. For trending of relative SV changes, a concordance rate of 80.9% and an angular error of -1.0 ± 23.0° were obtained. These performances are insufficient for most clinical uses. Similar conclusions were derived from lung-related estimates. Our findings indicate that the key difficulty in EIT-based SV monitoring is that purely amplitude-based features are strongly influenced by other factors (such as posture, electrode contact impedance and lung or heart conductivity). All the data of the present study are made publicly available for further investigations.

Ventilation inhomogeneity in obstructive lung diseases measured by electrical impedance tomography: a simulation study.

Electrical impedance tomography (EIT) has mostly been used in the Intensive Care Unit (ICU) to monitor ventilation distribution but is also promising for the diagnosis in spontaneously breathing patients with obstructive lung diseases. Beside tomographic images, several numerical measures have been proposed to quantitatively assess the lung state. In this study two common measures, the 'Global Inhomogeneity Index' and the 'Coefficient of Variation' were compared regarding their capability to reflect the severity of lung obstruction. A three-dimensional simulation model was used to simulate obstructed lungs, whereby images were reconstructed on a two-dimensional domain. Simulations revealed that minor obstructions are not adequately recognized in the reconstructed images and that obstruction above and below the electrode plane may result in misleading values of inhomogeneity measures. EIT measurements on several electrode planes are necessary to apply these measures in patients with obstructive lung diseases in a promising manner.

Temporal Unmixing of Dynamic Fluorescent Images by Blind Source Separation Method with a Convex Framework.

By recording a time series of tomographic images, dynamic fluorescence molecular tomography (FMT) allows exploring perfusion, biodistribution, and pharmacokinetics of labeled substances in vivo. Usually, dynamic tomographic images are first reconstructed frame by frame, and then unmixing based on principle component analysis (PCA) or independent component analysis (ICA) is performed to detect and visualize functional structures with different kinetic patterns. PCA and ICA assume sources are statistically uncorrelated or independent and don't perform well when correlated sources are present. In this paper, we deduce the relationship between the measured imaging data and the kinetic patterns and present a temporal unmixing approach, which is based on nonnegative blind source separation (BSS) method with a convex analysis framework to separate the measured data. The presented method requires no assumption on source independence or zero correlations. Several numerical simulations and phantom experiments are conducted to investigate the performance of the proposed temporal unmixing method. The results indicate that it is feasible to unmix the measured data before the tomographic reconstruction and the BSS based method provides better unmixing quality compared with PCA and ICA.

Performance Enhancement of Pharmacokinetic Diffuse Fluorescence Tomography by Use of Adaptive Extended Kalman Filtering.

Due to both the physiological and morphological differences in the vascularization between healthy and diseased tissues, pharmacokinetic diffuse fluorescence tomography (DFT) can provide contrast-enhanced and comprehensive information for tumor diagnosis and staging. In this regime, the extended Kalman filtering (EKF) based method shows numerous advantages including accurate modeling, online estimation of multiparameters, and universal applicability to any optical fluorophore. Nevertheless the performance of the conventional EKF highly hinges on the exact and inaccessible prior knowledge about the initial values. To address the above issues, an adaptive-EKF scheme is proposed based on a two-compartmental model for the enhancement, which utilizes a variable forgetting-factor to compensate the inaccuracy of the initial states and emphasize the effect of the current data. It is demonstrated using two-dimensional simulative investigations on a circular domain that the proposed adaptive-EKF can obtain preferable estimation of the pharmacokinetic-rates to the conventional-EKF and the enhanced-EKF in terms of quantitativeness, noise robustness, and initialization independence. Further three-dimensional numerical experiments on a digital mouse model validate the efficacy of the method as applied in realistic biological systems.

Recent progress on the factorization method for electrical impedance tomography.

The Factorization Method is a noniterative method to detect the shape and position of conductivity anomalies inside an object. The method was introduced by Kirsch for inverse scattering problems and extended to electrical impedance tomography (EIT) by Brühl and Hanke. Since these pioneering works, substantial progress has been made on the theoretical foundations of the method. The necessary assumptions have been weakened, and the proofs have been considerably simplified. In this work, we aim to summarize this progress and present a state-of-the-art formulation of the Factorization Method for EIT with continuous data. In particular, we formulate the method for general piecewise analytic conductivities and give short and self-contained proofs.

A local region of interest imaging method for electrical impedance tomography with internal electrodes.

Electrical Impedance Tomography (EIT) is a very attractive functional imaging method despite the low sensitivity and resolution. The use of internal electrodes with the conventional reconstruction algorithms was not enough to enhance image resolution and accuracy in the region of interest (ROI). We propose a local ROI imaging method with internal electrodes developed from careful analysis of the sensitivity matrix that is designed to reduce the sensitivity of the voxels outside the local region and optimize the sensitivity of the voxel inside the local region. We perform numerical simulations and physical measurements to demonstrate the localized EIT imaging method. In preliminary results with multiple objects we show the benefits of using an internal electrode and the improved resolution due to the local ROI image reconstruction method. The sensitivity is further increased by allowing the surface electrodes to be unevenly spaced with a higher density of surface electrodes near the ROI. Also, we analyse how much the image quality is improved using several performance parameters for comparison. While these have not yet been studied in depth, it convincingly shows an improvement in local sensitivity in images obtained with an internal electrode in comparison to a standard reconstruction method.

The use of electrical impedance tomography to the differential diagnosis of pathological mammographic/sonographic findings.

Our study involved 870 eligible women with suspected pathological breast lesion discovered by mammography (MMG) or ultrasound examination (USG) which were recommended to pass histological examination to verify the diagnosis. All patients included in our study were divided into two age groups: the 1st group - patients older than 40 years (total of 724 patients) , the 2nd group - patients younger than 40 years (total of 146 patients). The purpose of our study was to analyze the possibilities of electrical impedance tomography (EIT) implementation to the differential diagnosis of pathologic lesions of the breast either solely, or in a combination with MMG/USG. The following results were obtained: in the 1st group the average specificity of MMG was 79.5%; when added EIT the average specificity decreased to 72.8%. The sensitivity of MMG, by contrast, increased from 87.8% when using it as an independent method to 94.5% when added EIT. In the 2nd group the average specificity of USG was 90.2%; when added EIT the average specificity decreased to 86.4%. Similarly, as in the 1st group the sensitivity of USG increased from 86.7% when using it as an independent method to 93.3% when added EIT.Analysis of false-negative results of electrical impedance tomography depending on the stage of the process has shown that as the earlier stage of the disease and as the smaller is the dimensions of the tumor, the higher is the number of false-negative results. In addition, we observed the dependence of the false-negative results of the tumor grade. The results of our study show that the use of EIT in addition to MMG/USG can improve the sensitivity of these methods and to increase the rate of early detection of breast cancer with minimal economic costs and highly qualified staff time expenditures.