Cloud Deployment of High-Resolution Medical Image Analysis With TOMAAT

CloudBrain-MRS: An intelligent cloud computing platform for in vivo magnetic resonance spectroscopy preprocessing, quantification, and analysis

Magnetic resonance spectroscopy (MRS) is an important clinical imaging method for diagnosis of diseases. MRS spectrum is used to observe the signal intensity of metabolites or further infer their concentrations. Although the magnetic resonance vendors commonly provide basic functions of spectrum plots and metabolite quantification, the spread of clinical research of MRS is still limited due to the lack of easy-to-use processing software or platform. To address this issue, we have developed CloudBrain-MRS, a cloud-based online platform that provides powerful hardware and advanced algorithms. The platform can be accessed simply through a web browser, without the need of any program installation on the user side. CloudBrain-MRS also integrates the classic LCModel and advanced artificial intelligence algorithms and supports batch preprocessing, quantification, and analysis of MRS data from different vendors. Additionally, the platform offers useful functions: (1) Automatically statistical analysis to find biomarkers for diseases; (2) Consistency verification between the classic and artificial intelligence quantification algorithms; (3) Colorful three-dimensional visualization for easy observation of individual metabolite spectrum. Last, data of both healthy subjects and patients with mild cognitive impairment are used to demonstrate the functions of the platform. To the best of our knowledge, this is the first cloud computing platform for in vivo MRS with artificial intelligence processing. We have shared our cloud platform at MRSHub, providing at least two years of free access and service. If you are interested, please visit https://mrshub.org/software_all/#CloudBrain-MRS or https://csrc.xmu.edu.cn/CloudBrain.html.

Endolymphatic space is age-dependent

Knowledge of the physiological endolymphatic space (ELS) is necessary to estimate endolymphatic hydrops (ELH) in patients with vestibulocochlear syndromes. Therefore, the current study investigated age-dependent changes in the ELS of participants with normal vestibulocochlear testing. Sixty-four ears of 32 participants with normal vestibulocochlear testing aged between 21 and 75 years (45.8 ± 17.2 years, 20 females, 30 right-handed, two left-handed) were examined by intravenous delayed gadolinium-enhanced magnetic resonance imaging of the inner ear (iMRI). Clinical diagnostics included neuro-otological assessment, video-oculography during caloric stimulation, and head-impulse test. iMRI data analysis provided semi-quantitative visual grading and automatic algorithmic quantitative segmentation of ELS volume (3D, mm³) using a deep learning-based segmentation of the inner ear's total fluid space (TFS) and volumetric local thresholding, as described earlier. As a result, following a 4-point ordinal scale, a mild ELH (grade 1) was found in 21/64 (32.8%) ears uni- or bilaterally in either cochlear, vestibulum, or both. Age and ELS were found to be positively correlated for the inner ear (r(64) = 0.33, p < 0.01), and vestibulum (r(64) = 0.25, p < 0.05). For the cochlea, the values correlated positively without reaching significance (r(64) = 0.21). In conclusion, age-dependent increases of the ELS should be considered when evaluating potential ELH in single subjects and statistical group comparisons.

Vestibular paroxysmia entails vestibular nerve function, microstructure and endolymphatic space changes linked to root-entry zone neurovascular compression

Combining magnetic resonance imaging (MRI) sequences that permit the determination of vestibular nerve angulation (NA = change of nerve caliber or direction), structural nerve integrity via diffusion tensor imaging (DTI), and exclusion of endolymphatic hydrops (ELH) via delayed gadolinium-enhanced MRI of the inner ear (iMRI) could increase the diagnostic accuracy in patients with vestibular paroxysmia (VP). Thirty-six participants were examined, 18 with VP (52.6 ± 18.1 years) and 18 age-matched with normal vestibulocochlear testing (NP 50.3 ± 16.5 years). This study investigated whether (i) NA, (ii) DTI changes, or (iii) ELH occur in VP, and (iv) to what extent said parameters relate. Methods included vestibulocochlear testing and MRI data analyses for neurovascular compression (NVC) and NA verification, DTI and ELS quantification. As a result, (i) NA increased NVC specificity. (ii) DTI structural integrity was reduced on the side affected by VP (p < 0.05). (iii) 61.1% VP showed mild ELH and higher asymmetry indices than NP (p > 0.05). (iv) "Disease duration" and "total number of attacks" correlated with the decreased structural integrity of the affected nerve in DTI (p < 0.001). NVC distance within the nerve's root-entry zone correlated with nerve function (Roh = 0.72, p < 0.001), nerve integrity loss (Roh = - 0.638, p < 0.001), and ELS volume (Roh = - 0.604, p < 0.001) in VP. In conclusion, this study is the first to link eighth cranial nerve function, microstructure, and ELS changes in VP to clinical features and increased vulnerability of NVC in the root-entry zone. Combined MRI with NVC or NA verification, DTI and ELS quantification increased the diagnostic accuracy at group-level but did not suffice to diagnose VP on a single-subject level due to individual variability and lack of diagnostic specificity.

Artificial Intelligence in Dermatology Image Analysis: Current Developments and Future Trends

BACKGROUND

Thanks to the rapid development of computer-based systems and deep-learning-based algorithms, artificial intelligence (AI) has long been integrated into the healthcare field. AI is also particularly helpful in image recognition, surgical assistance and basic research. Due to the unique nature of dermatology, AI-aided dermatological diagnosis based on image recognition has become a modern focus and future trend. Key scientific concepts of review: The use of 3D imaging systems allows clinicians to screen and label skin pigmented lesions and distributed disorders, which can provide an objective assessment and image documentation of lesion sites. Dermatoscopes combined with intelligent software help the dermatologist to easily correlate each close-up image with the corresponding marked lesion in the 3D body map. In addition, AI in the field of prosthetics can assist in the rehabilitation of patients and help to restore limb function after amputation in patients with skin tumors.

THE AIM OF THE STUDY

For the benefit of patients, dermatologists have an obligation to explore the opportunities, risks and limitations of AI applications. This study focuses on the application of emerging AI in dermatology to aid clinical diagnosis and treatment, analyzes the current state of the field and summarizes its future trends and prospects so as to help dermatologists realize the impact of new technological innovations on traditional practices so that they can embrace and use AI-based medical approaches more quickly.

ColoRectalCADx: Expeditious Recognition of Colorectal Cancer with Integrated Convolutional Neural Networks and Visual Explanations Using Mixed Dataset Evidence

Colorectal cancer typically affects the gastrointestinal tract within the human body. Colonoscopy is one of the most accurate methods of detecting cancer. The current system facilitates the identification of cancer by computer-assisted diagnosis (CADx) systems with a limited number of deep learning methods. It does not imply the depiction of mixed datasets for the functioning of the system. The proposed system, called ColoRectalCADx, is supported by deep learning (DL) models suitable for cancer research. The CADx system comprises five stages: convolutional neural networks (CNN), support vector machine (SVM), long short-term memory (LSTM), visual explanation such as gradient-weighted class activation mapping (Grad-CAM), and semantic segmentation phases. Here, the key components of the CADx system are equipped with 9 individual and 12 integrated CNNs, implying that the system consists mainly of investigational experiments with a total of 21 CNNs. In the subsequent phase, the CADx has a combination of CNNs of concatenated transfer learning functions associated with the machine SVM classification. Additional classification is applied to ensure effective transfer of results from CNN to LSTM. The system is mainly made up of a combination of CVC Clinic DB, Kvasir2, and Hyper Kvasir input as a mixed dataset. After CNN and LSTM, in advanced stage, malignancies are detected by using a better polyp recognition technique with Grad-CAM and semantic segmentation using U-Net. CADx results have been stored on Google Cloud for record retention. In these experiments, among all the CNNs, the individual CNN DenseNet-201 (87.1% training and 84.7% testing accuracies) and the integrated CNN ADaDR-22 (84.61% training and 82.17% testing accuracies) were the most efficient for cancer detection with the CNN+LSTM model. ColoRectalCADx accurately identifies cancer through individual CNN DesnseNet-201 and integrated CNN ADaDR-22. In Grad-CAM's visual explanations, CNN DenseNet-201 displays precise visualization of polyps, and CNN U-Net provides precise malignant polyps.

IE-Vnet: Deep Learning-Based Segmentation of the Inner Ear's Total Fluid Space

Background

In-vivo MR-based high-resolution volumetric quantification methods of the endolymphatic hydrops (ELH) are highly dependent on a reliable segmentation of the inner ear's total fluid space (TFS). This study aimed to develop a novel open-source inner ear TFS segmentation approach using a dedicated deep learning (DL) model.

Methods

The model was based on a V-Net architecture (IE-Vnet) and a multivariate (MR scans: T1, T2, FLAIR, SPACE) training dataset (D1, 179 consecutive patients with peripheral vestibulocochlear syndromes). Ground-truth TFS masks were generated in a semi-manual, atlas-assisted approach. IE-Vnet model segmentation performance, generalizability, and robustness to domain shift were evaluated on four heterogenous test datasets (D2-D5, n = 4 × 20 ears).

Results

The IE-Vnet model predicted TFS masks with consistently high congruence to the ground-truth in all test datasets (Dice overlap coefficient: 0.9 ± 0.02, Hausdorff maximum surface distance: 0.93 ± 0.71 mm, mean surface distance: 0.022 ± 0.005 mm) without significant difference concerning side (two-sided Wilcoxon signed-rank test, p>0.05), or dataset (Kruskal-Wallis test, p>0.05; post-hoc Mann-Whitney U, FDR-corrected, all p>0.2). Prediction took 0.2 s, and was 2,000 times faster than a state-of-the-art atlas-based segmentation method.

Conclusion

IE-Vnet TFS segmentation demonstrated high accuracy, robustness toward domain shift, and rapid prediction times. Its output works seamlessly with a previously published open-source pipeline for automatic ELS segmentation. IE-Vnet could serve as a core tool for high-volume trans-institutional studies of the inner ear. Code and pre-trained models are available free and open-source under https://github.com/pydsgz/IEVNet.

Intravenous Delayed Gadolinium-Enhanced MR Imaging of the Endolymphatic Space: A Methodological Comparative Study

In-vivo non-invasive verification of endolymphatic hydrops (ELH) by means of intravenous delayed gadolinium (Gd) enhanced magnetic resonance imaging of the inner ear (iMRI) is rapidly developing into a standard clinical tool to investigate peripheral vestibulo-cochlear syndromes. In this context, methodological comparative studies providing standardization and comparability between labs seem even more important, but so far very few are available. One hundred eight participants [75 patients with Meniere's disease (MD; 55.2 ± 14.9 years) and 33 vestibular healthy controls (HC; 46.4 ± 15.6 years)] were examined. The aim was to understand (i) how variations in acquisition protocols influence endolymphatic space (ELS) MR-signals; (ii) how ELS quantification methods correlate to each other or clinical data; and finally, (iii) how ELS extent influences MR-signals. Diagnostics included neuro-otological assessment, video-oculography during caloric stimulation, head-impulse test, audiometry, and iMRI. Data analysis provided semi-quantitative (SQ) visual grading and automatic algorithmic quantitative segmentation of ELS area [2D, mm²] and volume [3D, mm³] using deep learning-based segmentation and volumetric local thresholding. Within the range of 0.1-0.2 mmol/kg Gd dosage and a 4 h ± 30 min time delay, SQ grading and 2D- or 3D-quantifications were independent of signal intensity (SI) and signal-to-noise ratio (SNR; FWE corrected, p < 0.05). The ELS quantification methods used were highly reproducible across raters or thresholds and correlated strongly (0.3-0.8). However, 3D-quantifications showed the least variability. Asymmetry indices and normalized ELH proved the most useful for predicting quantitative clinical data. ELH size influenced SI (cochlear basal turn p < 0.001), but not SNR. SI could not predict the presence of ELH. In conclusion, (1) Gd dosage of 0.1-0.2 mmol/kg after 4 h ± 30 min time delay suffices for ELS quantification. (2) A consensus is needed on a clinical SQ grading classification including a standardized level of evaluation reconstructed to anatomical fixpoints. (3) 3D-quantification methods of the ELS are best suited for correlations with clinical variables and should include both ears and ELS values reported relative or normalized to size. (4) The presence of ELH increases signal intensity in the basal cochlear turn weakly, but cannot predict the presence of ELH.

VOLT: a novel open-source pipeline for automatic segmentation of endolymphatic space in inner ear MRI

Background

Objective and volumetric quantification is a necessary step in the assessment and comparison of endolymphatic hydrops (ELH) results. Here, we introduce a novel tool for automatic volumetric segmentation of the endolymphatic space (ELS) for ELH detection in delayed intravenous gadolinium-enhanced magnetic resonance imaging of inner ear (iMRI) data.

Methods

The core component is a novel algorithm based on Volumetric Local Thresholding (VOLT). The study included three different data sets: a real-world data set (D1) to develop the novel ELH detection algorithm and two validating data sets, one artificial (D2) and one entirely unseen prospective real-world data set (D3). D1 included 210 inner ears of 105 patients (50 male; mean age 50.4 ± 17.1 years), and D3 included 20 inner ears of 10 patients (5 male; mean age 46.8 ± 14.4 years) with episodic vertigo attacks of different etiology. D1 and D3 did not differ significantly concerning age, gender, the grade of ELH, or data quality. As an artificial data set, D2 provided a known ground truth and consisted of an 8-bit cuboid volume using the same voxel-size and grid as real-world data with different sized cylindrical and cuboid-shaped cutouts (signal) whose grayscale values matched the real-world data set D1 (mean 68.7 ± 7.8; range 48.9–92.8). The evaluation included segmentation accuracy using the Sørensen-Dice overlap coefficient and segmentation precision by comparing the volume of the ELS.

Results

VOLT resulted in a high level of performance and accuracy in comparison with the respective gold standard. In the case of the artificial data set, VOLT outperformed the gold standard in higher noise levels. Data processing steps are fully automated and run without further user input in less than 60 s. ELS volume measured by automatic segmentation correlated significantly with the clinical grading of the ELS (p < 0.01).

Conclusion

VOLT enables an open-source reproducible, reliable, and automatic volumetric quantification of the inner ears’ fluid space using MR volumetric assessment of endolymphatic hydrops. This tool constitutes an important step towards comparable and systematic big data analyses of the ELS in patients with the frequent syndrome of episodic vertigo attacks. A generic version of our three-dimensional thresholding algorithm has been made available to the scientific community via GitHub as an ImageJ-plugin.