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Recent advances in artificial intelligence have enabled promising applications in neurosurgery that can enhance patient outcomes and minimize risks. This paper presents a novel system that utilizes AI to aid neurosurgeons in precisely identifying and localizing brain tumors. The system was trained on a dataset of brain MRI scans and utilized deep learning algorithms for segmentation and classification. Evaluation of the system on a separate set of brain MRI scans demonstrated an average Dice similarity coefficient of 0.87. The system was also evaluated through a user experience test involving the Department of Neurosurgery at the University Hospital Ulm, with results showing significant improvements in accuracy, efficiency, and reduced cognitive load and stress levels. Additionally, the system has demonstrated adaptability to various surgical scenarios and provides personalized guidance to users. These findings indicate the potential for AI to enhance the quality of neurosurgical interventions and improve patient outcomes. Future work will explore integrating this system with robotic surgical tools for minimally invasive surgeries.
Automatic segmentation is essential for the brain tumor diagnosis, disease prognosis, and follow-up therapy of patients with gliomas. Still, accurate detection of gliomas and their sub-regions in multimodal MRI is very challenging due to the variety of scanners and imaging protocols. Over the last years, the BraTS Challenge has provided a large number of multi-institutional MRI scans as a benchmark for glioma segmentation algorithms. This paper describes our contribution to the BraTS 2022 Continuous Evaluation challenge. We propose a new ensemble of multiple deep learning frameworks namely, DeepSeg, nnU-Net, and DeepSCAN for automatic glioma boundaries detection in pre-operative MRI. It is worth noting that our ensemble models took first place in the final evaluation on the BraTS testing dataset with Dice scores of 0.9294, 0.8788, and 0.8803, and Hausdorf distance of 5.23, 13.54, and 12.05, for the whole tumor, tumor core, and enhancing tumor, respectively. Furthermore, the proposed ensemble method ranked first in the final ranking on another unseen test dataset, namely Sub-Saharan Africa dataset, achieving mean Dice scores of 0.9737, 0.9593, and 0.9022, and HD95 of 2.66, 1.72, 3.32 for the whole tumor, tumor core, and enhancing tumor, respectively.
Purpose
Artificial intelligence (AI), in particular deep neural networks, has achieved remarkable results for medical image analysis in several applications. Yet the lack of explainability of deep neural models is considered the principal restriction before applying these methods in clinical practice.
Methods
In this study, we propose a NeuroXAI framework for explainable AI of deep learning networks to increase the trust of medical experts. NeuroXAI implements seven state-of-the-art explanation methods providing visualization maps to help make deep learning models transparent.
Results
NeuroXAI has been applied to two applications of the most widely investigated problems in brain imaging analysis, i.e., image classification and segmentation using magnetic resonance (MR) modality. Visual attention maps of multiple XAI methods have been generated and compared for both applications. Another experiment demonstrated that NeuroXAI can provide information flow visualization on internal layers of a segmentation CNN.
Conclusion
Due to its open architecture, ease of implementation, and scalability to new XAI methods, NeuroXAI could be utilized to assist radiologists and medical professionals in the detection and diagnosis of brain tumors in the clinical routine of cancer patients. The code of NeuroXAI is publicly accessible at https://github.com/razeineldin/NeuroXAI.
Accurate and safe neurosurgical intervention can be affected by intra-operative tissue deformation, known as brain-shift. In this study, we propose an automatic, fast, and accurate deformable method, called iRegNet, for registering pre-operative magnetic resonance images to intra-operative ultrasound volumes to compensate for brain-shift. iRegNet is a robust end-to-end deep learning approach for the non-linear registration of MRI-iUS images in the context of image-guided neurosurgery. Pre-operative MRI (as moving image) and iUS (as fixed image) are first appended to our convolutional neural network, after which a non-rigid transformation field is estimated. The MRI image is then transformed using the output displacement field to the iUS coordinate system. Extensive experiments have been conducted on two multi-location databases, which are the BITE and the RESECT. Quantitatively, iRegNet reduced the mean landmark errors from pre-registration value of (4.18 ± 1.84 and 5.35 ± 4.19 mm) to the lowest value of (1.47 ± 0.61 and 0.84 ± 0.16 mm) for the BITE and RESECT datasets, respectively. Additional qualitative validation of this study was conducted by two expert neurosurgeons through overlaying MRI-iUS pairs before and after the deformable registration. Experimental findings show that our proposed iRegNet is fast and achieves state-of-the-art accuracies outperforming state-of-the-art approaches. Furthermore, the proposed iRegNet can deliver competitive results, even in the case of non-trained images as proof of its generality and can therefore be valuable in intra-operative neurosurgical guidance.
Purpose: Gliomas are the most common and aggressive type of brain tumors due to their infiltrative nature and rapid progression. The process of distinguishing tumor boundaries from healthy cells is still a challenging task in the clinical routine. Fluid attenuated inversion recovery (FLAIR) MRI modality can provide the physician with information about tumor infiltration. Therefore, this paper proposes a new generic deep learning architecture, namely DeepSeg, for fully automated detection and segmentation of the brain lesion using FLAIR MRI data.
Methods: The developed DeepSeg is a modular decoupling framework. It consists of two connected core parts based on an encoding and decoding relationship. The encoder part is a convolutional neural network (CNN) responsible for spatial information extraction. The resulting semantic map is inserted into the decoder part to get the full-resolution probability map. Based on modified U-Net architecture, different CNN models such as residual neural network (ResNet), dense convolutional network (DenseNet), and NASNet have been utilized in this study.
Results: The proposed deep learning architectures have been successfully tested and evaluated on-line based on MRI datasets of brain tumor segmentation (BraTS 2019) challenge, including s336 cases as training data and 125 cases for validation data. The dice and Hausdorff distance scores of obtained segmentation results are about 0.81 to 0.84 and 9.8 to 19.7 correspondingly.
Conclusion: This study showed successful feasibility and comparative performance of applying different deep learning models in a new DeepSeg framework for automated brain tumor segmentation in FLAIR MR images. The proposed DeepSeg is open source and freely available at https://github.com/razeineldin/DeepSeg/.
Intraoperative brain deformation, so called brain shift, affects the applicability of preoperative magnetic resonance imaging (MRI) data to assist the procedures of intraoperative ultrasound (iUS) guidance during neurosurgery. This paper proposes a deep learning-based approach for fast and accurate deformable registration of preoperative MRI to iUS images to correct brain shift. Based on the architecture of 3D convolutional neural networks, the proposed deep MRI-iUS registration method has been successfully tested and evaluated on the retrospective evaluation of cerebral tumors (RESECT) dataset. This study showed that our proposed method outperforms other registration methods in previous studies with an average mean squared error (MSE) of 85. Moreover, this method can register three 3D MRI-US pair in less than a second, improving the expected outcomes of brain surgery.
A hybrid deep registration of MR scans to interventional ultrasound for neurosurgical guidance
(2021)
Despite the recent advances in image-guided neurosurgery, reliable and accurate estimation of the brain shift still remains one of the key challenges. In this paper, we propose an automated multimodal deformable registration method using hybrid learning-based and classical approaches to improve neurosurgical procedures. Initially, the moving and fixed images are aligned using classical affine transformation (MINC toolkit), and then the result is provided to the convolutional neural network, which predicts the deformation field using backpropagation. Subsequently, the moving image is transformed using the resultant deformation into a moved image. Our model was evaluated on two publicly available datasets: the retrospective evaluation of cerebral tumors (RESECT) and brain images of tumors for evaluation (BITE). The mean target registration errors have been reduced from 5.35 ± 4.29 to 0.99 ± 0.22 mm in the RESECT and from 4.18 ± 1.91 to 1.68 ± 0.65 mm in the BITE. Experimental results showed that our method improved the state-of-the-art in terms of both accuracy and runtime speed (170 ms on average). Hence, the proposed method provides a fast runtime for 3D MRI to intra-operative US pair in a GPU-based implementation, which shows a promise for its applicability in assisting the neurosurgical procedures compensating for brain shift.
Glioblastomas are the most aggressive fast-growing primary brain cancer which originate in the glial cells of the brain. Accurate identification of the malignant brain tumor and its sub-regions is still one of the most challenging problems in medical image segmentation. The Brain Tumor Segmentation Challenge (BraTS) has been a popular benchmark for automatic brain glioblastomas segmentation algorithms since its initiation. In this year, BraTS 2021 challenge provides the largest multi-parametric (mpMRI) dataset of 2,000 pre-operative patients. In this paper, we propose a new aggregation of two deep learning frameworksnamely, DeepSeg and nnU-Net for automatic glioblastoma recognition in pre-operative mpMRI. Our ensemble method obtains Dice similarity scores of 92.00, 87.33, and 84.10 and Hausdorff Distances of 3.81, 8.91, and 16.02 for the enhancing tumor, tumor core, and whole tumor regions, respectively, on the BraTS 2021 validation set, ranking us among the top ten teams. These experimental findings provide evidence that it can be readily applied clinically and thereby aiding in the brain cancer prognosis, therapy planning, and therapy response monitoring. A docker image for reproducing our segmentation results is available online at (https://hub.docker.com/r/razeineldin/deepseg21).
Intraoperative imaging can assist neurosurgeons to define brain tumours and other surrounding brain structures. Interventional ultrasound (iUS) is a convenient modality with fast scan times. However, iUS data may suffer from noise and artefacts which limit their interpretation during brain surgery. In this work, we use two deep learning networks, namely UNet and TransUNet, to make automatic and accurate segmentation of the brain tumour in iUS data. Experiments were conducted on a dataset of 27 iUS volumes. The outcomes show that using a transformer with UNet is advantageous providing an efficient segmentation modelling long-range dependencies between each iUS image. In particular, the enhanced TransUNet was able to predict cavity segmentation in iUS data with an inference rate of more than 125 FPS. These promising results suggest that deep learning networks can be successfully deployed to assist neurosurgeons in the operating room.
Purpose
Computerized medical imaging processing assists neurosurgeons to localize tumours precisely. It plays a key role in recent image-guided neurosurgery. Hence, we developed a new open-source toolkit, namely Slicer-DeepSeg, for efficient and automatic brain tumour segmentation based on deep learning methodologies for aiding clinical brain research.
Methods
Our developed toolkit consists of three main components. First, Slicer-DeepSeg extends the 3D Slicer application and thus provides support for multiple data input/ output data formats and 3D visualization libraries. Second, Slicer core modules offer powerful image processing and analysis utilities. Third, the Slicer-DeepSeg extension provides a customized GUI for brain tumour segmentation using deep learning-based methods.
Results
The developed Slicer-DeepSeg was validated using a public dataset of high-grade glioma patients. The results showed that our proposed platform’s performance considerably outperforms other 3D Slicer cloud-based approaches.
Conclusions
Developed Slicer-DeepSeg allows the development of novel AI-assisted medical applications in neurosurgery. Moreover, it can enhance the outcomes of computer-aided diagnosis of brain tumours. Open-source Slicer-DeepSeg is available at github.com/razeineldin/Slicer-DeepSeg.
Background
The actual task of electrocardiographic examinations is to increase the reliability of diagnosing the condition of the heart. Within the framework of this task, an important direction is the solution of the inverse problem of electrocardiography, based on the processing of electrocardiographic signals of multichannel cardio leads at known electrode coordinates in these leads (Titomir et al. Noninvasiv electrocardiotopography, 2003), (Macfarlane et al. Comprehensive Electrocardiology, 2nd ed. (Chapter 9), 2011).
Results
In order to obtain more detailed information about the electrical activity of the heart, we carry out a reconstruction of the distribution of equivalent electrical sources on the heart surface. In this area, we hold reconstruction of the equivalent sources during the cardiac cycle at relatively low hardware cost. ECG maps of electrical potentials on the surface of the torso (TSPM) and electrical sources on the surface of the heart (HSSM) were studied for different times of the cardiac cycle. We carried out a visual and quantitative comparison of these maps in the presence of pathological regions of different localization. For this purpose we used the model of the heart electrical activity, based on cellular automata.
Conclusions
The model of cellular automata allows us to consider the processes of heart excitation in the presence of pathological regions of various sizes and localization. It is shown, that changes in the distribution of electrical sources on the surface of the epicardium in the presence of pathological areas with disturbances in the conduction of heart excitation are much more noticeable than changes in ECG maps on the torso surface.
Mit dem Kunstbegriff "Virtuelle Realität" beschreibt man die Darstellung von künstlichen Welten und die Interaktion mit den selbigen. Meist verbindet man damit teure Spiel- und Filmproduktionen. Doch durch derzeitige Entwicklungen können auch kleine Entwicklerstudios und Endanwender auf Bewegungserkennungssysteme zurückgreifen. In dieser Ausarbeitung werden zwei Prototypen vorgestellt, die auf eben diese Systeme zurückgreifen. In den Prototypen soll eine Interaktion mit der Umwelt und ein "Mittendringefühl" im Rahmen von Serious Games ermöglicht werden.
The digitization of our society changes the way we live, work, learn, communicate, and collaborate. This disruptive change interacts with all information processes and systems that are important business enablers for the context of digitization since years. Our aim is to support flexibility and agile transformations for both business domains and related information technology with more flexible enterprise information systems through adaptation and evolution of digital enterprise architectures. The present research paper investigates the continuous bottom-up integration of micro-granular architectures for a huge amount of dynamically growing systems and services, like microservices and the Internet of Things, as part of a new digital enterprise architecture. To integrate micro granular architecture models to living architectural model versions we are extending more traditional enterprise architecture reference models with state of art elements for agile architectural engineering to support the digitization of products, services, and processes.
SmartLife ecosystems are emerging as intelligent user-centered systems that will shape future trends in technology and communication. Biological metaphors of living adaptable ecosystems provide the logical foundation for self-optimizing and self-healing run-time environments for intelligent adaptable business services and related information systems with service-oriented enterprise architectures. The present research in progress work investigates mechanisms for adaptable enterprise architectures for the development of service-oriented ecosystems with integrated technologies like Semantic Technologies, Web Services, Cloud Computing and Big Data Management. With a large and diverse set of ecosystem services with different owners, our scenario of service-based SmartLife ecosystems can pose challenges in their development, and more importantly, for maintenance and software evolution. Our research explores the use of knowledge modeling using ontologies and flexible metamodels for adaptable enterprise architectures to support program comprehension for software engineers during maintenance and evolution tasks of service-based applications. Our previous reference enterprise architecture model ESARC -- Enterprise Services Architecture Reference Cube -- and the Open Group SOA Ontology was extended to support agile semantic analysis, program comprehension and software evolution for a SmartLife applications scenario. The Semantic Browser is a semantic search tool that was developed to provide knowledge-enhanced investigation capabilities for service-oriented applications and their architectures.
The internet of things, enterprise social networks, adaptive case management, mobility systems, analytics for big data, and cloud environments are emerging to support smart connected i.e. digital products and services and the digital transformation. Biological metaphors for living and adaptable ecosystems are currently providing the logical foundation for resilient run-time environments with serviceoriented digitization architectures and for self-optimizing intelligent business services and related distributed information systems. We are investigating mechanisms for flexible adaptation and evolution of information systems with digital architecture in the context of the ongoing digital transformation. The goal is to support flexible and agile transformations for both business and related information systems through adaptation and dynamical evolution of their digital architectures. The present research paper investigates mechanisms of decision analytics for digitization architectures, putting a spotlight to internet of things micro-granular architectures, by extending original enterprise architecture reference models with digitization architectures and their multi-perspective architectural decision management.
The digitization of our society changes the way we live, work, learn, communicate, and collaborate. The Internet of Things, enterprise social networks, adaptive case management, mobility systems, analytics for big data, and cloud services environments are emerging to support smart connected products and services and the digital transformation. Biological metaphors of living and adaptable ecosystems provide the logical foundation for self-optimizing and resilient run-time environments for intelligent business services and service-oriented enterprise architectures. Our aim is to support flexibility and agile transformations for both business domains and related information technology. The present research paper investigates mechanisms for decision analytics in the context of multi-perspective explorations of enterprise services and their digital enterprise architectures by extending original architecture reference models with state of art elements for agile architectural engineering for the digitization and collaborative architectural decision support. The paper’s context focuses on digital transformations of business and IT and integrates fundamental mappings between adaptable digital enterprise architectures and service-oriented information systems. We are putting a spotlight on the example domain – Internet of Things.
The digitization of our society changes the way we live, work, learn, communicate, and collaborate. This disruptive change interacts with all information processes and systems that are important business enablers for the context of digitization since years. Our aim is to support flexibility and agile transformations for both business domains and related information technology and enterprise systems through adaptation and evolution of digital enterprise architectures. The present research paper investigates collaborative decision mechanisms for adaptive digital enterprise architectures by extending original architecture reference models with state of art elements for agile architectural engineering for the digitization and collaborative architectural decision support.
Handling complexity in modern software engineering : editorial introduction to issue 32 of CSIMQ
(2022)
The potential of the Internet and related digital technologies, such as the Internet of Things (IoT), cognition and artificial intelligence, data analytics, services computing, cloud computing, mobile systems, collaboration networks, and cyber-physical systems, are both strategic drivers and enablers of modern digital platforms with fast-evolving ecosystems of intelligent services for digital products. This issue of CSIMQ presents three recent articles on modern software engineering. First, we focus on continuous software development and place it in the context of software architectures and digital transformation. The first contribution is followed by the description of the basis of specific security requirements and adequate digital monitoring mechanisms. Finally, we present a practical example of the digital management of livestock farming.
Today, many companies are adapting their strategy, business models, products, services as well as business processes and information systems in order to expand their digitalization level through intelligent systems and services. The paper raises an important question: What are cognitive co-creation mechanisms for extending digital services and architectures to readjust the usage value of smart services? Typically, extensions of digital services and products and their architectures are manual design tasks that are complex and require specialized, rare experts. The current publication explores the basic idea of extending specific digital artifacts, such as intelligent service architectures, through mechanisms of cognitive co-creation to enable a rapid evolutionary path and better integration of humans and intelligent systems. We explore the development of intelligent service architectures through a combined, iterative, and permanent task of co-creation between humans and intelligent systems as part of a new concept of cognitively adapted smart services. In this paper, we present components of a new platform for the joint co-creation of cognitive services for an ecosystem of intelligent services that enables the adaptation of digital services and architectures.