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Radiofrequency ablation is an ablation technique to treat tumors with focused heat. Computer tomography, ultrasound and magnetic resonance imaging (MRI) are imaging modalities which can be used for image-guided procedures. MRI offers several advantages in comparison to the other imaging modalities, such as radiation-free fluoroscopic imaging, temperature mapping, a high-soft-tissue contrast and free selection of imaging planes. This work addresses the application of 3Dcontrollers for controlling interventional, fluoroscopic MR sequences at the scenario of MR guided radiofrequency ablation of hepatic malignancies. During this procedure, the interventionalist can monitor the targeting of the tumor with near-real time fluoroscopic sequences. In general, adjustments of the imaging planes are necessary during tumor targeting, which is performed by an assistant in the control room. Therefore, communication between the interventionalist in the scanner room and the assistant in the control room is essential. However, verbal communication is impaired due to the loud scanning noises. Alternatively, non-verbal communication between the two persons is possible, however limited to a few gestures and susceptible to misunderstandings. This work is analyzing different 3D-controllers to enable control of interventional MR sequences during MR-guided procedures directly by the interventionalist. Leap Motion, Wii Remote, SpaceNavigator, Phantom Omni and Foot Switch were selected. For that a simulation was built in C++ with VTK to feign the real scenario for test purposes. Previous results showed that Leap Motion is not suitable for the application while Wii Remote and Foot Switch are possible input devices. Final evaluation showed a generally time reduction with the use of 3D-controllers. Best results were reached with Wii Remote in 34 seconds. Handholding input devices like Wii Remote have further potential to integrate them in real environment to reduce intervention time.
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).
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 learning (DL), has achieved remarkable results for medical image analysis in several applications. Yet the lack of human-like explanations of such systems is considered the principal restriction before utilizing these methods in clinical practice (Yang, Ye, & Xia, 2022).
Methods
Explainable Artificial Intelligence (XAI) provides a human-explainable and interpretable description of the “black-box” nature of DL (Gulum, Trombley, & Kantardzic, 2021). An effective XAI diagnosis generator, namely NeuroXAI (refer to Fig. 1), has been developed to extract 3D explanations from convolutional neural networks (CNN) models of brain gliomas (Zeineldin et al., 2022). By providing visual justification maps, NeuroXAI can help make DL models transparent and thus increase the trust of medical experts.
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 imaging (MRI). Visual attention maps of multiple XAI methods have been generated and compared for both applications, which could help to provide transparency about the performance of DL systems.
Conclusion
NeuroXAI helps to understand the prediction process of 3D CNN networks for brain glioma using human-understandable explanations. Results revealed that the investigated DL models behave in a logical human-like manner and can improve the analytical process of the MRI images systematically. Due to its open architecture, ease of implementation, and scalability to new XAI methods, NeuroXAI could be utilized to assist medical professionals in the detection and diagnosis of brain tumors. NeuroXAI code is publicly accessible at https://github.com/razeineldin/NeuroXAI
The metric and qualitative analysis of models of the upper and lower dental arches is an important aspect of orthodontic treatment planning. Currently available eLearning systems for dental education only allow access to digital learning materials, and do not interactively support the learning progress. Moreover, to date no study compared the efficiency of learning methods based on physical or digital study models. For this pilot study, 18 dental students were separated into two groups to investigate whether the learning success in study model analysis with an interactive elearning system is higher based on digital models or on conventional plaster models. The results show that with the digital method less time is needed per model analysis. Moreover, the digital approach leads to higher total scores than that based on plaster models. We conclude that interactive eLearning using digital dental arch models is a promising tool for dental education.
Diese Arbeit liefert einen Konzeptentwurf, der die Integration verschiedener Systeme mit prozessrelevanten klinischen Diensten gewährleistet. Chirurgische Abläufe werden in Form von Prozessen modelliert. Die Wahl der Notation und die Art der Modellierung dieser Prozesse spielt in der heutigen Forschung in diesem Gebiet eine zentrale Rolle. Sind diese Prozesse modelliert, besteht die Möglichkeit, diese in einer Workflow-Engine automatisiert auszuführen. Im Rahmen der Entwicklung eines Workflow-Managment-Systems stellt sich die Frage, wie die Anbindung dieser Workflow-Engine mit anderen Systemen erfolgen soll. In der Arbeit werden Schnittstellen abstrakt in der Web Services Description Language (WSDL) definiert. Darum werden automatisiert Artefakte erzeugt. Auf der Grundlage dieser Artefakte erfolgt die Integration der Systeme. Die Workflow-Engine kommunizieren über SOAP-Nachrichten (Simple Object Access Protocol) mit den entsprechenden Systemen. Dieser Ansatz wurde mithilfe eines Prototyps validiert und umgesetzt.
Informationstechnische Systeme, die den Arbeitsablauf im klinischen Bereich unterstützen, sind aktuell auf organisatorische Abläufe beschränkt. Diese Arbeit stellt einen ersten Ansatz vor, wie solch ein System in den perioperativen Bereich eingebracht werden kann. Hierzu wurde eine Workflow Engine mit einer perioperativen Prozess-Visualisierung verknüpft. Das System wurde nach Modell-View-Controller-Prinzip implementiert. Als "Controller" kommt die Workflow Engine zum Einsatz; also "Modell" ein Prozessmodell, mit den erforderlichen klinischen Daten. Der "View" wurde durch eine abgekoppelte Anwendung realisiert, welche auf Web-Technologien basiert. Drei Visualisierungen, die Workflow Engine sowie die Anbindung beider über eine Datenbankschnittstelle, wurden erfolgreich umgesetzt. Bei den drei Visualisierungen wurden jeweils eine Ansicht für den OP-Koordinator, den Springer und eine Ansicht für die Übersicht einer OP erstellt.
Information systems, which support the workflow in the clinical area, are currently limited to organizational processes. This work shows a first approach of an information system supporting all actors in the perioperative area. The first prototype and proof of concept was a task manager, giving all actors information about their task and the task of all other actors during an intervention. Based on this initial task manager, we implemented an information system based on a workflow engine controlling all processes and all information necessary for the intervention. A second part was the development of a perioperative process visualization which was developed based on a user centered approach jointly with clinicians and OR members.
An operation room is a stressful work environment. Nevertheless, all involved persons have to work safely as there is no space for making mistakes. To ensure a high level of concentration and seamless interaction, all involved persons have to know their own tasks and tasks of their colleagues. The entire team must work synchronously at all times. However, the operation room (OR) is a noisy environment and the actors have to set their focus on their work. To optimize the overall workflow, a task manager supporting the team was developed. Each actor is equipped with a client terminal showing a summary of their own tasks. Moreover, a big screen displays all tasks of all actors. The architecture is a distributed system based on a communication framework that supports the interaction of all clients with the task manager. A prototype of the task manager and several clients have been developed and implemented. The system represents a proof-of-concept for further development. This paper describes the concept of the task manager.