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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
For the modeling, execution, and control of complex, non-standardized intraoperative processes, a modeling language is needed that reflects the variability of interventions. As the established Business Process Model and Notation (BPMN) reaches its limits in terms of flexibility, the Case Management Model and Notation (CMMN) was considered as it addresses weakly structured processes.
Methods
To analyze the suitability of the modeling languages, BPMN and CMMN models of a Robot-Assisted Minimally Invasive Esophagectomy and Cochlea Implantation were derived and integrated into a situation recognition workflow. Test cases were used to contrast the differences and compare the advantages and disadvantages of the models concerning modeling, execution, and control. Furthermore, the impact on transferability was investigated.
Results
Compared to BPMN, CMMN allows flexibility for modeling intraoperative processes while remaining understandable. Although more effort and process knowledge are needed for execution and control within a situation recognition system, CMMN enables better transferability of the models and therefore the system. Concluding, CMMN should be chosen as a supplement to BPMN for flexible process parts that can only be covered insufficiently by BPMN, or otherwise as a replacement for the entire process.
Conclusion
CMMN offers the flexibility for variable, weakly structured process parts, and is thus suitable for surgical interventions. A combination of both notations could allow optimal use of their advantages and support the transferability of the situation recognition system.
One of the key challenges for automatic assistance is the support of actors in the operating room depending on the status of the procedure. Therefore, context information collected in the operating room is used to gain knowledge about the current situation. In literature, solutions already exist for specific use cases, but it is doubtful to what extent these approaches can be transferred to other conditions. We conducted a comprehensive literature research on existing situation recognition systems for the intraoperative area, covering 274 articles and 95 cross-references published between 2010 and 2019. We contrasted and compared 58 identified approaches based on defined aspects such as used sensor data or application area. In addition, we discussed applicability and transferability. Most of the papers focus on video data for recognizing situations within laparoscopic and cataract surgeries. Not all of the approaches can be used online for real-time recognition. Using different methods, good results with recognition accuracies above 90% could be achieved. Overall, transferability is less addressed. The applicability of approaches to other circumstances seems to be possible to a limited extent. Future research should place a stronger focus on adaptability. The literature review shows differences within existing approaches for situation recognition and outlines research trends. Applicability and transferability to other conditions are less addressed in current work.
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.
Purpose
Context awareness in the operating room (OR) is important to realize targeted assistance to support actors during surgery. A situation recognition system (SRS) is used to interpret intraoperative events and derive an intraoperative situation from these. To achieve a modular system architecture, it is desirable to de-couple the SRS from other system components. This leads to the need of an interface between such an SRS and context-aware systems (CAS). This work aims to provide an open standardized interface to enable loose coupling of the SRS with varying CAS to allow vendor-independent device orchestrations.
Methods
A requirements analysis investigated limiting factors that currently prevent the integration of CAS in today's ORs. These elicited requirements enabled the selection of a suitable base architecture. We examined how to specify this architecture with the constraints of an interoperability standard. The resulting middleware was integrated into a prototypic SRS and our system for intraoperative support, the OR-Pad, as exemplary CAS for evaluating whether our solution can enable context-aware assistance during simulated orthopedical interventions.
Results
The emerging Service-oriented Device Connectivity (SDC) standard series was selected to specify and implement a middleware for providing the interpreted contextual information while the SRS and CAS are loosely coupled. The results were verified within a proof of concept study using the OR-Pad demonstration scenario. The fulfillment of the CAS’ requirements to act context-aware, conformity to the SDC standard series, and the effort for integrating the middleware in individual systems were evaluated. The semantically unambiguous encoding of contextual information depends on the further standardization process of the SDC nomenclature. The discussion of the validity of these results proved the applicability and transferability of the middleware.
Conclusion
The specified and implemented SDC-based middleware shows the feasibility of loose coupling an SRS with unknown CAS to realize context-aware assistance in the OR.
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).
Background
Personalized medicine requires the integration and analysis of vast amounts of patient data to realize individualized care. With Surgomics, we aim to facilitate personalized therapy recommendations in surgery by integration of intraoperative surgical data and their analysis with machine learning methods to leverage the potential of this data in analogy to Radiomics and Genomics.
Methods
We defined Surgomics as the entirety of surgomic features that are process characteristics of a surgical procedure automatically derived from multimodal intraoperative data to quantify processes in the operating room. In a multidisciplinary team we discussed potential data sources like endoscopic videos, vital sign monitoring, medical devices and instruments and respective surgomic features. Subsequently, an online questionnaire was sent to experts from surgery and (computer) science at multiple centers for rating the features’ clinical relevance and technical feasibility.
Results
In total, 52 surgomic features were identified and assigned to eight feature categories. Based on the expert survey (n = 66 participants) the feature category with the highest clinical relevance as rated by surgeons was “surgical skill and quality of performance” for morbidity and mortality (9.0 ± 1.3 on a numerical rating scale from 1 to 10) as well as for long-term (oncological) outcome (8.2 ± 1.8). The feature category with the highest feasibility to be automatically extracted as rated by (computer) scientists was “Instrument” (8.5 ± 1.7). Among the surgomic features ranked as most relevant in their respective category were “intraoperative adverse events”, “action performed with instruments”, “vital sign monitoring”, and “difficulty of surgery”.
Conclusion
Surgomics is a promising concept for the analysis of intraoperative data. Surgomics may be used together with preoperative features from clinical data and Radiomics to predict postoperative morbidity, mortality and long-term outcome, as well as to provide tailored feedback for surgeons.
Purpose
Supporting the surgeon during surgery is one of the main goals of intelligent ORs. The OR-Pad project aims to optimize the information flow within the perioperative area. A shared information space should enable appropriate preparation and provision of relevant information at any time before, during, and after surgery.
Methods
Based on previous work on an interaction concept and system architecture for the sterile OR-Pad system, we designed a user interface for mobile and intraoperative (stationary) use, focusing on the most important functionalities like clear information provision to reduce information overload. The concepts were transferred into a high-fidelity prototype for demonstration purposes. The prototype was evaluated from different perspectives, including a usability study.
Results
The prototype’s central element is a timeline displaying all available case information chronologically, like radiological images, labor findings, or notes. This information space can be adapted for individual purposes (e.g., highlighting a tumor, filtering for own material). With the mobile and intraoperative mode of the system, relevant information can be added, preselected, viewed, and extended during the perioperative process. Overall, the evaluation showed good results and confirmed the vision of the information system.
Conclusion
The high-fidelity prototype of the information system OR-Pad focuses on supporting the surgeon via a timeline making all available case information accessible before, during, and after surgery. The information space can be personalized to enable targeted support. Further development is reasonable to optimize the approach and address missing or insufficient aspects, like the holding arm and sterility concept or new desired features.
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.
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/.
The increasing heterogenecity of students at German Universities of Applied Sciences and the growing importance of digitization call for a rethinking of teaching and learning within higher education. In the next years, changing the learning ecosystem by developing and reflecting upon new teaching and learning techniques using methods of digitalization will be both - most relevant and very challenging. The following article introduces two different learning scenarios, which exemplify the implementation of new educational models that allow discontinuity of time and place, technology and process in teaching and learning. Within a blended learning apporach, the first learning scenario aims at adapting and individualizing the knowledge transfer in the course Foundations of Computer Science by providing knowledge individually and situation-specifically. The second learning scenario proposes a web-based tool to facilitate digital learning environments and thus digital learning communities and the possibility of computer-supported learning. The overall aim of both learning scenarios is to enhance learning for diverse groups by providing a different smart learning ecosystem in stepping away from a teacher-based to a student-centered approach. Both learning scenarios exemplarily represent the educational vision of Reutlingen University - its development into an interactive university.
The focus of the developed maturity model was set on processes. The concept of the widespread CMM and its practices has been transferred to the perioperative domain and the concept of the new maturity model. Additional optimization goals and technological as well as networking-specific aspects enable a process- and object-focused view of the maturity model in order to ensure broad coverage of different subareas. The evaluation showed that the model is applicable to the perioperative field. Adjustments and extensions of the maturity model are future steps to improve the rating and classification of the new maturity model.
In this paper a method for the generation of gSPM with ontology-based generalization was presented. The resulting gSPM was modeled with BPMN/BPMNsix in an efficient way and could be executed with BPMN workflow engines. In the next step the implementation of resource concepts, anatomical structures, and transition probabilities for workflow execution will be realized.
Stent graft visualization and planning tool for endovascular surgery using finite element analysis
(2014)
Purpose: A new approach to optimize stent graft selection for endovascular aortic repair is the use of finite element analysis. Once the finite element model is created and solved, a software module is needed to view the simulation results in the clinical work environment. A new tool for Interpretation of simulation results, named Medical Postprocessor, that enables comparison of different stent graft configurations and products was designed, implemented and tested. Methods Aortic endovascular stent graft ring forces and sealing states in the vessel landing zone of three different configurations were provided in a surgical planning software using the Medical Imaging Interaction Tool Kit (MITK) Software system. For data interpretation, software modules for 2D and 3D presentations were implemented. Ten surgeons evaluated the software features of the Medical Postprocessor. These surgeons performed usability tests and answered questionnaires based on their experience with the system.
Results: The Medical Postprocessor visualization system enabled vascular surgeons to determine the configuration with the highest overall fixation force in 16 ± 6 s, best proximal sealing in 56±24 s and highest proximal fixation force in 38 ± 12 s. The majority considered the multiformat data provided helpful and found the Medical Postprocessor to be an efficient decision support system for stent graft selection. The evaluation of the user interface results in an ISONORMconform user interface (113.5 points).
Conclusion: The Medical Postprocessor visualization Software tool for analyzing stent graft properties was evaluated by vascular surgeons. The results show that the software can assist the interpretation of simulation results to optimize stent graft configuration and sizing.
Intra-operative fluoroscopy-guided assistance system for transcatheter aortic valve implantation
(2014)
A new surgical assistance system has been developed to assist the correct positioning of the AVP during transapical TAVI. The developed assistance system automatically defines the target area for implanting the AVP under live 2-D fluoroscopy guidance. Moreover, this surgical assistance system works with low levels of contrast agent for the final deployment of AVP, reducing therefore long-term negative effects, such as renal failure in the elderly and high-risk patients.