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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.
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
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.