Slicer-DeepSeg: Open-Source Deep Learning Toolkit for Brain Tumour Segmentation

Ramy A. Zeineldin, Pauline Weimann, Mohamed E. Karar, Franziska Mathis-Ullrich, Oliver Burgert
2021 Current Directions in Biomedical Engineering  
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
more » ... t 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 AIassisted medical applications in neurosurgery. Moreover, it can enhance the outcomes of computer-aided diagnosis of brain tumours. Open-source Slicer-DeepSeg is available at
doi:10.1515/cdbme-2021-1007 fatcat:pbnytnvqpzcd7jojwdyyjr3uzu