PWD-3DNet: A deep learning-based fully-automated segmentation of multiple structures on temporal bone CT scans

The temporal bone is a part of the lateral skull surface that contains organs responsible for hearing and balance. Mastering surgery of the temporal bone is challenging because of this complex and microscopic three-dimensional anatomy. Segmentation of intra-temporal anatomy based on computed tomography (CT) images is necessary for applications such as surgical training and rehearsal, amongst others. However, temporal bone segmentation is challenging due to the similar intensities and complicated anatomical relationships among crit- ical structures, undetectable small structures on standard clinical CT, and the amount of time required for manual segmentation. This paper describes a single multi-class deep learning-based pipeline as the first fully automated algorithm for segmenting multiple temporal bone structures from CT volumes, including the sigmoid sinus, facial nerve, inner ear, malleus, incus, stapes, internal carotid artery and internal auditory canal. The proposed fully convolutional network, PWD-3DNet, is a patch-wise densely connected (PWD) three-dimensional (3D) network. The accuracy and speed of the proposed algorithm was shown to surpass current manual and semi-automated segmentation techniques. The experimental results yielded significantly high Dice similar- ity scores and low Hausdorff distances for all temporal bone structures with an average of 86% and 0.755 millimeter (mm), respectively. We illustrated that overlapping in the inference sub-volumes improves the segmentation performance. Moreover, we proposed augmentation layers by using samples with various transformations and image artefacts to increase the robustness of PWD-3DNet against image acquisition protocols, such as smoothing caused by soft tissue scanner settings and larger voxel sizes used for radiation reduction. The proposed algorithm was tested on low-resolution CTs acquired by another center with different scanner parameters than the ones used to create the algorithm and shows potential for application beyond the particular training data used in the study

PWD-3DNet: A Deep Learning-Based Fully-Automated Segmentation of Multiple Structures on Temporal Bone CT Scans

The temporal bone is a part of the lateral skull surface that contains organs responsible for hearing and balance. Mastering surgery of the temporal bone is challenging because of this complex and microscopic three-dimensional anatomy. Segmentation of intra-temporal anatomy based on computed tomography (CT) images is necessary for applications such as surgical training and rehearsal, amongst others. However, temporal bone segmentation is challenging due to the similar intensities and complicated anatomical relationships among critical structures, undetectable small structures on standard clinical CT, and the amount of time required for manual segmentation. This paper describes a single multi-class deep learning-based pipeline as the first fully automated algorithm for segmenting multiple temporal bone structures from CT volumes, including the sigmoid sinus, facial nerve, inner ear, malleus, incus, stapes, internal carotid artery and internal auditory canal. The proposed fully convolutional network, PWD-3DNet, is a patch-wise densely connected (PWD) three-dimensional (3D) network. The accuracy and speed of the proposed algorithm was shown to surpass current manual and semi-automated segmentation techniques. The experimental results yielded significantly high Dice similarity scores and low Hausdorff distances for all temporal bone structures with an average of 86% and 0.755 millimeter (mm), respectively. We illustrated that overlapping in the inference sub-volumes improves the segmentation performance. Moreover, we proposed augmentation layers by using samples with various transformations and image artefacts to increase the robustness of PWD-3DNet against image acquisition protocols, such as smoothing caused by soft tissue scanner settings and larger voxel sizes used for radiation reduction. The proposed algorithm was tested on low-resolution CTs acquired by another center with different scanner parameters than the ones used to create the algorithm and shows potential for application beyond the particular training data used in the study

Automatic Segmentation of the Mandible for Three-Dimensional Virtual Surgical Planning

Three-dimensional (3D) medical imaging techniques have a fundamental role in the field of oral and maxillofacial surgery (OMFS). 3D images are used to guide diagnosis, assess the severity of disease, for pre-operative planning, per-operative guidance and virtual surgical planning (VSP). In the field of oral cancer, where surgical resection requiring the partial removal of the mandible is a common treatment, resection surgery is often based on 3D VSP to accurately design a resection plan around tumor margins. In orthognathic surgery and dental implant surgery, 3D VSP is also extensively used to precisely guide mandibular surgery. Image segmentation from the radiography images of the head and neck, which is a process to create a 3D volume of the target tissue, is a useful tool to visualize the mandible and quantify geometric parameters. Studies have shown that 3D VSP requires accurate segmentation of the mandible, which is currently performed by medical technicians. Mandible segmentation was usually done manually, which is a time-consuming and poorly reproducible process. This thesis presents four algorithms for mandible segmentation from CT and CBCT and contributes to some novel ideas for the development of automatic mandible segmentation for 3D VSP. We implement the segmentation approaches on head and neck CT/CBCT datasets and then evaluate the performance. Experimental results show that our proposed approaches for mandible segmentation in CT/CBCT datasets exhibit high accuracy

METGAN: Generative Tumour Inpainting and Modality Synthesis in Light Sheet Microscopy

Novel multimodal imaging methods are capable of generating extensive, super high resolution datasets for preclinical research. Yet, a massive lack of annotations prevents the broad use of deep learning to analyze such data. So far, existing generative models fail to mitigate this problem because of frequent labeling errors. In this paper, we introduce a novel generative method which leverages real anatomical information to generate realistic image-label pairs of tumours. We construct a dual-pathway generator, for the anatomical image and label, trained in a cycle-consistent setup, constrained by an independent, pretrained segmentor. The generated images yield significant quantitative improvement compared to existing methods. To validate the quality of synthesis, we train segmentation networks on a dataset augmented with the synthetic data, substantially improving the segmentation over baseline

Review on Augmented Reality in Oral and Cranio-Maxillofacial Surgery: Toward 'Surgery-Specific' Head-Up Displays

In recent years, there has been an increasing interest towards the augmented reality as applied to the surgical field. We conducted a systematic review of literature classifying the augmented reality applications in oral and cranio-maxillofacial surgery (OCMS) in order to pave the way to future solutions that may ease the adoption of AR guidance in surgical practice. Publications containing the terms 'augmented reality' AND 'maxillofacial surgery', and the terms 'augmented reality' AND 'oral surgery' were searched in the PubMed database. Through the selected studies, we performed a preliminary breakdown according to general aspects, such as surgical subspecialty, year of publication and country of research; then, a more specific breakdown was provided according to technical features of AR-based devices, such as virtual data source, visualization processing mode, tracking mode, registration technique and AR display type. The systematic search identified 30 eligible publications. Most studies (14) were in orthognatic surgery, the minority (2) concerned traumatology, while 6 studies were in oncology and 8 in general OCMS. In 8 of 30 studies the AR systems were based on a head-mounted approach using smart glasses or headsets. In most of these cases (7), a video-see-through mode was implemented, while only 1 study described an optical-see-through mode. In the remaining 22 studies, the AR content was displayed on 2D displays (10), full-parallax 3D displays (6) and projectors (5). In 1 case the AR display type is not specified. AR applications are of increasing interest and adoption in oral and cranio-maxillofacial surgery, however, the quality of the AR experience represents the key requisite for a successful result. Widespread use of AR systems in the operating room may be encouraged by the availability of 'surgery-specific' head-mounted devices that should guarantee the accuracy required for surgical tasks and the optimal ergonomics

Automated Segmentation of Temporal Bone Structures

Mastoidectomy is a challenging surgical procedure that is difficult to perform and practice. As supplementation to current training techniques, surgical simulators have been developed with the ability to visualize and operate on temporal bone anatomy. Medical image segmentation is done to create three-dimensional models of anatomical structures for simulation. Manual segmentation is an accurate but time-consuming process that requires an expert to label each structure on images. An automatic method for segmentation would allow for more practical model creation. The objective of this work was to create an automated segmentation algorithm for structures of the temporal bone relevant to mastoidectomy. The first method explored was multi-atlas based segmentation of the sigmoid sinus which produced accurate and consistent results. In order to segment other structures and improve robustness and accuracy, two convolutional neural networks were compared. The convolutional neural network implementation produced results that were more accurate than previously published work