In novelty detection, the goal is to decide if a new data point should be categorized as an inlier or an outlier, given a training dataset that primarily captures the inlier distribution. Recent approaches typically use deep encoder and decoder network frameworks to derive a reconstruction error, and employ this error either to determine a novelty score, or as the basis for a one-class classifier. In this research, we use a similar framework but with a lightweight deep network, and we adopt a probabilistic score with reconstruction error. Our methodology calculates the probability of whether the sample comes from the inlier distribution or not. This work makes two key contributions. The first is that we compute the novelty probability by linearizing the manifold that holds the structure of the inlier distribution. This allows us to interpret how the probability is distributed and can be determined in relation to the local coordinates of the manifold tangent space. The second contribution is that we improve the training protocol for the network. Our results indicate that our approach is effective at learning the target class, and it outperforms recent state-of-the-art methods on several benchmark datasets.

Automatic segmentation of medical images is a key step for diagnostic and interventional tasks. However, achieving this requires large amounts of annotated volumes, which can be tedious and time-consuming task for expert annotators. In this paper, we introduce DeepEdit, a deep learning-based method for volumetric medical image annotation, that allows automatic and semi-automatic segmentation, and click-based refinement. DeepEdit combines the power of two methods: a non-interactive (i.e. automatic segmentation using nnU-Net, UNET or UNETR) and an interactive segmentation method (i.e. DeepGrow), into a single deep learning model. It allows easy integration of uncertainty-based ranking strategies (i.e. aleatoric and epistemic uncertainty computation) and active learning. We propose and implement a method for training DeepEdit by using standard training combined with user interaction simulation. Once trained, DeepEdit allows clinicians to quickly segment their datasets by using the algorithm in auto segmentation mode or by providing clicks via a user interface (i.e. 3D Slicer, OHIF). We show the value of DeepEdit through evaluation on the PROSTATEx dataset for prostate/prostatic lesions and the Multi-Atlas Labeling Beyond the Cranial Vault (BTCV) dataset for abdominal CT segmentation, using state-of-the-art network architectures as baseline for comparison. DeepEdit could reduce the time and effort annotating 3D medical images compared to DeepGrow alone. Source code is available at https://github.com/Project-MONAI/MONAILabel

The lack of annotated datasets is a major bottleneck for training new task-specific supervised machine learning models, considering that manual annotation is extremely expensive and time-consuming. To address this problem, we present MONAI Label, a free and open-source framework that facilitates the development of applications based on artificial intelligence (AI) models that aim at reducing the time required to annotate radiology datasets. Through MONAI Label, researchers can develop AI annotation applications focusing on their domain of expertise. It allows researchers to readily deploy their apps as services, which can be made available to clinicians via their preferred user interface. Currently, MONAI Label readily supports locally installed (3D Slicer) and web-based (OHIF) frontends and offers two active learning strategies to facilitate and speed up the training of segmentation algorithms. MONAI Label allows researchers to make incremental improvements to their AI-based annotation application by making them available to other researchers and clinicians alike. Additionally, MONAI Label provides sample AI-based interactive and non-interactive labeling applications, that can be used directly off the shelf, as plug-and-play to any given dataset. Significant reduced annotation times using the interactive model can be observed on two public datasets.

Hyperspectral imaging has the potential to improve intraoperative decision making if tissue characterisation is performed in real-time and with high-resolution. Hyperspectral snapshot mosaic sensors offer a promising approach due to their fast acquisition speed and compact size. However, a demosaicking algorithm is required to fully recover the spatial and spectral information of the snapshot images. Most state-of-the-art demosaicking algorithms require ground-truth training data with paired snapshot and high-resolution hyperspectral images, but such imagery pairs with the exact same scene are physically impossible to acquire in intraoperative settings. In this work, we present a fully unsupervised hyperspectral image demosaicking algorithm which only requires exemplar snapshot images for training purposes. We regard hyperspectral demosaicking as an ill-posed linear inverse problem which we solve using a deep neural network. We take advantage of the spectral correlation occurring in natural scenes to design a novel inter spectral band regularisation term based on spatial gradient consistency. By combining our proposed term with standard regularisation techniques and exploiting a standard data fidelity term, we obtain an unsupervised loss function for training deep neural networks, which allows us to achieve real-time hyperspectral image demosaicking. Quantitative results on hyperspetral image datasets show that our unsupervised demosaicking approach can achieve similar performance to its supervised counter-part, and significantly outperform linear demosaicking. A qualitative user study on real snapshot hyperspectral surgical images confirms the results from the quantitative analysis. Our results suggest that the proposed unsupervised algorithm can achieve promising hyperspectral demosaicking in real-time thus advancing the suitability of the modality for intraoperative use.

Vestibular Schwannoma (VS) typically grows from the inner ear to the brain. It can be separated into two regions, intrameatal and extrameatal respectively corresponding to being inside or outside the inner ear canal. The growth of the extrameatal regions is a key factor that determines the disease management followed by the clinicians. In this work, a VS segmentation approach with subdivision into intra-/extra-meatal parts is presented. We annotated a dataset consisting of 227 T2 MRI instances, acquired longitudinally on 137 patients, excluding post-operative instances. We propose a staged approach, with the first stage performing the whole tumour segmentation and the second stage performing the intra-/extra-meatal segmentation using the T2 MRI along with the mask obtained from the first stage. To improve on the accuracy of the predicted meatal boundary, we introduce a task-specific loss which we call Boundary Distance Loss. The performance is evaluated in contrast to the direct intrameatal extrameatal segmentation task performance, i.e. the Baseline. Our proposed method, with the two-stage approach and the Boundary Distance Loss, achieved a Dice score of 0.8279+-0.2050 and 0.7744+-0.1352 for extrameatal and intrameatal regions respectively, significantly improving over the Baseline, which gave Dice score of 0.7939+-0.2325 and 0.7475+-0.1346 for the extrameatal and intrameatal regions respectively.

Automatic segmentation of lung lesions associated with COVID-19 in CT images requires large amount of annotated volumes. Annotations mandate expert knowledge and are time-intensive to obtain through fully manual segmentation methods. Additionally, lung lesions have large inter-patient variations, with some pathologies having similar visual appearance as healthy lung tissues. This poses a challenge when applying existing semi-automatic interactive segmentation techniques for data labelling. To address these challenges, we propose an efficient convolutional neural networks (CNNs) that can be learned online while the annotator provides scribble-based interaction. To accelerate learning from only the samples labelled through user-interactions, a patch-based approach is used for training the network. Moreover, we use weighted cross-entropy loss to address the class imbalance that may result from user-interactions. During online inference, the learned network is applied to the whole input volume using a fully convolutional approach. We compare our proposed method with state-of-the-art using synthetic scribbles and show that it outperforms existing methods on the task of annotating lung lesions associated with COVID-19, achieving 16% higher Dice score while reducing execution time by 3$\times$ and requiring 9000 lesser scribbles-based labelled voxels. Due to the online learning aspect, our approach adapts quickly to user input, resulting in high quality segmentation labels. Source code for ECONet is available at: https://github.com/masadcv/ECONet-MONAILabel.