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Determining early-stage prognostic markers and stratifying patients for effective treatment are two key challenges for improving outcomes for melanoma patients. Previous studies have used tumour transcriptome data to stratify patients into immune subgroups, which were associated with differential melanoma specific survival and potential treatment strategies. However, acquiring transcriptome data is a time-consuming and costly process. Moreover, it is not routinely used in the current clinical workflow. Here we attempt to overcome this by developing deep learning models to classify gigapixel H&E stained pathology slides, which are well established in clinical workflows, into these immune subgroups. Previous subtyping approaches have employed supervised learning which requires fully annotated data, or have only examined single genetic mutations in melanoma patients. We leverage a multiple-instance learning approach, which only requires slide-level labels and uses an attention mechanism to highlight regions of high importance to the classification. Moreover, we show that pathology-specific self-supervised models generate better representations compared to pathology-agnostic models for improving our model performance, achieving a mean AUC of 0.76 for classifying histopathology images as high or low immune subgroups. We anticipate that this method may allow us to find new biomarkers of high importance and could act as a tool for clinicians to infer the immune landscape of tumours and stratify patients, without needing to carry out additional expensive genetic tests., 8 pages (without appendices), 2 figures, submitted to MIDL 2022 conference proceedings

International audience; This book constitutes the refereed proceedings of the 4th International Workshop on Simulation and Synthesis in Medical Imaging, SASHIMI 2019, held in conjunction with MICCAI 2019, in Shenzhen, China, in October 2019.

Nuclear segmentation in histology images is a challenging task due to significant variations in the shape and appearance of nuclei. One of the main hurdles in nuclear instance segmentation is overlapping nuclei where a smart algorithm is needed to separate each nucleus. In this paper, we introduce a proposal-free deep learning based framework to address these challenges. To this end, we propose a spatially-aware network (SpaNet) to capture spatial information in a multi-scale manner. A dual-head variation of the SpaNet is first utilized to predict the pixel-wise segmentation and centroid detection maps of nuclei. Based on these outputs, a single-head SpaNet predicts the positional information related to each nucleus instance. Spectral clustering method is applied on the output of the last SpaNet, which utilizes the nuclear mask and the Gaussian-like detection map for determining the connected components and associated cluster identifiers, respectively. The output of the clustering method is the final nuclear instance segmentation mask. We applied our method on a publicly available multi-organ data set and achieved state-of-the-art performance for nuclear segmentation.

Computer-aided diagnosis systems for classification of different type of skin lesions have been an active field of research in recent decades. It has been shown that introducing lesions and their attributes masks into lesion classification pipeline can greatly improve the performance. In this paper, we propose a framework by incorporating transfer learning for segmenting lesions and their attributes based on the convolutional neural networks. The proposed framework is based on the encoder-decoder architecture which utilizes a variety of pre-trained networks in the encoding path and generates the prediction map by combining multi-scale information in decoding path using a pyramid pooling manner. To address the lack of training data and increase the proposed model generalization, an extensive set of novel domain-specific augmentation routines have been applied to simulate the real variations in dermoscopy images. Finally, by performing broad experiments on three different data sets obtained from International Skin Imaging Collaboration archive (ISIC2016, ISIC2017, and ISIC2018 challenges data sets), we show that the proposed method outperforms other state-of-the-art approaches for ISIC2016 and ISIC2017 segmentation task and achieved the first rank on the leader-board of ISIC2018 attribute detection task., 18 pages

Nuclei detection is an important task in the histology domain as it is a main step toward further analysis such as cell counting, cell segmentation, study of cell connections, etc. This is a challenging task due to the complex texture of histology image, variation in shape, and touching cells. To tackle these hurdles, many approaches have been proposed in the literature where deep learning methods stand on top in terms of performance. Hence, in this paper, we propose a novel framework for nuclei detection based on Mixture Density Networks (MDNs). These networks are suitable to map a single input to several possible outputs and we utilize this property to detect multiple seeds in a single image patch. A new modified form of a cost function is proposed for training and handling patches with missing nuclei. The probability maps of the nuclei in the individual patches are next combined to generate the final image-wide result. The experimental results show the state-of-the-art performance on complex colorectal adenocarcinoma dataset., Comment: 8 pages, 3 figures

A fundamental assumption in prosthetic dentistry is that the axis-orbital plane will usually be parallel to the horizontal reference plane. Most articulator systems have incorporated this concept into their designs and use orbitale as the anterior reference point for transferring the vertical position of the maxilla to the articulator. Clinical observations of Cantonese patients suggest that in some individuals the Frankfort plane may not be horizontal, thus the orientation of the casts in the articulator is incorrect with respect to the horizontal plane. The purpose of this study was to introduce a simple method for converting the conventional face-bow to postural face-bow to reproduce the orientation of the occlusal plane relative to the true horizontal plane with the patient in Natural Head Posture (NHP).

Screw-retained implant restorations have an advantage of predictable retention as well as retrievability, and obviate the risk of excessive sub-gingival cement commonly associated with cement retained implant restorations. Screw-retained restorations generally have screw access holes, which can compromise esthetics and weaken the porcelain around the holes. The purpose of this study is to describe the use of a separate overcasting crown design to cover the screw access hole of implant screw-retained prosthesis for improved esthetics.

Statistical shape modeling is a powerful tool for visualizing and quantifying geometric and functional patterns of the heart. After myocardial infarction (MI), the left ventricle typically remodels in response to physiological challenges. Several methods have been proposed in the literature to describe statistical shape changes. Which method best characterizes the left ventricular remodeling after MI is an open research question. A better descriptor of remodeling is expected to provide a more accurate evaluation of disease status in MI patients. We therefore designed a challenge to test shape characterization in MI given a set of three-dimensional left ventricular surface points. The training set comprised 100 MI patients, and 100 asymptomatic volunteers (AV). The challenge was initiated in 2015 at the Statistical Atlases and Computational Models of the Heart workshop, in conjunction with the MICCAI conference. The training set with labels was provided to participants, who were asked to submit the likelihood of MI from a different (validation) set of 200 cases (100 AV and 100 MI). Sensitivity, specificity, accuracy, and area under the receiver operating characteristic curve were used as the outcome measures. The goals of this challenge were to 1) establish a common dataset for evaluating statistical shape modeling algorithms in MI, and 2) test whether statistical shape modeling provides additional information characterizing MI patients over standard clinical measures. Eleven groups with a wide variety of classification and feature extraction approaches participated in this challenge. All methods achieved excellent classification results with accuracy ranges from 0.83 to 0.98. The areas under the receiver operating characteristic curves were all above 0.90. Four methods showed significantly higher performance than standard clinical measures. The dataset and software for evaluation are available from the Cardiac Atlas Project website. 1 1 http://www.cardiacatlas.org .

This paper demonstrates the potential for synthesis of medical images in one modality (e.g. MR) from images in another (e.g. CT) using a CycleGAN [24] architecture. The synthesis can be learned from unpaired images, and applied directly to expand the quantity of available training data for a given task. We demonstrate the application of this approach in synthesising cardiac MR images from CT images, using a dataset of MR and CT images coming from different patients. Since there can be no direct evaluation of the synthetic images, as no ground truth images exist, we demonstrate their utility by leveraging our synthetic data to achieve improved results in segmentation. Specifically, we show that training on both real and synthetic data increases accuracy by 15% compared to real data. Additionally, our synthetic data is of sufficient quality to be used alone to train a segmentation neural network, that achieves 95% of the accuracy of the same model trained on real data.