Fiducial marker recovery and detection from severely truncated data in navigation assisted spine surgery

Fiducial markers are commonly used in navigation assisted minimally invasive spine surgery (MISS) and they help transfer image coordinates into real world coordinates. In practice, these markers might be located outside the field-of-view (FOV), due to the limited detector sizes of C-arm cone-beam computed tomography (CBCT) systems used in intraoperative surgeries. As a consequence, reconstructed markers in CBCT volumes suffer from artifacts and have distorted shapes, which sets an obstacle for navigation. In this work, we propose two fiducial marker detection methods: direct detection from distorted markers (direct method) and detection after marker recovery (recovery method). For direct detection from distorted markers in reconstructed volumes, an efficient automatic marker detection method using two neural networks and a conventional circle detection algorithm is proposed. For marker recovery, a task-specific learning strategy is proposed to recover markers from severely truncated data. Afterwards, a conventional marker detection algorithm is applied for position detection. The two methods are evaluated on simulated data and real data, both achieving a marker registration error smaller than 0.2 mm. Our experiments demonstrate that the direct method is capable of detecting distorted markers accurately and the recovery method with task-specific learning has high robustness and generalizability on various data sets. In addition, the task-specific learning is able to reconstruct other structures of interest accurately, e.g. ribs for image-guided needle biopsy, from severely truncated data, which empowers CBCT systems with new potential applications.

Module-Power Prediction from PL Measurements using Deep Learning

The individual causes for power loss of photovoltaic modules are investigated for quite some time. Recently, it has been shown that the power loss of a module is, for example, related to the fraction of inactive areas. While these areas can be easily identified from electroluminescense (EL) images, this is much harder for photoluminescence (PL) images. With this work, we close the gap between power regression from EL and PL images. We apply a deep convolutional neural network to predict the module power from PL images with a mean absolute error (MAE) of 4.4% or 11.7WP. Furthermore, we depict that regression maps computed from the embeddings of the trained network can be used to compute the localized power loss. Finally, we show that these regression maps can be used to identify inactive regions in PL images as well.

InSE-NET: A Perceptually Coded Audio Quality Model based on CNN

Automatic coded audio quality assessment is an important task whose progress is hampered by the scarcity of human annotations, poor generalization to unseen codecs, bitrates, content-types, and a lack of flexibility of existing approaches. One of the typical human-perception-related metrics, ViSQOL v3 (ViV3), has been proven to provide a high correlation to the quality scores rated by humans. In this study, we take steps to tackle problems of predicting coded audio quality by completely utilizing programmatically generated data that is informed with expert domain knowledge. We propose a learnable neural network, entitled InSE-NET, with a backbone of Inception and Squeeze-and-Excitation modules to assess the perceived quality of coded audio at a 48kHz sample rate. We demonstrate that synthetic data augmentation is capable of enhancing the prediction. Our proposed method is intrusive, i.e. it requires Gammatone spectrograms of unencoded reference signals. Besides a comparable performance to ViV3, our approach provides a more robust prediction towards higher bitrates.

Inter-Species Cell Detection: Datasets on pulmonary hemosiderophages in equine, human and feline specimens

Pulmonary hemorrhage (P-Hem) occurs among multiple species and can have various causes. Cytology of bronchoalveolarlavage fluid (BALF) using a 5-tier scoring system of alveolar macrophages based on their hemosiderin content is considered the most sensitive diagnostic method. We introduce a novel, fully annotated multi-species P-Hem dataset which consists of 74 cytology whole slide images (WSIs) with equine, feline and human samples. To create this high-quality and high-quantity dataset, we developed an annotation pipeline combining human expertise with deep learning and data visualisation techniques. We applied a deep learning-based object detection approach trained on 17 expertly annotated equine WSIs, to the remaining 39 equine, 12 human and 7 feline WSIs. The resulting annotations were semi-automatically screened for errors on multiple types of specialised annotation maps and finally reviewed by a trained pathologists. Our dataset contains a total of 297,383 hemosiderophages classified into five grades. It is one of the largest publicly availableWSIs datasets with respect to the number of annotations, the scanned area and the number of species covered.

Known Operator Learning and Hybrid Machine Learning in Medical Imaging --- A Review of the Past, the Present, and the Future

In this article, we perform a review of the state-of-the-art of hybrid machine learning in medical imaging. We start with a short summary of the general developments of the past in machine learning and how general and specialized approaches have been in competition in the past decades. A particular focus will be the theoretical and experimental evidence pro and contra hybrid modelling. Next, we inspect several new developments regarding hybrid machine learning with a particular focus on so-called known operator learning and how hybrid approaches gain more and more momentum across essentially all applications in medical imaging and medical image analysis. As we will point out by numerous examples, hybrid models are taking over in image reconstruction and analysis. Even domains such as physical simulation and scanner and acquisition design are being addressed using machine learning grey box modelling approaches. Towards the end of the article, we will investigate a few future directions and point out relevant areas in which hybrid modelling, meta learning, and other domains will likely be able to drive the state-of-the-art ahead.

Deep Iterative 2D/3D Registration

Deep Learning-based 2D/3D registration methods are highly robust but often lack the necessary registration accuracy for clinical application. A refinement step using the classical optimization-based 2D/3D registration method applied in combination with Deep Learning-based techniques can provide the required accuracy. However, it also increases the runtime. In this work, we propose a novel Deep Learning driven 2D/3D registration framework that can be used end-to-end for iterative registration tasks without relying on any further refinement step. We accomplish this by learning the update step of the 2D/3D registration framework using Point-to-Plane Correspondences. The update step is learned using iterative residual refinement-based optical flow estimation, in combination with the Point-to-Plane correspondence solver embedded as a known operator. Our proposed method achieves an average runtime of around 8s, a mean re-projection distance error of 0.60 $\pm$ 0.40 mm with a success ratio of 97 percent and a capture range of 60 mm. The combination of high registration accuracy, high robustness, and fast runtime makes our solution ideal for clinical applications.

Automatic and explainable grading of meningiomas from histopathology images

Meningioma is one of the most prevalent brain tumors in adults. To determine its malignancy, it is graded by a pathologist into three grades according to WHO standards. This grade plays a decisive role in treatment, and yet may be subject to inter-rater discordance. In this work, we present and compare three approaches towards fully automatic meningioma grading from histology whole slide images. All approaches are following a two-stage paradigm, where we first identify a region of interest based on the detection of mitotic figures in the slide using a state-of-the-art object detection deep learning network. This region of highest mitotic rate is considered characteristic for biological tumor behavior. In the second stage, we calculate a score corresponding to tumor malignancy based on information contained in this region using three different settings. In a first approach, image patches are sampled from this region and regression is based on morphological features encoded by a ResNet-based network. We compare this to learning a logistic regression from the determined mitotic count, an approach which is easily traceable and explainable. Lastly, we combine both approaches in a single network. We trained the pipeline on 951 slides from 341 patients and evaluated them on a separate set of 141 slides from 43 patients. All approaches yield a high correlation to the WHO grade. The logistic regression and the combined approach had the best results in our experiments, yielding correct predictions in 32 and 33 of all cases, respectively, with the image-based approach only predicting 25 cases correctly. Spearman's correlation was 0.716, 0.792 and 0.790 respectively. It may seem counterintuitive at first that morphological features provided by image patches do not improve model performance. Yet, this mirrors the criteria of the grading scheme, where mitotic count is the only unequivocal parameter.

FlexParser -- the adaptive log file parser for continuous results in a changing world

Any modern system writes events into files, called log files. Those contain crucial information which are subject to various analyses. Examples range from cybersecurity, intrusion detection over usage analyses to trouble shooting. Before data analysis is possible, desired information needs to be extracted first out of the semi-structured log messages. State of the art event parsing often assumes static log events. However, any modern system is updated consistently and with updates also log file structures can change. We call those changes 'mutations' and study parsing performance for different mutation cases. Latest research discovers mutations using anomaly detection post mortem, however, does not cover actual continuous parsing. Thus, we propose a novel, flexible parser, called FlexParser which can extract desired values despite gradual changes in the log messages. It implies basic text preprocessing followed by a supervised Deep Learning method. We train a stateful LSTM on parsing one event per data set. Statefulness enforces the model to learn log message structures across several messages. Our model was tested on seven different, publicly available log file data sets and various kinds of mutations. Exhibiting an average F1-Score of 0.98, it outperforms other Deep Learning methods as well as state-of-the-art unsupervised parsers.

SmartPatch: Improving Handwritten Word Imitation with Patch Discriminators

As of recent generative adversarial networks have allowed for big leaps in the realism of generated images in diverse domains, not the least of which being handwritten text generation. The generation of realistic-looking hand-written text is important because it can be used for data augmentation in handwritten text recognition (HTR) systems or human-computer interaction. We propose SmartPatch, a new technique increasing the performance of current state-of-the-art methods by augmenting the training feedback with a tailored solution to mitigate pen-level artifacts. We combine the well-known patch loss with information gathered from the parallel trained handwritten text recognition system and the separate characters of the word. This leads to a more enhanced local discriminator and results in more realistic and higher-quality generated handwritten words.

Robust partial Fourier reconstruction for diffusion-weighted imaging using a recurrent convolutional neural network

Purpose: To develop an algorithm for robust partial Fourier (PF) reconstruction applicable to diffusion-weighted (DW) images with non-smooth phase variations. Methods: Based on an unrolled proximal splitting algorithm, a neural network architecture is derived which alternates between data consistency operations and regularization implemented by recurrent convolutions. In order to exploit correlations, multiple repetitions of the same slice are jointly reconstructed under consideration of permutation-equivariance. The proposed method is trained on DW liver data of 60 volunteers and evaluated on retrospectively and prospectively sub-sampled data of different anatomies and resolutions. In addition, the benefits of using a recurrent network over other unrolling strategies is investigated. Results: Conventional PF techniques can be significantly outperformed in terms of quantitative measures as well as perceptual image quality. The proposed method is able to generalize well to brain data with contrasts and resolution not present in the training set. The reduction in echo time (TE) associated with prospective PF-sampling enables DW imaging with higher signal. Also, the TE increase in acquisitions with higher resolution can be compensated for. It can be shown that unrolling by means of a recurrent network produced better results than using a weight-shared network or a cascade of networks. Conclusion: This work demonstrates that robust PF reconstruction of DW data is feasible even at strong PF factors in applications with severe phase variations. Since the proposed method does not rely on smoothness priors of the phase but uses learned recurrent convolutions instead, artifacts of conventional PF methods can be avoided.