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4D CT imaging is an essential component of radiotherapy of thoracic/abdominal tumors. 4D CT images are, however, often affected by artifacts that compromise treatment planning quality. In this work, deep learning (DL)-based conditional inpainting is proposed to restore anatomically correct image information of artifact-affected areas. The restoration approach consists of a two-stage process: DL-based detection of common interpolation (INT) and double structure (DS) artifacts, followed by conditional inpainting applied to the artifact areas. In this context, conditional refers to a guidance of the inpainting process by patient-specific image data to ensure anatomically reliable results. The study is based on 65 in-house 4D CT images of lung cancer patients (48 with only slight artifacts, 17 with pronounced artifacts) and two publicly available 4D CT data sets that serve as independent external test sets. Automated artifact detection revealed a ROC-AUC of 0.99 for INT and of 0.97 for DS artifacts (in-house data). The proposed inpainting method decreased the average root mean squared error (RMSE) by 52%(INT) and 59% (DS) for the in-house data. For the external test data sets, the RMSE improvement is similar (50% and 59 %, respectively). Applied to 4D CT data with pronounced artifacts (not part of the training set), 72% of the detectable artifacts were removed. The results highlight the potential of DL-based inpainting for restoration of artifact-affected 4D CT data. Compared to recent 4D CT inpainting and restoration approaches, the proposed methodology illustrates the advantages of exploiting patient-specific prior image information., Comment: 13 pages

Histopathologic diagnosis relies on simultaneous integration of information from a broad range of scales, ranging from nuclear aberrations ($\approx \mathcal{O}(0.1{\mu m})$) through cellular structures ($\approx \mathcal{O}(10{\mu m})$) to the global tissue architecture ($\gtrapprox \mathcal{O}(1{mm})$). To explicitly mimic how human pathologists combine multi-scale information, we introduce a family of multi-encoder FCNs with deep fusion. We present a simple block for merging model paths with differing spatial scales in a spatial relationship-preserving fashion, which can readily be included in standard encoder-decoder networks. Additionally, a context classification gate block is proposed as an alternative for the incorporation of global context. Our experiments were performed on three publicly available whole-slide images of recent challenges (PAIP 2019, BACH 2020, CAMELYON 2016). The multi-scale architectures consistently outperformed the baseline single-scale U-Nets by a large margin. They benefit from local as well as global context and particularly a combination of both. If feature maps from different scales are fused, doing so in a manner preserving spatial relationships was found to be beneficial. Deep guidance by a context classification loss appeared to improve model training at low computational costs. All multi-scale models had a reduced GPU memory footprint compared to ensembles of individual U-Nets trained on different image scales. Additional path fusions were shown to be possible at low computational cost, opening up possibilities for further, systematic and task-specific architecture optimization. The findings demonstrate the potential of the presented family of human-inspired, end-to-end trainable, multi-scale multi-encoder FCNs to improve deep histopathologic diagnosis by extensive integration of largely different spatial scales., Comment: Accepted for Medical Image Analysis

Objective: This work addresses two key problems of skin lesion classification. The first problem is the effective use of high-resolution images with pretrained standard architectures for image classification. The second problem is the high class imbalance encountered in real-world multi-class datasets. Methods: To use high-resolution images, we propose a novel patch-based attention architecture that provides global context between small, high-resolution patches. We modify three pretrained architectures and study the performance of patch-based attention. To counter class imbalance problems, we compare oversampling, balanced batch sampling, and class-specific loss weighting. Additionally, we propose a novel diagnosis-guided loss weighting method which takes the method used for ground-truth annotation into account. Results: Our patch-based attention mechanism outperforms previous methods and improves the mean sensitivity by 7%. Class balancing significantly improves the mean sensitivity and we show that our diagnosis-guided loss weighting method improves the mean sensitivity by 3% over normal loss balancing. Conclusion: The novel patch-based attention mechanism can be integrated into pretrained architectures and provides global context between local patches while outperforming other patch-based methods. Hence, pretrained architectures can be readily used with high-resolution images without downsampling. The new diagnosis-guided loss weighting method outperforms other methods and allows for effective training when facing class imbalance. Significance: The proposed methods improve automatic skin lesion classification. They can be extended to other clinical applications where high-resolution image data and class imbalance are relevant., Comment: Accepted for publication in IEEE Transactions on Biomedical Engineering

In this paper we present the methods of our submission to the ISIC 2018 challenge for skin lesion diagnosis (Task 3). The dataset consists of 10000 images with seven image-level classes to be distinguished by an automated algorithm. We employ an ensemble of convolutional neural networks for this task. In particular, we fine-tune pretrained state-of-the-art deep learning models such as Densenet, SENet and ResNeXt. We identify heavy class imbalance as a key problem for this challenge and consider multiple balancing approaches such as loss weighting and balanced batch sampling. Another important feature of our pipeline is the use of a vast amount of unscaled crops for evaluation. Last, we consider meta learning approaches for the final predictions. Our team placed second at the challenge while being the best approach using only publicly available data., Comment: ISIC Skin Image Analysis Workshop and Challenge @ MICCAI 2018. Second place at challenge, best with public data, see https://challenge2018.isic-archive.com/leaderboards/