The availability of massive amounts of data in histopathological whole-slide images (WSIs) has enabled the application of deep learning models and especially convolutional neural networks (CNNs), which have shown a high potential for improvement in cancer diagnosis. However, storage and transmission of large amounts of data such as gigapixel histopathological WSIs are challenging. Exploiting lossy compression algorithms for medical images is controversial but, as long as the clinical diagnosis is not affected, is acceptable. We study the impact of JPEG 2000 compression on our proposed CNN-based algorithm, which has produced performance comparable to that of pathologists and which was ranked second place in the CAMELYON17 challenge. Detecting tumor metastases in hematoxylin and eosin-stained tissue sections of breast lymph nodes is evaluated and compared with the pathologists’ diagnoses in three different experimental setups. Our experiments show that the CNN model is robust against compression ratios up to 24:1 when it is trained on uncompressed high-quality images. We demonstrate that a model trained on lower quality images—i.e., lossy compressed images—depicts a classification performance that is significantly improved for the corresponding compression ratio. Moreover, it is also observed that the model performs equally well on all higher-quality images. These properties will help to design cloud-based computer-aided diagnosis (CAD) systems, e.g., telemedicine that employ deep CNN models that are more robust to image quality variations due to compression required to address data storage and transmission constraints. However, the results presented are specific to the CAD system and application described, and further work is needed to examine whether they generalize to other systems and applications.
Imaging mass spectrometry (IMS) is a novel molecular imaging technique to investigate how molecules are distributed between tumors and within tumor region in order to shed light into tumor biology or find potential biomarkers. Convolutional neural networks (CNNs) have proven to be very potent classifiers often outperforming other machine learning algorithms, especially in computational pathology. To overcome the challenge of complexity and high-dimensionality of the IMS data, the proposed CNNs are either very deep or use large kernels, which results in large amount of parameters and therefore a high computational complexity. An alternative is down-sampling the data, which inherently leads to a loss of information. In this paper, we propose using dilated CNNs as a possible solution to this challenge, since it allows for an increase of the receptive field size, neither by increasing the network parameters nor by decreasing the input signal resolution. Since the mass signature of cancer biomarkers are distributed over the whole mass spectrum, both locally- and globally-distributed patterns need to be captured to correctly classify the spectrum. By experiment, we show that employing dilated convolutions in the architecture of a CNN leads to a higher performance in tumor classification. Our proposed model outperforms the state-of-the-art for tumor classification in both clinical lung and bladder datasets by 1-3%.
3D ultrasound (US) transducers will improve the quality of image-guided medical interventions if an automated detection of the needle becomes possible. Image-based detection of the needle is challenging due to the presence of other echogenic structures in the acquired data, inconsistent visibility of needle parts and the low quality in US imaging. As the currently applied approaches for needle detection classify each voxel individually, they do not consider the global relations between the voxels. In this work, we introduce coherent needle labeling by using dense conditional random fields over a volume, along with 3D space-frequency features. The proposal includes long-distance dependencies in voxel pairs according to their similarities in the feature space and their spatial distance. This post-processing stage leads to better label assignment of volume voxels and a more compact and coherent segmented region. Our ex-vivo experiments based on measuring the F-1, F-2 and IoU scores show that the performance improves a significant 10-20 % compared with only using the linear SVM as a baseline for voxel classification.
Advanced image analysis can lead to automated examination to histopatholgy images which is essential for ob- jective and fast cancer diagnosis. Recently deep learning methods, in particular Convolutional Neural Networks (CNNs), have shown exceptionally successful performance on medical image analysis as well as computational histopathology. Because Whole-Slide Images (WSIs) have a very large size, the CNN models are commonly applied to classify WSIs per patch. Although a CNN is trained on a large part of the input space, the spatial dependencies between patches are ignored and the inference is performed only on appearance of the individual patches. Therefore, prediction on the neighboring regions can be inconsistent. In this paper, we apply Con- ditional Random Fields (CRFs) over latent spaces of a trained deep CNN in order to jointly assign labels to the patches. In our approach, extracted compact features from intermediate layers of a CNN are considered as observations in a fully-connected CRF model. This leads to performing inference on a wider context rather than appearance of individual patches. Experiments show an improvement of approximately 3.9% on average FROC score for tumorous region detection in histopathology WSIs. Our proposed model, trained on the Camelyon171 ISBI challenge dataset, won the 2nd place with a kappa score of 0.8759 in patient-level pathologic lymph node classification for breast cancer detection.
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