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Register a new userFastSurfer -- A fast and accurate deep learning based neuroimaging pipeline
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Traditional neuroimage analysis pipelines involve computationally intensive, time-consuming optimization steps, and thus, do not scale well to large cohort studies with thousands or tens of thousands of individuals. In this work we propose a fast and accurate deep learning based neuroimaging pipeline for the automated processing of structural human brain MRI scans, replicating FreeSurfers anatomical segmentation including surface reconstruction and cortical parcellation. To this end, we introduce an advanced deep learning architecture capable of whole brain segmentation into 95 classes. The network architecture incorporates local and global competition via competitive dense blocks and competitive skip pathways, as well as multi-slice information aggregation that specifically tailor network performance towards accurate segmentation of both cortical and sub-cortical structures. Further, we perform fast cortical surface reconstruction and thickness analysis by introducing a spectral spherical embedding and by directly mapping the cortical labels from the image to the surface. This approach provides a full FreeSurfer alternative for volumetric analysis (in under 1 minute) and surface-based thickness analysis (within only around 1h runtime). For sustainability of this approach we perform extensive validation: we assert high segmentation accuracy on several unseen datasets, measure generalizability and demonstrate increased test-retest reliability, and high sensitivity to group differences in dementia.
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The relationship between cognition and white matter hyperintensities (WMH) volumes often depends on the accuracy of the lesion segmentation algorithm used. As such, accurate detection and quantification of WMH is of great interest. Here, we use a deep learning-based WMH segmentation algorithm, StackGen-Net, to detect and quantify WMH on 3D FLAIR volumes from ADNI. We used a subset of subjects (n=20) and obtained manual WMH segmentations by an experienced neuro-radiologist to demonstrate the accuracy of our algorithm. On a larger cohort of subjects (n=290), we observed that larger WMH volumes correlated with worse performance on executive function (P=.004), memory (P=.01), and language (P=.005).
We present an automated method to track and identify neurons in C. elegans, called fast Deep Learning Correspondence or fDLC, based on the transformer network architecture. The model is trained once on empirically derived synthetic data and then predicts neural correspondence across held-out real animals via transfer learning. The same pre-trained model both tracks neurons across time and identifies corresponding neurons across individuals. Performance is evaluated against hand-annotated datasets, including NeuroPAL [1]. Using only position information, the method achieves 80.0% accuracy at tracking neurons within an individual and 65.8% accuracy at identifying neurons across individuals. Accuracy is even higher on a published dataset [2]. Accuracy reaches 76.5% when using color information from NeuroPAL. Unlike previous methods, fDLC does not require straightening or transforming the animal into a canonical coordinate system. The method is fast and predicts correspondence in 10 ms making it suitable for future real-time applications.
Brain tumor segmentation is a challenging problem in medical image analysis. The goal of brain tumor segmentation is to generate accurate delineation of brain tumor regions with correctly located masks. In recent years, deep learning methods have shown very promising performance in solving various computer vision problems, such as image classification, object detection and semantic segmentation. A number of deep learning based methods have been applied to brain tumor segmentation and achieved impressive system performance. Considering state-of-the-art technologies and their performance, the purpose of this paper is to provide a comprehensive survey of recently developed deep learning based brain tumor segmentation techniques. The established works included in this survey extensively cover technical aspects such as the strengths and weaknesses of different approaches, pre- and post-processing frameworks, datasets and evaluation metrics. Finally, we conclude this survey by discussing the potential development in future research work.
AI-powered automatic camera scene detection mode is nowadays available in nearly any modern smartphone, though the problem of accurate scene prediction has not yet been addressed by the research community. This paper for the first time carefully defines this problem and proposes a novel Camera Scene Detection Dataset (CamSDD) containing more than 11K manually crawled images belonging to 30 different scene categories. We propose an efficient and NPU-friendly CNN model for this task that demonstrates a top-3 accuracy of 99.5% on this dataset and achieves more than 200 FPS on the recent mobile SoCs. An additional in-the-wild evaluation of the obtained solution is performed to analyze its performance and limitation in the real-world scenarios. The dataset and pre-trained models used in this paper are available on the project website.
Deep learning based Quantitative Susceptibility Mapping (QSM) has shown great potential in recent years, outperforming traditional non-learning approaches in speed and accuracy. However, many of the current deep learning approaches are not data consistent, require in vivo training data or do not solve all steps of the QSM processing pipeline. Here we aim to overcome these limitations and developed a framework to solve the QSM processing steps jointly. We developed a new hybrid training data generation method that enables the end-to-end training for solving background field correction and dipole inversion in a data-consistent fashion using a variational network that combines the QSM model term and a learned regularizer. We demonstrate that NeXtQSM overcomes the limitations of previous model-agnostic deep learning methods and show that NeXtQSM offers a complete deep learning based pipeline for computing robust, fast and accurate quantitative susceptibility maps.
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