We present a rotation-equivariant unsupervised learning framework for the sparse deconvolution of non-negative scalar fields defined on the unit sphere. Spherical signals with multiple peaks naturally arise in Diffusion MRI (dMRI), where each voxel consists of one or more signal sources corresponding to anisotropic tissue structure such as white matter. Due to spatial and spectral partial voluming, clinically-feasible dMRI struggles to resolve crossing-fiber white matter configurations, leading to extensive development in spherical deconvolution methodology to recover underlying fiber directions. However, these methods are typically linear and struggle with small crossing-angles and partial volume fraction estimation. In this work, we improve on current methodologies by nonlinearly estimating fiber structures via unsupervised spherical convolutional networks with guaranteed equivariance to spherical rotation. Experimentally, we first validate our proposition via extensive single and multi-shell synthetic benchmarks demonstrating competitive performance against common baselines. We then show improved downstream performance on fiber tractography measures on the Tractometer benchmark dataset. Finally, we show downstream improvements in terms of tractography and partial volume estimation on a multi-shell dataset of human subjects.
Confocal histology provides an opportunity to establish intra-voxel fiber orientation distributions that can be used to quantitatively assess the biological relevance of diffusion weighted MRI models, e.g., constrained spherical deconvolution (CSD). Here, we apply deep learning to investigate the potential of single shell diffusion weighted MRI to explain histologically observed fiber orientation distributions (FOD) and compare the derived deep learning model with a leading CSD approach. This study (1) demonstrates that there exists additional information in the diffusion signal that is not cu…
In single-molecule super-resolution microscopy, engineered point-spread functions (PSFs) are designed to efficiently encode new molecular properties, such as 3D orientation, into complex spatial features captured by a camera. To fully benefit from their optimality, algorithms must estimate multi-dimensional parameters such as molecular position and orientation in the presence of PSF overlap and model-experiment mismatches. Here, we present a novel joint sparse deconvolution algorithm based on the decomposition of fluorescence images into six basis images that characterize molecular orientation…
Deforestation has become a significant contributing factor to climate change and, due to this, both classifying the drivers and predicting segmentation maps of deforestation has attracted significant interest. In this work, we develop a rotation equivariant convolutional neural network model to predict the drivers and generate segmentation maps of deforestation events from Landsat 8 satellite images. This outperforms previous methods in classifying the drivers and predicting the segmentation map of deforestation, offering a 9% improvement in classification accuracy and a 7% improvement in segm…
Vanderbilt University（范德堡大学）；University of Pittsburgh（匹兹堡大学）；Vanderbilt University Medical Center（范德堡大学医学中心）
Diffusion-weighted magnetic resonance imaging (DW-MRI) is the only non-invasive approach for estimation of intra-voxel tissue microarchitecture and reconstruction of in vivo neural pathways for the human brain. With improvement in accelerated MRI acquisition technologies, DW-MRI protocols that make use of multiple levels of diffusion sensitization have gained popularity. A well-known advanced method for reconstruction of white matter microstructure that uses multi-shell data is multi-tissue constrained spherical deconvolution (MT-CSD). MT-CSD substantially improves the resolution of intra-voxe…
Ground-truth effects in learning-based fiber orientation distribution estimation in neonatal brains
Signal Processing Laboratory (LTS5)（信号处理实验室）；École Polytechnique Fédérale de Lausanne (EPFL)（瑞士联邦理工学院洛桑分校）；Department of Radiology, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL)（洛桑大学医院放射科及洛桑大学）；College of Electronic and Information Engineering, Tongji University（同济大学电子与信息学院）；CIBM Center for Biomedical Imaging（生物医学成像中心）；Computational Radiology Laboratory, Department of Radiology, Boston Children’s Hospital and Harvard Medical School（波士顿儿童医院放射科计算放射实验室及哈佛医学院）；Department of Radiological Sciences, University of California Irvine（加州大学 Irvine 分校放射科学系）
Equivariant Imaging Biomarkers for Robust Unsupervised Segmentation of Histopathology
Department of Biomedical Engineering, Yale University（生物医学工程系，耶鲁大学）；Department of Radiology & Biomedical Imaging, Yale University（放射科与生物医学成像系，耶鲁大学）；Department of Urology, Yale University（泌尿外科系，耶鲁大学）；Medical Scientist Training Program, Yale University（医学科学家培训计划，耶鲁大学）
Unsupervised learning enables modeling complex images without the need for annotations. The representation learned by such models can facilitate any subsequent analysis of large image datasets. However, some generative factors that cause irrelevant variations in images can potentially get entangled in such a learned representation causing the risk of negatively affecting any subsequent use. The orientation of imaged objects, for instance, is often arbitrary/irrelevant, thus it can be desired to learn a representation in which the orientation information is disentangled from all other factors. …
King’s College London（伦敦国王学院）；University College London（伦敦大学学院）；National Hospital for Neurology and Neurosurgery（国立神经病学和神经外科医院）；King’s College Hospital Foundation Trust（国王学院医院基金会信托）；Epilepsy Society（癫痫协会）
Accurate local fiber orientation distribution (FOD) modeling based on diffusion magnetic resonance imaging (dMRI) capable of resolving complex fiber configurations benefits from specific acquisition protocols that sample a high number of gradient directions (b-vecs), a high maximum b-value(b-vals), and multiple b-values (multi-shell). However, acquisition time is limited in a clinical setting and commercial scanners may not provide such dMRI sequences. Therefore, dMRI is often acquired as single-shell (single b-value). In this work, we learn improved FODs for commercially acquired MRI. We eval…
Histology images are inherently symmetric under rotation, where each orientation is equally as likely to appear. However, this rotational symmetry is not widely utilised as prior knowledge in modern Convolutional Neural Networks (CNNs), resulting in data hungry models that learn independent features at each orientation. Allowing CNNs to be rotation-equivariant removes the necessity to learn this set of transformations from the data and instead frees up model capacity, allowing more discriminative features to be learned. This reduction in the number of required parameters also reduces the risk …
