Data-driven Parameter Optimization and Spatial Awareness for Uniform Manifold Approximation and Projection (UMAP) of IMS data sets: A step towards parameter-free dimensionality reduction

Imaging Mass Spectrometry (IMS) is a powerful technique capable of extracting unlabeled spatial and chemical information from a biological tissue sample. Ever-increasing technological advancements have resulted in rapid growth of IMS data set sizes, scaling quadratically with the increasingly refined spatial resolution of its ion images....

Recurrent Inference Machines for accelerated MRI acquisition trained using simulated undersampled k-space data

Recently, many advancements have been made in accelerated MRI reconstruction with the use of neural networks. Such deep learning methods learn a suitable MRI prior distribution from large sets of training data. For MRI images acquired with an uncommon scanning sequence, large datasets required for training are not available. Additionally, deep...

On the Atoms of Robustness: Robust Matrix Decomposition for Spectral Imaging

Modern imaging modalities across many application domains increasingly acquire a large number of very high-dimensional measurements, commonly collecting hundreds to millions of variables per spatial resolution element. That high-dimensional nature can severely challenge traditional (often Euclidean distance based) approaches to noise and...

Data-Driven Soft Discriminant Maps: Class-aware Linear Feature Extraction in Imaging Mass Spectrometry

Retrieving actionable information from large datasets is increasingly computationally expensive due to the current trend of ever-increasing dataset sizes. Reducing dataset sizes with dimensionality reduction techniques is often necessary for statistical analysis techniques, such as classification, to be computationally feasible. Most...

Filtering Quasiperiodic Noise from Biomedical Images

In the field of biomedical imaging, images often report a combination of biologically induced variation, usually the goal of the imaging process (e.g. outlining an anatomical region or disease pattern), and non-biological variation, such as instrument or acquisition method-induced noise patterns. <br/>Since some medical decisions are made based...

Intensity-Aware Rank Estimation for Dimensionality Reduction in Imaging Mass Spectrometry

Imaging Mass Spectrometry (IMS) is a spectral imaging technique, which enables detection of the spatial distribution of molecules by collecting a mass spectrum for every pixel across a tissue sample. As such, IMS enables the detection of disease-introduced anomalies in tissue samples as well as the gaining of deeper insight on a molecular level...