Ahmed M. Raslan | Searcharxiv

arXiv2021

Human Brain Mapping with Multi-Thousand Channel PtNRGrids Resolves Novel Spatiotemporal Dynamics

Electrophysiological devices are critical for mapping eloquent and diseased brain regions and for therapeutic neuromodulation in clinical settings and are extensively utilized for research in brain-machine interfaces. However, the existing devices are often limited in either spatial resolution or cortical coverage, even including those with thousands of channels used in animal experiments. Here, we developed scalable manufacturing processes and dense connectorization to achieve reconfigurable thin-film, multi-thousand channel neurophysiological recording grids using platinum-nanorods (PtNRGrids). With PtNRGrids, we have achieved a multi-thousand channel array of small (30 μm) contacts with low impedance, providing unparalleled spatial and temporal resolution over a large cortical area. We demonstrate that PtNRGrids can resolve sub-millimeter functional organization of the barrel cortex in anesthetized rats that captured the histochemically-demonstrated structure. In the clinical setting, PtNRGrids resolved fine, complex temporal dynamics from the cortical surface in an awake human patient performing grasping tasks. Additionally, the PtNRGrids identified the spatial spread and dynamics of epileptic discharges in a patient undergoing epilepsy surgery at 1 mm spatial resolution, including activity induced by direct electrical stimulation. Collectively, these findings demonstrate the power of the PtNRGrids to transform clinical mapping and research with brain-machine interfaces and highlights a path toward novel therapeutics.

physics.app-ph↗

arXiv2021

NuCLS: A scalable crowdsourcing, deep learning approach and dataset for nucleus classification, localization and segmentation

High-resolution mapping of cells and tissue structures provides a foundation for developing interpretable machine-learning models for computational pathology. Deep learning algorithms can provide accurate mappings given large numbers of labeled instances for training and validation. Generating adequate volume of quality labels has emerged as a critical barrier in computational pathology given the time and effort required from pathologists. In this paper we describe an approach for engaging crowds of medical students and pathologists that was used to produce a dataset of over 220,000 annotations of cell nuclei in breast cancers. We show how suggested annotations generated by a weak algorithm can improve the accuracy of annotations generated by non-experts and can yield useful data for training segmentation algorithms without laborious manual tracing. We systematically examine interrater agreement and describe modifications to the MaskRCNN model to improve cell mapping. We also describe a technique we call Decision Tree Approximation of Learned Embeddings (DTALE) that leverages nucleus segmentations and morphologic features to improve the transparency of nucleus classification models. The annotation data produced in this study are freely available for algorithm development and benchmarking at: https://sites.google.com/view/nucls.

eess.IV↗