14 papers · ranked by Valyu relevance
Inbal Shainer, Enrico Kuehn, Eva Laurell, Mariam Al Kassar + 5 more
The advent of multimodal brain atlases promises to accelerate discoveries in neuroscience by offering in silico queries of cell types, connectivity and gene expression in regions of interest. We employed multiplexed fluorescent in situ RNA hybridization chain reaction (HCR) to generate expression maps for an initial…
Zachary Hemminger, Gabriela Sanchez-Tam, Haley De Ocampo, Aihui Wang + 7 more
Genetic variation can alter brain structure and, consequently, function. Comparative statistical analysis of mouse brains across genetic backgrounds requires spatial, single-cell, atlas-scale data, in replicates—a challenge for current technologies. We introduce Atlas-scale Transcriptome Localization using Aggregate…
Zachary Hemminger, Gaby Tam, Haley De Ocampo, Aihui Wang + 7 more
Genetic variation can alter organ structure and, in turn, function. Comparative statistical analysis of organs across genetic backgrounds requires spatial, single-cell, atlas-scale data in replicates, which current technologies do not provide at scale. We introduce Atlas-scale Transcriptome Localization using Aggregate…
Cantin Ortiz, Jose Fernandez Navarro, Aleksandra Jurek, Antje Märtin + 2 more
Brain maps are essential for integrating information and interpreting the structure-function relationship of circuits and behavior. We aimed to generate a systematic classification of the adult mouse brain organization based on unbiased extraction of spatially-defining features. Applying whole-brain spatial…
Ying Xu, Catherine Gatt, Esra Kaymak, Kensei Kikuchi + 2 more
Whole-organism cell atlases have painted the cellular landscapes of individual species, however comparing cells across the tree of life remains challenging. Most cross-species analyses are restricted to orthologous genes, while the complexity of atlas data constitutes an access barrier for many researchers. We…
Aurina Arnatkevičiūtė, Ben D. Fulcher, Alex Fornito
The recent availability of comprehensive, brain-wide gene expression atlases such as the Allen Human Brain Atlas (AHBA) has opened new opportunities for understanding how spatial variations on the molecular scale relate to the macroscopic neuroimaging phenotypes. A rapidly growing body of literature is demonstrating…
Hugo Mantion, Zhao Zhang, Diego Serra, Lætitia Lebrun + 2 more
Descriptions of tissues by histopathologists rest on verbal statements limited by quantitative inaccuracies and personal cognitive biases. Here we propose an unsupervised computational framework that transposes to histology the concepts and methods of RNA-seq gene expression analysis, setting histology on an unbiased…
Ameer Sarwar, Mara Rue, Leon French, Helen Cross + 3 more
Spatial transcriptomics promises to transform our understanding of tissue biology by molecularly profiling individual cells in situ. A fundamental question they allow us to ask is how nearby cells orchestrate their gene expression. Rather than focus on how these cells (samples) communicate with each other, we reframe…
Kaitlin M. Stouffer, Alain Trouvé, Laurent Younes, Michael Kunst + 6 more
This paper explicates a solution to the problem of building correspondences between molecular-scale transcriptomics and tissue-scale atlases. The central model represents spatial transcriptomics as generalized functions encoding molecular position and high-dimensional transcriptomic-based (gene, cell type) identity. We…
Tyler Roberts, Yong Zhong Liang, Gerald C. Cupchik, Jonathan S. Cant + 1 more
Expression recognition relies on the ability to distinguish subtle visual differences across a range of facial expressions. Here, we examine the neural representation of dynamic expressions as reflected by electroencephalography (EEG) data in human adults. We find that a wide range of expressions (i.e., 14 emotional…
Susan J. Tappan, Brian S. Eastwood, Nathan O’Connor, Quanxin Wang + 7 more
Identification and delineation of brain regions in histologic mouse brain sections is especially pivotal for many neurogenomics, transcriptomics, proteomics and connectomics studies, yet this process is prone to observer error and bias. Here we present a novel brain navigation system, named NeuroInfo, whose general…
Heidi Kleven, Thomas H. Gillespie, Lyuba Zehl, Timo Dickscheid + 3 more
Brain atlases are important reference resources for accurate anatomical description of neuroscience data. Open access, three-dimensional atlases serve as spatial frameworks for integrating experimental data and defining regions-of-interest in analytic workflows. However, naming conventions, parcellation criteria, area…
John G. Samuelsson, Jeremy D. Schmahmann, Martin Sereno, Bruce Rosen + 1 more
Scientific interest in the cerebellum has surged in the last few decades with an emerging consensus on a multifaceted functionality and intricate, but not yet fully understood, functional topography over the cerebellar cortex. To further refine this structure-function relationship and quantify its inter-subject…
Siobhan Ewert, Andreas Horn
Three-dimensional atlases of subcortical brain structures are valuable tools to reference anatomy in neuroscience and neurology. In the special case of deep brain stimulation (DBS), the two most prominent targets are the subthalamic nucleus (STN) and the internal part of the pallidum (GPi). With the help of atlases…