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Improved spatially resolved single cell transcriptomic imaging in archival tissues with MERSCOPE® Abstract:  The advent of tools enabling researchers to easily perform spatial transcriptomics with single cell resolution has enabled a revolution in the understanding…

Highlights: MERFISH reveals cellular and spatial remodeling during intestinal inflammation Inflammation-associated fibroblast response is more diverse than expected Neighborhoods define distinct cellular collections that evolve toward ulceration Hallmarks of inflammatory fibroblast states are found in…

Abstract Advances in the development of largely automated microscopy methods such as MERFISH for imaging cellular structures in mouse brains are providing spatial detection of micron resolution gene expression. While there has been tremendous progress made in the field…

Abstract Imaging-based spatial transcriptomics techniques generate image data that, once processed, results in a set of spatial points with categorical labels for different mRNA species. A crucial part of analyzing downstream data involves the analysis…

Abstract BACKGROUND: Mature endothelial cells (ECs) are heterogeneous, with subtypes defined by tissue origin and position within the vascular bed (ie, artery, capillary, vein, and lymphatic). How this heterogeneity is established during the development of…

Abstract The lateral septum (LS) is a nucleus in the ventral forebrain that modulates complex social and affective behaviors. Several distinct neuronal types have been described in the LS; however, the full extent of this…

Abstract Motivation Spatial omics data demand computational analysis but many analysis tools have computational resource requirements that increase with the number of cells analyzed. This presents scalability challenges as researchers use spatial omics technologies to profile…

Abstract The identification of spot-like structures in large and noisy microscopy images is an important task in many life science techniques, and it is essential to their quantitative performance. For example, imaging-based spatial transcriptomics (iST)…

Abstract Single-cell RNA sequencing (scRNA-seq) has advanced our understanding of cell types and their heterogeneity within the human liver, but the spatial organization at single-cell resolution has not yet been described. Here we apply multiplexed…

Abstract Spatially resolved single-cell transcriptomics have provided unprecedented insights into gene expression in situ, particularly in the context of cell interactions or organization of tissues. However, current technologies for profiling spatial gene expression at single-cell resolution…

Abstract Single-cell atlases are critical for unraveling the cellular basis of health and disease, yet their sheer diversity and vast data landscape in time and space pose daunting computational challenges pertaining to the delineation of…

Abstract Targeted spatial transcriptomics hold particular promise in analyzing complex tissues. Most such methods, however, measure only a limited panel of transcripts, which need to be selected in advance to inform on the cell types…

Abstract:  Our understanding of molecular biology and pathology has been greatly facilitated by recent advances in multiple sequencing technologies, coupled with computational analysis, to detect and count proteins and transcripts. However, these tools lack spatial…

Abstract:  Understanding the spatial complexities within cancer provides crucial information for evaluating individual tumor development and progression; recent research in prostate cancer has shown how critical it is for oncologists to maintain a spatial context…

Abstract:  The neuronal system consists of various molecularly unique cell types arranged into different anatomical structures. Over the past decade, single-cell sequencing has made considerable strides in elucidating the cell heterogeneity of the nervous system….

Abstract Mounting evidence implicated the classical complement pathway (CP) in normal brain development, and the pathogenesis of neuropsychiatric and neurodegenerative diseases. However the source and regulation of complement in the brain remain unclear. Using MERFISH,…

Abstract 3D organization of the genome plays a critical role in regulating gene expression. However, it remains unclear how chromatin organization differs among different cell types in the brain. Here we used genome-scale DNA and…

Abstract Brains come in various sizes and shapes, yet how neuronal position constrains the type of circuits that they can form remains largely unknown. The spatial layout of anatomical structures with corresponding functions varies widely…

ABSTRACT Astrocyte specification during development is influenced by both intrinsic and extrinsic factors, but the precise contribution of each remains poorly understood. Here we show that septal astrocytes from Nkx2.1 and Zic4 expressing progenitor zones…

Abstract The prefrontal cortex (PFC) is a complex brain region that regulates diverse functions ranging from cognition, emotion and executive action to even pain processing. To decode the cellular and circuit organization of such diverse…