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Introduction In situ profiling of cancer tissue facilitates the preservation of spatial context among the various substates of tumor cells, as well as their interactions with the immune system and the surrounding landscape of stroma,…

Abstract Abstract: Single cell spatial-omics data visualization plays a pivotal role in unraveling the intricate spatial organization and heterogeneity of cellular systems. Various software tools and packages have been developed to effectively visualize and interpret…

Abstract Single-cell spatial transcriptomics such as in-situ hybridization or sequencing technologies can provide subcellular resolution that enables the identification of individual cell identities, locations, and a deep understanding of subcellular mechanisms. However, accurate segmentation and…

Abstract Duplication 15q (dup15q) syndrome is the most common genetic cause of autism spectrum disorder (ASD). Due to a higher genetic and phenotypic homogeneity compared to idiopathic autism, dup15q syndrome provides a well-defined setting to…

Abstract We analyze more than 700,000 single-nucleus RNA-seq profiles from 106 donors during prenatal and postnatal developmental stages and identify lineage-specific programs that underlie the development of specific subtypes of excitatory cortical neurons, interneurons, glial…

Abstract Spatial transcriptomics technologies enable the spatially resolved measurement of gene expression within a tissue specimen. With these technologies, researchers can investigate how cells organize into cellular niches which are defined as distinct regions in…

Abstract Proper brain function requires the assembly and function of diverse populations of neurons and glia. Single cell gene expression studies have mostly focused on characterization of neuronal cell diversity; however, recent studies have revealed…

ABSTRACT An accurate characterization of cell-cell communication (CCC) in the local tissue microenvironment is critical for elucidating the diverse biological processes that coordinate normal physiological development and disease progression. Emerging spatially resolved transcriptomics (SRT) techniques…

ABSTRACT The “dorsal pons”, or “dorsal pontine tegmentum” (dPnTg), is part of the brainstem. It is a complex, densely packed region whose nuclei are involved in the regulation of many vital functions. Notable among them…

Abstract 3D standard reference brains serve as key resources to understand the spatial organization of the brain and promote interoperability across different studies. However, unlike the adult mouse brain, the lack of standard 3D reference…