Cytosplore MTG Viewer
Cytosplore MTG Viewer is an interactive visual analysis system for the exploration of single cell data gathered from nuclear sequencing of the human Middle Temporal Gyrus (MTG). The included RNA-Seq dataset on over 15 thousand cell nuclei taken from human brain tissue was published through the Allen Cell Types Database by the Allen Institute for Brain Science. Cytosplore MTG Viewer allows to interactively explore the cellular hierarchy of the human MTG cell types data, inspect transcriptome-wide gene expression in combination with metadata of individual cells, perform differential analyses and statistics between manual selections of cells, or between pre-defined clusters throughout the cellular hierarchy and more. Cytosplore MTG Viewer is based on Cytosplore and provides many of the analysis tools presented in the previous Cytosplore publications. Download and try Cytosplore MTG Viewer yourself!
TU Delft / LUMC
Project Lead Cytosplore
Cytosplore MTG Viewer is being developed by a team consisting of members from the Leiden Computational Biology Center, the Division of Image Processing at the Leiden University Medical Center, and the Computer Graphics and Visualization Group at the TU Delft in a research project, carried out in close collaboration with Trygve Bakken, Jeremy Miller, Rebecca Hodge, and Ed Lein from the Allen Institute for Brain Science. The research has been made possible through the NWO-AES grants 12720 (VanPIRE, PI Vilanova) and 12721 (Genes in Space, PI Lelieveldt).
Conserved cell types with divergent features between human and mouse cortex. , bioRxiv, 2018.
Abstract: Elucidating the cellular architecture of the human neocortex is central to understanding our cognitive abilities and susceptibility to disease. Here we applied single nucleus RNA-sequencing to perform a comprehensive analysis of cell types in the middle temporal gyrus of human cerebral cortex. We identify a highly diverse set of excitatory and inhibitory neuronal types that are mostly sparse, with excitatory types being less layer-restricted than expected. Comparison to a similar mouse cortex single cell RNA-sequencing dataset revealed a surprisingly well-conserved cellular architecture that enables matching of homologous types and predictions of human cell type properties. Despite this general conservation, we also find extensive differences between homologous human and mouse cell types, including dramatic alterations in proportions, laminar distributions, gene expression, and morphology. These species-specific features emphasize the importance of directly studying human brain.
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Disclaimer: Cytosplore MTG Viewer is a research project between TU Delft and Leiden University Medical Center. We do our best to provide support but cannot guarantee it. If you have any suggestions, problems, want to share your success stories or papers published using Cytosplore MTG Viewer, we would love to get feedback! Please do not hesitate to get in touch.
Cytosplore MTG Viewer is free to use.
If you use Cytosplore MTG Viewer within the scope of a scientific article you must cite the original publications:
Hodge, Bakken, et al. Conserved cell types with divergent features between human and mouse cortex, bioRxiv, 2018.