Cytosplore Viewer is an interactive visual analysis system for the exploration of single cell data that was published in the Allen Cell Types Database by the Allen Institute for Brain Science. Currently, Cytosplore Viewer includes sequencing data of over 15 thousand nuclei gathered from the human Middle Temporal Gyrus (MTG). It also includes single cell sequencing data of the Primary Visual Cortex (VISp) and Anterior Lateral Motor Cortex (ALM) in mouse brain. Cytosplore Viewer allows one 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 Viewer is based on Cytosplore and provides many of the analysis tools presented in the previous Cytosplore publications. Download and try Cytosplore Viewer yourself!
TU Delft / LUMC
Project Lead Cytosplore
Cytosplore 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, Bosiljka Tasic, Zizhen Yao, Lucas T. Graybuck, Hongkui Zeng, Mike Hawrylycz , 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 ...
Shared and Distinct Transcriptomic Cell Types Across Neocortical Areas. , Nature, 2018.
Abstract: The neocortex contains a multitude of cell types that are segregated into layers and functionally distinct areas. To investigate the diversity of cell types across the mouse neocortex, here we analysed 23,822 cells from two areas at distant poles of the mouse neocortex: the primary visual cortex and the anterior lateral motor cortex. We define 133 transcriptomic cell types by deep, single-cell RNA sequencing ...
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Disclaimer: Cytosplore 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 Viewer, we would love to get feedback! Please do not hesitate to get in touch.
Cytosplore Viewer is free to use.
If you use Cytosplore 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.
B. Tasic et al., Shared and distinct transcriptomic cell types across neocortical areas, Nature, 563, pp. 72—78, 2018.