Cytosplore Simian Viewer

The Cytosplore Simian Viewer system is designed to enable researchers to analyze and compare cell and gene expression variations across multiple species. ##Repositories Used

The Cytosplore Simian Viewer system makes use of the following repositories:

1. Core

   • Description: Core application manages data sets and plugins.
   • Repository Link: ManiVaultCore

2. Scatterplot View Plugin

   • Repository Link: ScatterplotPlugin

3. Differential Expression View Plugin

   • Repository Link: ClusterDifferentialExpressionPlugin

4. Pairwise Expression Comparison View Plugin

   • Repository Link: SimianViewerPairExpCompPlugin

5. Multi-species Expression Comparison View Plugin

   • Repository Link: SimianViewerMultExpCompPlugin

6. Distancemap View Plugin

   • Repository Link: SimianViewerPlugin

7. ChartLegend View Plugin

   • Repository Link: ChartLegendPlugin

Installers

Installer executables are available for download on the Cytosplore Viewer website.

Publications

If you use this project in your research or find it helpful, please consider citing the publications:

• Cytosplore Simian Viewer: Visual Exploration for Multi-Species Single-Cell RNA Sequencing Data

  • Authors: Soumyadeep Basu, Jeroen Eggermont, Thomas Kroes, Nicholas L. Jorstad, Trygve Bakken, Ed Lein, Boudewijn P.F. Lelieveldt, Thomas Höllt
  • Published in: Eurographics Workshop on Visual Computing for Biology and Medicine, page 111-120 - Sep 2023
  • Link: Publisher
  • BibTeX:

    @article{10.2312:vcbm.20231219,
      booktitle = {Eurographics Workshop on Visual Computing for Biology and Medicine},
      editor = {Hansen, Christian and Procter, James and Renata G. Raidou and Jönsson, Daniel and Höllt, Thomas},
      title = {{Cytosplore Simian Viewer: Visual Exploration for Multi-Species Single-Cell RNA Sequencing Data}},
      author = {Basu, Soumyadeep and Eggermont, Jeroen and Kroes, Thomas and Jorstad, Nikolas and Bakken, Trygve and Lein, Ed and Lelieveldt, Boudewijn and Höllt, Thomas},
      year = {2023},
      publisher = {The Eurographics Association},
      ISSN = {2070-5786},
      ISBN = {978-3-03868-216-5},
      DOI = {10.2312/vcbm.20231219}
    }

  -Abstract: With the rapid advances in single-cell sequencing technologies, novel types of studies into the cell-type makeup of the brain have become possible. Biologists often analyze large and complex single-cell transcriptomic datasets to enhance knowledge of the intricate features of cellular and molecular tissue organization. A particular area of interest is the study of whether cell types and their gene regulation are conserved across species during evolution. However, in-depth comparisons across species of such high-dimensional, multi-modal single-cell data pose considerable visualization challenges. This paper introduces Cytosplore Simian Viewer, a visualization system that combines various views and linked interaction methods for comparative analysis of single-cell transcriptomic datasets across multiple species. Cytosplore Simian Viewer enables biologists to help gain insights into the cell type and gene expression differences and similarities among different species, particularly focusing on comparing human data to other species. The system validation in discovery research on real-world datasets demonstrates its utility in visualizing valuable results related to the evolutionary development of the middle temporal gyrus.

• Comparative transcriptomics reveals human-specific cortical features

  • Authors: Nikolas L Jorstad, Janet HT Song, David Exposito-Alonso, Hamsini Suresh, Nathan Castro, et al.
  • Published in: Science, 2023
  • Link: Publisher
  • BibTeX:

    @article{10.1126:science.ade9516,
      DOI={10.1126/science.ade9516},
      author = {Nikolas L. Jorstad  and Janet H. T. Song  and David Exposito-Alonso  and Hamsini Suresh  and Nathan Castro-Pacheco  and Fenna M. Krienen  and Anna Marie Yanny  and Jennie Close  and Emily Gelfand  and Brian Long  and Stephanie C. Seeman  and Kyle J. Travaglini  and Soumyadeep Basu  and Marc Beaudin  and Darren Bertagnolli  and Megan Crow  and Song-Lin Ding  and Jeroen Eggermont  and Alexandra Glandon  and Jeff Goldy  and Katelyn Kiick  and Thomas Kroes  and Delissa McMillen  and Trangthanh Pham  and Christine Rimorin  and Kimberly Siletti  and Saroja Somasundaram  and Michael Tieu  and Amy Torkelson  and Guoping Feng  and William D. Hopkins  and Thomas Höllt  and C. Dirk Keene  and Sten Linnarsson  and Steven A. McCarroll  and Boudewijn P. Lelieveldt  and Chet C. Sherwood  and Kimberly Smith  and Christopher A. Walsh  and Alexander Dobin  and Jesse Gillis  and Ed S. Lein  and Rebecca D. Hodge  and Trygve E. Bakken },
      title = {Comparative transcriptomics reveals human-specific cortical features},
      journal = {Science},
      volume = {382},
      number = {6667},
      pages = {eade9516},
      year = {2023},
      doi = {10.1126/science.ade9516},
      URL = {https://www.science.org/doi/abs/10.1126/science.ade9516},
      eprint = {https://www.science.org/doi/pdf/10.1126/science.ade9516},
    }
       

  -Abstract: The cognitive abilities of humans are distinctive among primates, but their molecular and cellular substrates are poorly understood. We used comparative single-nucleus transcriptomics to analyze samples of the middle temporal gyrus (MTG) from adult humans, chimpanzees, gorillas, rhesus macaques, and common marmosets to understand human-specific features of the neocortex. Human, chimpanzee, and gorilla MTG showed highly similar cell-type composition and laminar organization as well as a large shift in proportions of deep-layer intratelencephalic-projecting neurons compared with macaque and marmoset MTG. Microglia, astrocytes, and oligodendrocytes had more-divergent expression across species compared with neurons or oligodendrocyte precursor cells, and neuronal expression diverged more rapidly on the human lineage. Only a few hundred genes showed human-specific patterning, suggesting that relatively few cellular and molecular changes distinctively define adult human cortical structure.

Connecting Actions Used

This plugin uses the Manivault action system to communicate between plugins. Below is a list of published actions and their connections:

Published Actions Table

PublishedFrom	Type	ToName	FromName	PublishedName	ConcernedPlugin
DifferentialExpression	TriggerAction	CalculateDifferentialExpression		Cluster Differential Expression 1::CalculateDifferentialExpression	Connect
DifferentialExpression	VariantAction	TableViewLeftSideInfo		Cluster Differential Expression 1::TableViewLeftSideInfo	Connect
DifferentialExpression	VariantAction	InvokeMethods		Cluster Differential Expression 1::InvokeMethods	Connect
DifferentialExpression	DatasetPickerAction	Cross-species Dataset1		Cluster Differential Expression 1::Dataset1	Connect
DifferentialExpression	DatasetPickerAction	Cross-species Dataset2		Cluster Differential Expression 1::Dataset2	Connect
DifferentialExpression	StringAction	Species1Name		Cluster Differential Expression 1::DatasetName1	Connect
DifferentialExpression	StringAction	Species2Name		Cluster Differential Expression 1::DatasetName2	Connect
DifferentialExpression	OptionsAction	Select cross-species Clusters1		Cluster Differential Expression 1::SelectClusters1	Connect
DifferentialExpression	OptionsAction	Select cross-species Clusters2		Cluster Differential Expression 1::SelectClusters2	Connect
DifferentialExpression	StringAction	Har-Hcondel IntoText		Cluster Differential Expression 1::IntoText	Connect
SimianViewer	OptionAction	Scatterplot color control		Simian::ScatterplotColorControl	Publish
SimianViewer	ColorAction	Selection color		Simian::SelectionColor	Publish
SimianViewer	StringAction	Selected Crossspecies Cluster		Simian::SelectedCrossspeciesCluster	Publish
SimianViewer	DatasetPickerAction	ScatterplotView1Color		Simian::ScatterplotView1Color	Publish
SimianViewer	DatasetPickerAction	ScatterplotView1Position		Simian::ScatterplotView1Position	Publish
SimianViewer	DatasetPickerAction	ScatterplotView2Color		Simian::ScatterplotView2Color	Publish
SimianViewer	DatasetPickerAction	ScatterplotView2Position		Simian::ScatterplotView2Position	Publish
SimianViewer	OptionAction	Neighborhood		Simian::Neighborhood	Publish
SimianViewer	ToggleAction	ParallelBarPluginVisibility		Simian::ParallelBarsVisibility	Publish
SimianViewer	DatasetPickerAction	DE Dataset1		Simian::DE Dataset1	Publish
SimianViewer	DatasetPickerAction	DE Dataset2		Simian::DE Dataset2	Publish
SimianViewer	ToggleAction	PopPyramidPluginVisibility		Simian::PopPyramidVisibility	Publish
SimianViewer	ColorAction	Selection color		Simian::SelectionColor	Connect
SimianViewer	StringAction	Selected CrossSpecies Cluster		Simian::SelectedCrossspeciesCluster	Connect
SimianViewer	OptionAction	Neighborhood		Simian::Neighbhorhood	Connect
DifferentialExpression	StringAction	SelectedID		Cluster Differential Expression 1::LastSelectedId	Connect
DifferentialExpression	StringAction	Species1Name		Cluster Differential Expression 1::DatasetName1	Connect
DifferentialExpression	StringAction	Species2Name		Cluster Differential Expression 1::DatasetName2	Connect
SimianViewer	DatasetPickerAction	DE Dataset1		Simian::DE Dataset1	Connect
SimianViewer	DatasetPickerAction	DE Dataset2		Simian::DE Dataset2	Connect
SimianViewer	ToggleAction	Visible		Simian::ParallelBarsVisibility	Connect
SimianViewer	ColorAction	Selection color		Simian::SelectionColor	Connect
SimianViewer	StringAction	Selected CrossSpecies Cluster		Simian::SelectedCrossspeciesCluster	Connect
SimianViewer	DatasetPickerAction	DE Dataset1		Simian::DE Dataset1	Connect
SimianViewer	DatasetPickerAction	DE Dataset2		Simian::DE Dataset2	Connect
DifferentialExpression	StringAction	SelectedID		Cluster Differential Expression 1::LastSelectedId	Connect
DifferentialExpression	StringAction	Species1Name		Cluster Differential Expression 1::DatasetName1	Connect
DifferentialExpression	StringAction	Species2Name		Cluster Differential Expression 1::DatasetName2	Connect
SimianViewer	ToggleAction	Visible		Simian::PopPyramidVisibility	Connect
SimianViewer	DatasetPickerAction	Settings/Datasets/Color		Simian::ScatterplotView1Color	Connect
SimianViewer	DatasetPickerAction	Settings/Datasets/Position		Simian::ScatterplotView1Position	Connect
Scatterplot1	ColorAction	Settings/Coloring/1D Color map/Current color map		Scatterplot::1DColormap	Publish
Scatterplot1	ScalarAction	Settings/Plot/Point/Point Size		Scatterplot::PointSize	Publish
Scatterplot1	ScalarAction	Settings/Plot/Point/Point opacity		Scatterplot::PointOpacity	Publish
SimianViewer	OptionsAction	Scatterplot Expression color control		Simian::ScatterplotColorControl	Connect
SimianViewer	ColorAction	Settings/Selection/Point Selection/Color		Simian::SelectionColor	Connect
Scatterplot1	ScalarAction	Focus Selection		Scatterplot::FocusSelection	Publish
Scatterplot1	ScalarAction	Settings/Selection/Opacity		Scatterplot::SelectionOpacity	Publish
SimianViewer	DatasetPickerAction	Cluster dataset		Simian::ScatterplotView1Color	Publish
Scatterplot1	StringAction	Color map		Scatterplot::1DColormap	Publish
SimianViewer	StringAction	Cluster Selection String		Simian::SelectedCrossspeciesCluster	Publish
DifferentialExpression	StringAction	Chart Title		Cluster Differential Expression 1::DatasetName1	Publish
SimianViewer	DatasetPickerAction	Settings/Datasets/Color		Simian::ScatterplotView2Color	Connect
SimianViewer	DatasetPickerAction	Settings/Datasets/Position		Simian::ScatterplotView2Position	Connect
Scatterplot1	ColorAction	Settings/Coloring/1D Color map/Current color map		Scatterplot::1DColormap	Connect
Scatterplot1	ScalarAction	Settings/Plot/Point/Point Size		Scatterplot::PointSize	Connect
Scatterplot1	ScalarAction	Settings/Plot/Point/Point opacity		Scatterplot::PointOpacity	Connect
SimianViewer	OptionsAction	Scatterplot Expression color control		Simian::ScatterplotColorControl	Connect
SimianViewer	ColorAction	Settings/Selection/Point Selection/Color		Simian::SelectionColor	Connect
Scatterplot1	ScalarAction	Focus Selection		Scatterplot::FocusSelection	Connect
Scatterplot1	ScalarAction	Settings/Selection/Opacity		Scatterplot::SelectionOpacity	Connect
SimianViewer	DatasetPickerAction	Cluster dataset		Simian::ScatterplotView2Color	Connect
Scatterplot1	StringAction	Color map		Scatterplot::1DColormap	Connect
SimianViewer	StringAction	Cluster Selection String		Simian::SelectedCrossspeciesCluster	Connect
DifferentialExpression	StringAction	Chart Title		Cluster Differential Expression 1::DatasetName2	Connect