Cytosplore Viewer is an interactive visual analysis system for the exploration of single cell data published in the Allen Cell Types Database and for a number of the single cell data resources of the Brain Initiative Cell Census Network (BICCN), and the Brain Initiative Cell Atlas Network (BICAN).

Currently supported datasets include the October 2019 data releases in the Allen Cell Types Database of the Allen Institute for Brain Science: nuclear sequencing data of several areas of the human cortex, and single cell sequencing data of the mouse cortex and hippocampus.

Also supported are special modes for:

• cross-species comparison of cell types in the motor cortex between human, marmoset and mouse of BICCN (see Comparative cellular analysis of motor cortex in human, marmoset, and mouse below).
• comparing different spatial transcriptomics techniques of the SpaceTx Consortium (see SpaceTx: A Roadmap for Benchmarking Spatial Transcriptomics Exploration of the Brain below).

Cytosplore Viewer allows an interactive exploration of hierarchies of cell types. One can visualize 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.

To gain insights into the cell type and gene expression differences and similarities between humans and 4 different species of primates there is now a special version: Cytosplore Simian Viewer which was developed in for the Comparative transcriptomics reveals human-specific cortical features journal article published in Science, Volume 382, Issue 6667.

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, Brian Long, Nik L. Jorstad, Rebecca Hodge, Bosiljka Tasic, Zizhen Yao, Lucas T. Graybuck, Hongkui Zeng, Mike Hawrylycz , and Ed Lein from the Allen Institute for Brain Science.

This work was partially supported by an NWO Gravitation grant:BRAINSCAPES: A Roadmap from Neurogenetics to Neurobiology (NWO: 024.004.012) and NWO AES grants 3DOMICS (NWO: 17126), VANPIRE (NWO: 12720) and Genes in Space (NWO: 12721).