Cytosplore Viewer is an interactive visual analytics system for the exploration of single cell and spatial transcriptomics data published in the Allen Cell Types Database and for a number of the curated, authoritative data resources of the Brain Initiative Cell Atlas Network (BICAN), in particular the Human and Mammalian Brain Atlas (HMBA), the 2025 Basal Ganglia release.

Launched in 2019, Cytosplore Viewer is designed to leverage fast local compute and compressed data access for the linked exploration of multi-modal spatial and single cell datasets. Specific focus is multi-resolution detail analyses across multiple datasets, for instance:

• On-the-fly visual cross-species comparative visualization of cell types and their convergent and divergent features across species.
• On-the-fly multi-omics integration of ATAC-seq, Patch-seq, spatial and single-cell transcriptomics by leveraging standardized taxonomy mapping to cross-modal searches (e.g. spatial co-expression of ATAC and RNA seq data.
• Deepdives in single-cell and spatial data for in-depth re-analysis of subsets of cells. Specific niche functionalities are on-the-fly re-embedding using a complementary dimensionality reduction to UMAP, local gene expression gradients detection, differential expression analysis and manual annotation / correction facilities.

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 built in the ManiVault Studio application building toolkit, and provides many of the analysis tools and state-of-the-art visualization research outputs presented in the previous Cytosplore publications.

Visit the Projects page to see more details about the Cytosplore Viewer projects.

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).