Here, we present SpaceWalker, an interactive visual analytics tool for exploration of large patches of Spatial Transcriptomic data. SpaceWalker consists of two key innovations: a real-time spatial exploration of the HD gene expression space, and a gradient gene detector for on-the-fly retrieval of locally varying genes from the full gene set. We complement this with a suite of user-defined visualization options to inspect and query the data, and to project analysis results on the spatial data.
This software is described in the paper SpaceWalker: Interactive Gradient Exploration for Spatial Transcriptomics Data
SpaceWalker is built as a plug-in for the ManiVault application building system as described in ManiVault: A Flexible and Extensible Visual Analytics Framework for High-Dimensional Data.
The installer of this software which includes the SpaceWalker plugin can be downloaded below:
Currently, only a Windows installer is provided, Linux and Mac will follow in the coming period.
In the paper several datasets are discussed which are available here for exploring locally via downloading a ManiVault project file.
| smFISH & MERFISH1 | HybISS2 |
|---|---|
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| EEL FISH3 | ABC Atlas4 |
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- Long, B., Miller, J., and The SpaceTx Consortium. (2023). SpaceTx: A Roadmap for Benchmarking Spatial Transcriptomics Exploration of the Brain. arXiv preprint arXiv:2301.08436. https://viewer.cytosplore.org
- La Manno, G., Siletti, K., Furlan, A., Gyllborg, D., Vinsland, E., Mossi Albiach, A., Mattsson Langseth, C., Khven, I., Lederer, A.R., and Dratva, L.M. (2021). Molecular architecture of the developing mouse brain. Nature 596, 92-96. http://mousebrain.org/development/downloads.html
- Borm, L.E., Mossi Albiach, A., Mannens, C.C., Janusauskas, J., Özgün, C., Fernández-García, D., Hodge, R., Castillo, F., Hedin, C.R., Villablanca, E.J., et al. (2022). Scalable in situ single-cell profiling by electrophoretic capture of mRNA using EEL FISH. Nature Biotechnology, 1-10. http://mousebrain.org/adult/downloads.html
- Yao, Z., van Velthoven, C.T., Kunst, M., Zhang, M., McMillen, D., Lee, C., Jung, W., Goldy, J., Abdelhak, A., Baker, P., and Barkan, E. (2023). A high-resolution transcriptomic and spatial atlas of cell types in the whole mouse brain. bioRxiv, 2023.2003. 2006.531121. https://github.com/AllenInstitute/abc_atlas_access/blob/main/descriptions/MERFISH-C57BL6J-638850.md
SpaceWalker is licensed under LGPL v3.0, refer to the LICENSE file in the top level directory.
Copyright © 2023 BioVault (Biomedical Visual Analytics Unit LUMC)