GeneSurfer is an interactive interface for exploring localized transcriptome-wide gene co-expression patterns in the 3D spatial domain.
This software is described in GeneSurfer Enables Transcriptome-wide Exploration and Annotation of Gene Co-expression Modules in 3D Spatial Transcriptomics Data.
GeneSurfer is built as a plug-in for the ManiVault application building system. For more information about ManiVault Studio, see ManiVault.
The installer of this software which includes the GeneSurfer plugin can be downloaded here. After installation, the projects used in this paper are listed on the application's start page. Users can select a project, after which the corresponding file will be automatically downloaded and loaded.
Currently, only a Windows installer is provided, Linux and Mac will follow in the coming period.
Our main analysis and figures in the paper are demonstrated using the Allen Brain Cell Atlas (ABC Atlas)[1]. A minimum of 16GB memory is required, 32GB+ recommended.
To demonstrate GeneSurfer's general applicability, we also tested it on datasets from other spatial transcriptomics platforms. All data files and project files are available via our OSF repository. For detailed descriptions of the files and guidance on usage, please refer to the OSF project wiki.
[1] Yao, Z., van Velthoven, C.T.J., Kunst, M. et al. A high-resolution transcriptomic and spatial atlas of cell types in the whole mouse brain. Nature 624, 317–332 (2023). https://doi.org/10.1038/s41586-023-06812-z