# Welcome to Spateo documentation Cells do not live in a vacuum, but in a milieu defined by cell–cell communication that can be quantified via recent advances in spatial transcriptomics. Here we present *spateo*, a open source framework that welcomes community contributions for quantitative spatiotemporal modeling of spatial transcriptomics. Leveraging the ultra-high spatial-resolution, large field of view and high RNA capture sensitivity of Stereo-seq, *spateo* enables single cell resolution spatial transcriptomics via nuclei-staining and RNA signal based cell segmentation. *Spateo* also delivers novel methods for spatially constrained clustering to identify continuous tissue domains, spatial aware differential analyses to reveal spatial gene expression hotspots and modules, as well as the intricate ligand-receptor interactions. Importantly, *spateo* is equipped with sophisticated methods for building whole-body 3D models of embryogenesis by leveraging serial profilings of drosophila embryos across different stages. *Spateo* thus enables us to evolve from the reductionism of single cells to the holisticism of tissues and organs, heralding a paradigm shift in moving toward studying the ecology of tissue and organ while still offering us the opportunity to reveal associated molecular mechanisms. ```{attention} *Spateo* is currently in beta. Developers are hard at work implementing new features, fixing bugs, and improving the overall user experience. If you have a feature request and/or would like to report a bug, please feel free to open an issue on Github. *Spateo* will not be uploaded to Pypi until its first stable release. In the meantime, *spateo* may be installed directly from GitHub using [these instructions](installation.md#github). ``` ```{eval-rst} .. card:: Installation :octicon:`plug;1em;` :link: installation :link-type: doc Click here to view a brief *spateo* installation guide. ``` ```{eval-rst} .. card:: Tutorials :octicon:`play;1em;` :link: tutorials/index :link-type: doc End-to-end tutorials showcasing key features in the package. ``` ```{eval-rst} .. card:: Technicals :octicon:`info;1em;` :link: technicals/index :link-type: doc Technical information on algorithms and tools provided by *spateo*. ``` ```{eval-rst} .. card:: API reference :octicon:`book;1em;` :link: autoapi/spateo/index :link-type: doc Detailed descriptions of *spateo* API and internals. ``` ```{eval-rst} .. card:: GitHub :octicon:`mark-github;1em;` :link: https://github.com/aristoteleo/spateo-release Ask questions, report bugs, and contribute to *spateo* at our GitHub repository. ``` *This documentation was heavily inspired and adapted from the [scvi-tools documentation](https://docs.scvi-tools.org/en/stable/). Go check them out!* ```{toctree} :hidden: true :maxdepth: 3 :titlesonly: true Documentation home installation tutorials/index Technicals API references contributors contributing GitHub ```