Welcome to the spatiomic documentation!¶ Start spatiomic Installation Installation Options Workflow overview Workflow Diagram Explanation Loading and Processing Data Raw Data and Image Registration Weighted Subsampling Preprocessing Clustering Self-Organizing Maps Graph Construction and Clustering Label Transfer Interpretation Cluster Contributors Spatial Projection and Interpretation Differential Abundance Analysis Spatial Statistics Results Tutorials Full example Data loading Data preprocessing Self-organizing map training Cluster the SOM nodes Cluster composition Clustering of entire images Differential abundance analysis Spatial analysis Visualizing all clustered images Extended analyses Time evaluation Session info Image registration Load example data and shift it Detect the shift and correct it Evaluate the correction Pixel-based clustering SOM training Graph clustering Plotting & evaluation Statistics Spatial statistics Data loading Calculate spatial weights Calculate the autocorrelation Local statistics Getis-Ord Gi* Local Heteroskedasticity Join counts and vicinity graph Interoperability with esda Cell segmentation & clustering Data loading Cellpose segmentation Load a pixel-clustered image Quantify pixel-level features at the cell-level Cluster cells based on pixel-level clusters Cell-level clustering based on marker expression Plot the results Session info scverse interoperability Data loading Identify spatial neighbors Convert to AnnData Use AnnData with spatiomic Use with scverse tools SpatialData interoperability Pixel-level clustering using the data API Documentation spatiomic Submodules spatiomic.cluster Classes Package Contents spatiomic.data Classes Functions Package Contents spatiomic.dimension Classes Package Contents spatiomic.neighbor Classes Package Contents spatiomic.plot Functions Package Contents spatiomic.process Attributes Classes Package Contents spatiomic.segment Classes Functions Package Contents spatiomic.spatial Classes Functions Package Contents spatiomic.tool Functions Package Contents Attributes Functions Package Contents __dir__() __version__ GitHub spatiomic repository Other projects pytximport pyclustree BioContextAI Additional Information Complex Tissue Lab Test coverage Sunburst view Contributor Covenant Code of Conduct Our Pledge Our Standards Enforcement Responsibilities Scope Enforcement Enforcement Guidelines Attribution Legal Notice & TOS Website Terms and Conditions of Use Privacy Policy Indices and tables¶ Index Module Index Search Page
