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Spateo documentation
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  • Documentation home
  • Installation
  • Tutorials
    • Cell segmentation
      • Stain segmentation
      • RNA segmentation
    • Spatially variable genes identificaion
      • 1. Spatially variable genes identification within slice
    • Alignment
      • 1. Basic Usage of Spateo Alignment for 2D Slices
      • 2. Nonrigid alignment of Spateo alignment for 2D slices
      • 3. Partial alignment of Spateo for 2D slices
      • 4. Improve Efficiency and Scalibity
      • 5. 3D Reconstruction workflow
      • 5.1 3D Reconstruction with Pairwise Alignment on Drosophila Data (bin50)
      • 5.2 3D Reconstruction with Pairwise Alignment on Drosophila Data
    • Three dimensional reconstruction
      • Three dims models reconstruction
      • Axis & Backbone
      • Morphological features of 3D models
      • 3D spatial transcriptomics Interpolation
      • Animation of 3D models generated by spateo
    • Clustering and digitization
      • 1.Spatially constrained clustering (SCC) with binnning data
      • 2.Combined visualization of domains and segmented cells
      • 3.Basic spatial domain-cell analysis
      • 4.Identification of spatial variable genes and archetypes
      • 5.Borderline (under construction)
      • 6.Layer & column digitization
      • 7. Digitization of MESH surface in 3D space
    • Cell-cell interaction
      • Ligand-receptor interaction inference
      • Selecting “Target” Genes for Modeling
      • Fitting and Interpreting Cell-Cell Interaction Effect Models
    • Morphometric vector field and kinetics
      • 1.Alignment of 3D models between adjacent time points
      • 2.morphogenesis vector fields and trajectories
      • Characterizing Morphogenesis on Mouse Heart Organogenesis based on Gaussian Processes
      • 3.morphogenesis features
    • Interactive tools
      • 1.Auxiliary segmentation (AuxSeg): an interactive tool for ROI segmentation
      • 2.Enhancing visualization clarity for categorical spatial datasets using Spaco
  • Technicals
    • Cell segmentation
    • Tissue geometry digitization
  • API
    • spateo.align
    • spateo.alignment
      • spateo.alignment.deformation
      • spateo.alignment.methods
        • spateo.alignment.methods.backend
        • spateo.alignment.methods.backend_ot
        • spateo.alignment.methods.deprecated_morpho
        • spateo.alignment.methods.deprecated_morpho_sparse
        • spateo.alignment.methods.deprecated_morpho_sparse_utils
        • spateo.alignment.methods.deprecated_utils
        • spateo.alignment.methods.mesh_correction_utils
        • spateo.alignment.methods.morpho_class
        • spateo.alignment.methods.morpho_mesh_correction
        • spateo.alignment.methods.paste
        • spateo.alignment.methods.sampling
        • spateo.alignment.methods.utils
      • spateo.alignment.morpho_alignment
      • spateo.alignment.paste_alignment
      • spateo.alignment.transform
      • spateo.alignment.utils
    • spateo.configuration
    • spateo.cs
    • spateo.data_io
    • spateo.dd
    • spateo.digitization
      • spateo.digitization.borderline
      • spateo.digitization.boundary_old
      • spateo.digitization.contour
      • spateo.digitization.grid
      • spateo.digitization.utils
      • spateo.digitization.utils_old
    • spateo.errors
    • spateo.external
      • spateo.external.CAST
        • spateo.external.CAST.CAST_Mark
        • spateo.external.CAST.CAST_Projection
        • spateo.external.CAST.CAST_Stack
        • spateo.external.CAST.main
        • spateo.external.CAST.model
          • spateo.external.CAST.model.aug
          • spateo.external.CAST.model.model_GCNII
        • spateo.external.CAST.utils
        • spateo.external.CAST.visualize
      • spateo.external.MERFISHVI
        • spateo.external.MERFISHVI._model
        • spateo.external.MERFISHVI._module
        • spateo.external.MERFISHVI.multimodal_spatial_vae
        • spateo.external.MERFISHVI.scvi_spatial_module
      • spateo.external.STAGATE_pyG
        • spateo.external.STAGATE_pyG.STAGATE
        • spateo.external.STAGATE_pyG.Train_STAGATE
        • spateo.external.STAGATE_pyG.gat_conv
        • spateo.external.STAGATE_pyG.utils
      • spateo.external.lack
    • spateo.get_version
    • spateo.io
      • spateo.io.bbs
      • spateo.io.bgi
      • spateo.io.image
      • spateo.io.image_utils
      • spateo.io.merfish
      • spateo.io.nanostring
      • spateo.io.seqfish
      • spateo.io.seqscope
      • spateo.io.slideseq
      • spateo.io.starmap
      • spateo.io.tenx
      • spateo.io.utils
    • spateo.logging
    • spateo.pl
    • spateo.plotting
      • spateo.plotting.interactive
        • spateo.plotting.interactive.agg
      • spateo.plotting.static
        • spateo.plotting.static.agg
        • spateo.plotting.static.align
        • spateo.plotting.static.bbs
        • spateo.plotting.static.colorlabel
        • spateo.plotting.static.contour
        • spateo.plotting.static.dotplot
        • spateo.plotting.static.geo
        • spateo.plotting.static.glm
        • spateo.plotting.static.interactions
        • spateo.plotting.static.lisa
        • spateo.plotting.static.networks
        • spateo.plotting.static.polarity
        • spateo.plotting.static.position
        • spateo.plotting.static.scatters
        • spateo.plotting.static.space
        • spateo.plotting.static.three_d_plot
          • spateo.plotting.static.three_d_plot.align_plots
          • spateo.plotting.static.three_d_plot.backbone_plots
          • spateo.plotting.static.three_d_plot.morphometrics_plots
          • spateo.plotting.static.three_d_plot.pairwise_align_plots
          • spateo.plotting.static.three_d_plot.three_dims_plots
          • spateo.plotting.static.three_d_plot.three_dims_plotter
        • spateo.plotting.static.utils
    • spateo.pp
    • spateo.preprocessing
      • spateo.preprocessing._fast_utils
      • spateo.preprocessing.aggregate
      • spateo.preprocessing.auxseg
      • spateo.preprocessing.filter
      • spateo.preprocessing.image
      • spateo.preprocessing.normalize
      • spateo.preprocessing.transform
    • spateo.sample_data
    • spateo.segmentation
      • spateo.segmentation.align
      • spateo.segmentation.benchmark
      • spateo.segmentation.bp
      • spateo.segmentation.density
      • spateo.segmentation.em
      • spateo.segmentation.external
        • spateo.segmentation.external.cellpose
        • spateo.segmentation.external.deepcell
        • spateo.segmentation.external.stardist
      • spateo.segmentation.icell
      • spateo.segmentation.label
      • spateo.segmentation.moran
      • spateo.segmentation.qc
      • spateo.segmentation.simulation
      • spateo.segmentation.simulation_evaluation
        • spateo.segmentation.simulation_evaluation.allocate_cell
        • spateo.segmentation.simulation_evaluation.evaluation
        • spateo.segmentation.simulation_evaluation.prepare
      • spateo.segmentation.utils
      • spateo.segmentation.vi
    • spateo.svg
      • spateo.svg.get_svg
      • spateo.svg.get_svg_between_slice
      • spateo.svg.utils
    • spateo.tdr
      • spateo.tdr.interpolations
        • spateo.tdr.interpolations.interpolation_deeplearn
          • spateo.tdr.interpolations.interpolation_deeplearn.deep_interpolation
          • spateo.tdr.interpolations.interpolation_deeplearn.interpolation_nn
          • spateo.tdr.interpolations.interpolation_deeplearn.nn_losses
        • spateo.tdr.interpolations.interpolation_dl
        • spateo.tdr.interpolations.interpolation_gaussianprocess
          • spateo.tdr.interpolations.interpolation_gaussianprocess.gp_models
          • spateo.tdr.interpolations.interpolation_gaussianprocess.gp_train
        • spateo.tdr.interpolations.interpolation_gp
        • spateo.tdr.interpolations.interpolation_sparseVFC
        • spateo.tdr.interpolations.interpolation_vtk
        • spateo.tdr.interpolations.utils
      • spateo.tdr.models
        • spateo.tdr.models.models_backbone
          • spateo.tdr.models.models_backbone.backbone
          • spateo.tdr.models.models_backbone.backbone_methods
          • spateo.tdr.models.models_backbone.backbone_utils
        • spateo.tdr.models.models_individual
          • spateo.tdr.models.models_individual.mesh
          • spateo.tdr.models.models_individual.mesh_methods
          • spateo.tdr.models.models_individual.mesh_utils
          • spateo.tdr.models.models_individual.point_clouds
          • spateo.tdr.models.models_individual.voxel
        • spateo.tdr.models.models_migration
          • spateo.tdr.models.models_migration.arrow_model
          • spateo.tdr.models.models_migration.line_model
          • spateo.tdr.models.models_migration.morphofield_model
          • spateo.tdr.models.models_migration.morphopath_model
        • spateo.tdr.models.utilities
          • spateo.tdr.models.utilities.io
          • spateo.tdr.models.utilities.label_utils
          • spateo.tdr.models.utilities.model_utils
      • spateo.tdr.morphometrics
        • spateo.tdr.morphometrics.gene_similarity
        • spateo.tdr.morphometrics.morphofield
          • spateo.tdr.morphometrics.morphofield.gaussian_process
          • spateo.tdr.morphometrics.morphofield.sparsevfc
          • spateo.tdr.morphometrics.morphofield.trajectory
        • spateo.tdr.morphometrics.morphofield_dg
          • spateo.tdr.morphometrics.morphofield_dg.GPVectorField
          • spateo.tdr.morphometrics.morphofield_dg.differential_geometry
        • spateo.tdr.morphometrics.morphology
        • spateo.tdr.morphometrics.shape_similarity
      • spateo.tdr.widgets
        • spateo.tdr.widgets.clip
        • spateo.tdr.widgets.pick
        • spateo.tdr.widgets.slice
        • spateo.tdr.widgets.utils
    • spateo.tl
    • spateo.tools
      • spateo.tools.CCI_effects_modeling
        • spateo.tools.CCI_effects_modeling.MuSIC
        • spateo.tools.CCI_effects_modeling.MuSIC_downstream
        • spateo.tools.CCI_effects_modeling.MuSIC_upstream
        • spateo.tools.CCI_effects_modeling.SWR
        • spateo.tools.CCI_effects_modeling.distributions
        • spateo.tools.CCI_effects_modeling.regression_utils
      • spateo.tools.architype
      • spateo.tools.cci_fdr
      • spateo.tools.cci_two_cluster
      • spateo.tools.cell_communication
      • spateo.tools.cluster
        • spateo.tools.cluster._stagate
        • spateo.tools.cluster.cluster_spagcn
        • spateo.tools.cluster.find_clusters
        • spateo.tools.cluster.leiden
        • spateo.tools.cluster.spagcn_utils
        • spateo.tools.cluster.utils
      • spateo.tools.cluster_degs
      • spateo.tools.cluster_lasso
      • spateo.tools.coarse_align
      • spateo.tools.dimensionality_reduction
      • spateo.tools.find_neighbors
      • spateo.tools.gene_expression_variance
      • spateo.tools.glm
      • spateo.tools.labels
      • spateo.tools.lisa
      • spateo.tools.live_wire
      • spateo.tools.roi
      • spateo.tools.spatial_correlation
      • spateo.tools.spatial_degs
      • spateo.tools.spatial_smooth
      • spateo.tools.spatially_variable_gene_ot
      • spateo.tools.utils
    • spateo.utils
    • spateo.warnings
  • References
  • Contributors
  • Contributing
  • GitHub
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spateo.segmentation.external¶

Submodules¶

  • spateo.segmentation.external.cellpose
  • spateo.segmentation.external.deepcell
  • spateo.segmentation.external.stardist
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