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Spateo documentation

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Documentation home
Installation
Tutorials
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- Cell segmentation
  Toggle navigation of Cell segmentation
  - Stain segmentation
  - RNA segmentation
- Spatially variable genes identificaion
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  - 1. Spatially variable genes identification within slice
- Alignment
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- Three dimensional reconstruction
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- Clustering and digitization
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- Cell-cell interaction
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- Morphometric vector field and kinetics
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- Interactive tools
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  - 1.Auxiliary segmentation (AuxSeg): an interactive tool for ROI segmentation
  - 2.Enhancing visualization clarity for categorical spatial datasets using Spaco
Technicals
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- Cell segmentation
- Tissue geometry digitization
API
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- spateo.alignment
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- spateo.digitization
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- spateo.external
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  - spateo.external.CAST
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    - spateo.external.CAST.model
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      - spateo.external.CAST.model.aug
      - spateo.external.CAST.model.model_GCNII
    - spateo.external.CAST.CAST_Mark
    - spateo.external.CAST.CAST_Projection
    - spateo.external.CAST.CAST_Stack
    - spateo.external.CAST.main
    - spateo.external.CAST.utils
    - spateo.external.CAST.visualize
  - spateo.external.STAGATE_pyG
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  - spateo.external.lack
- spateo.io
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- spateo.plotting
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  - spateo.plotting.interactive
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    - spateo.plotting.interactive.agg
  - spateo.plotting.static
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- spateo.preprocessing
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- spateo.segmentation
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  - spateo.segmentation.external
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  - spateo.segmentation.simulation_evaluation
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  - spateo.segmentation.align
  - spateo.segmentation.benchmark
  - spateo.segmentation.bp
  - spateo.segmentation.density
  - spateo.segmentation.em
  - spateo.segmentation.icell
  - spateo.segmentation.label
  - spateo.segmentation.moran
  - spateo.segmentation.qc
  - spateo.segmentation.simulation
  - spateo.segmentation.utils
  - spateo.segmentation.vi
- spateo.svg
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- spateo.tdr
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  - spateo.tdr.interpolations
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    - spateo.tdr.interpolations.interpolation_deeplearn
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    - spateo.tdr.interpolations.interpolation_gaussianprocess
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      - spateo.tdr.interpolations.interpolation_gaussianprocess.gp_models
      - spateo.tdr.interpolations.interpolation_gaussianprocess.gp_train
    - spateo.tdr.interpolations.interpolation_dl
    - spateo.tdr.interpolations.interpolation_gp
    - spateo.tdr.interpolations.interpolation_sparseVFC
    - spateo.tdr.interpolations.interpolation_vtk
    - spateo.tdr.interpolations.utils
  - spateo.tdr.models
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    - spateo.tdr.models.models_backbone
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    - spateo.tdr.models.models_individual
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    - spateo.tdr.models.models_migration
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    - spateo.tdr.models.utilities
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  - spateo.tdr.morphometrics
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    - spateo.tdr.morphometrics.morphofield
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    - spateo.tdr.morphometrics.morphofield_dg
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      - spateo.tdr.morphometrics.morphofield_dg.GPVectorField
      - spateo.tdr.morphometrics.morphofield_dg.differential_geometry
    - spateo.tdr.morphometrics.gene_similarity
    - spateo.tdr.morphometrics.morphology
    - spateo.tdr.morphometrics.shape_similarity
  - spateo.tdr.widgets
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- spateo.tools
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- spateo.align
- spateo.configuration
- spateo.cs
- spateo.data_io
- spateo.dd
- spateo.errors
- spateo.get_version
- spateo.logging
- spateo.pl
- spateo.pp
- spateo.sample_data
- spateo.tl
- spateo.utils
- spateo.warnings
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