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Installation
API
spatialdata.SpatialData
spatialdata.bounding_box_query
spatialdata.polygon_query
spatialdata.get_values
spatialdata.get_extent
spatialdata.get_centroids
spatialdata.join_spatialelement_table
spatialdata.match_element_to_table
spatialdata.get_centroids
spatialdata.match_table_to_element
spatialdata.concatenate
spatialdata.transform
spatialdata.rasterize
spatialdata.to_circles
spatialdata.aggregate
spatialdata.unpad_raster
spatialdata.are_extents_equal
spatialdata.deepcopy
spatialdata.models.Image2DModel
spatialdata.models.Image3DModel
spatialdata.models.Labels2DModel
spatialdata.models.Labels3DModel
spatialdata.models.ShapesModel
spatialdata.models.PointsModel
spatialdata.models.TableModel
spatialdata.models.get_model
spatialdata.models.SpatialElement
spatialdata.models.get_axes_names
spatialdata.models.get_spatial_axes
spatialdata.models.points_geopandas_to_dask_dataframe
spatialdata.models.points_dask_dataframe_to_geopandas
spatialdata.models.get_channels
spatialdata.models.force_2d
spatialdata.transformations.BaseTransformation
spatialdata.transformations.Identity
spatialdata.transformations.MapAxis
spatialdata.transformations.Translation
spatialdata.transformations.Scale
spatialdata.transformations.Affine
spatialdata.transformations.Sequence
spatialdata.transformations.get_transformation
spatialdata.transformations.set_transformation
spatialdata.transformations.remove_transformation
spatialdata.transformations.get_transformation_between_coordinate_systems
spatialdata.transformations.get_transformation_between_landmarks
spatialdata.transformations.align_elements_using_landmarks
spatialdata.transformations.remove_transformations_to_coordinate_system
spatialdata.dataloader.ImageTilesDataset
spatialdata.read_zarr
spatialdata.save_transformations
spatialdata.get_dask_backing_files
spatialdata.testing.assert_spatial_data_objects_are_identical
spatialdata.testing.assert_elements_are_identical
spatialdata.testing.assert_elements_dict_are_identical
Tutorials
I. Use SpatialData with your data: the SpatialData object.
II. Use SpatialData with your data: SpatialElements and tables
Transformations and coordinate systems
Spatial query
Annotating regions of interest with
napari
Use landmark annotations to align multiple -omics layers
Working with annotations in SpatialData
Integrate/aggregate signals across spatial layers
Squidpy integration
Deep learning example on image tiles
Technology focus: 10x Genomics Visium
Technology focus: MIBI-TOF
Technology focus: MERFISH
Technology focus: CosMx
Technology focus: Visium HD
Technology focus: Xenium
Implicit performance improvements when plotting raster data
Spatial omics datasets
Design document for
SpatialData
Contributing guide
Changelog
References
.rst
.pdf
spatialdata.dataloader.ImageTilesDataset
Contents
ImageTilesDataset
spatialdata.dataloader.ImageTilesDataset
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spatialdata.dataloader.
ImageTilesDataset
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Contents
ImageTilesDataset
