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Multimodal spatial omics data Cross-modality aggregation Interactive annotation
Omics Data Automation  
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SpatialData: an open and universal data framework for spatial omics 
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(A) The SpatialData storage format provides uniform storage for raw and derived data of diverse spatial <t>omics</t> technologies. The format builds on five primitive elements (SpatialElements), stored to Zarr in an OME-NGFF compliant manner. (B) The SpatialData Python library implements core operations for data access, alignment, queries, and aggregation of spatial omics data. Transformations align multiple SpatialElements to a common coordinate system (CCS). The CCS allows unified spatial queries and aggregation operators to be deployed across datasets. (C) SpatialData provides access to various data formats, including vendor-specific file formats. Multiple datasets can be stored in a single file and together are represented as a SpatialData object. (D) Datasets stored in the SpatialData format can be annotated interactively using the integrated napari-spatialdata plugin. SpatialData also provides functionality for generating static plots. (E) Leveraging an implementation of the PyTorch Dataset class, deep learning models can be trained directly from SpatialData objects. (F) Since SpatialData builds upon established standards and software, it ties into the existing ecosystem for <t>multimodal</t> analysis including Squidpy , Scanpy , MONAI and scvi-tools , amongst others.
SpatialData: an open and universal data framework for spatial omics 
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(A) The SpatialData storage format builds on the OME-NGFF specification by prototyping new data types required to store spatial <t>omics</t> information. Coordinate systems and transforms as well as tables are currently in review by the community. Points and shapes will be submitted to the community for review in a next phase to ensure interoperability. (B) Storage format of SpatialData: it consists of one Zarr container with nested folder structure, one for each SpatialData element. Each of the elements is saved as Zarr arrays, except for the Points, which are stored as an Apache Parquet file. We want to highlight that the Parquet file storage for points might change in the near future when a Zarr alternative will be implemented.
SpatialData: an open and universal data framework for spatial omics bioRxiv, 2023 May 08
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