splisosm.io =========== .. py:module:: splisosm.io .. autoapi-nested-parse:: I/O loaders for SpatialData-based workflows. This module provides high-level wrappers for constructing SpatialData objects from platform-specific outputs. Functions --------- .. autoapisummary:: splisosm.io.load_visiumhd_probe splisosm.io.load_xenium_codeword Module Contents --------------- .. py:function:: load_visiumhd_probe(path, dataset_id = None, bin_sizes = None, bins_as_squares = True, fullres_image_file = None, load_all_images = False, var_names_make_unique = True, filtered_counts_file = True, counts_layer_name = 'counts', path_to_feature_2um_h5 = None) Load Visium HD outputs as SpatialData with probe-level binned tables. This wrapper uses ``binned_outputs/square_002um/raw_probe_bc_matrix.h5`` (or a custom ``path_to_feature_2um_h5``) as the source feature count matrix. It aggregates probe/peak/isoform counts to coarser bins or cells (``square_008um``, ``square_016um`` and, when available, ``cell_id``) according to the spatial mapping ``barcode_mappings.parquet`` (Space Ranger v4.0+ required). :param path: Path to Space Ranger ``outs`` directory for Visium HD. :param dataset_id: Optional dataset ID passed to the SpatialData reader. :param bin_sizes: Bin resolutions to include. Each entry can be ``int`` (for example ``8``) or Visium HD bin string (for example ``"square_008um"``). If ``None``, all available ``square_*um`` bins under ``binned_outputs`` are used. :param bins_as_squares: Whether bins are represented as squares when loading shapes. :param fullres_image_file: Path to the full-resolution image. :param load_all_images: Whether to load all optional images via ``spatialdata_io`` reader. :param var_names_make_unique: Whether to call ``var_names_make_unique()`` on probe table variables. :param filtered_counts_file: Whether to keep only in-tissue 2um barcodes prior to aggregation. If ``True``, barcodes are taken from the source bin table loaded by ``visium_hd`` (``square_002um``). If unavailable, the function falls back to ``binned_outputs/square_002um/filtered_feature_bc_matrix.h5``. :param counts_layer_name: Layer name used to store aggregated probe counts in each output table. :param path_to_feature_2um_h5: Optional path to the raw 2um probe/peak/isoform counts matrix H5 or H5AD. If not provided, will look for ``binned_outputs/square_002um/raw_feature_bc_matrix.h5``. :returns: A SpatialData object with probe-level tables for requested bins and, if available, cell-level segmentation. :rtype: spatialdata.SpatialData :raises ImportError: If required optional dependencies are not installed. :raises ValueError: If required files or requested bins are missing. .. py:function:: load_xenium_codeword(path, spatial_resolutions = (8.0, 16.0), quality_threshold = 20.0, n_jobs = -1, chunk_batch_size = 64, counts_layer_name = 'counts', build_cell_codeword_table = True, create_square_shapes = True, cells_boundaries = True, nucleus_boundaries = True, cells_as_circles = False, cells_labels = True, nucleus_labels = True, transcripts = True, morphology_mip = True, morphology_focus = True, aligned_images = True, cells_table = True, gex_only = True, show_progress = True) Load Xenium outputs and append multi-resolution codeword bin tables. This wrapper reads Xenium Ranger ``outs`` with ``spatialdata-io`` and then quantifies codewords into square spatial bins at one or more user-defined resolutions using transcript-level chunk data (``grids/0/*``). Counting is implemented with vectorized sparse aggregation over ``(spot, codeword)`` pairs to reduce Python overhead while avoiding dependence on optional precomputed density matrices. For each resolution, a table named ``square_XXXum`` is added to ``sdata.tables``; optional square geometries with a ``_bins`` suffix are added to ``sdata.shapes`` so the tables can be used directly with :func:`spatialdata.rasterize_bins`. ``transcripts.zarr.zip`` is expected to contain the ``density/codeword`` group for codeword indexing (Xenium Ranger v3.1+ required). If ``build_cell_codeword_table=True`` and the ``transcripts.parquet`` file is available, a cell-by-codeword anndata named ``table_codeword`` will also be built and added to ``sdata.tables``. :param path: Path to Xenium Ranger output directory, or its parent containing ``outs/``. :param spatial_resolutions: Spatial bin sizes in microns. :param quality_threshold: Minimum transcript quality score to retain. :param n_jobs: Parallel worker count for chunk processing. Use ``-1`` for all cores. :param chunk_batch_size: Number of transcript chunks submitted per processing batch. :param counts_layer_name: Layer name used to store codeword counts in each output table. :param build_cell_codeword_table: Whether to build a cell-by-codeword table from the transcripts parquet file. :param create_square_shapes: Whether to create square bin shapes for each table key. :param cells_boundaries: Passed to ``spatialdata_io.readers.xenium.xenium``. :param nucleus_boundaries: Passed to ``spatialdata_io.readers.xenium.xenium``. :param cells_as_circles: Passed to ``spatialdata_io.readers.xenium.xenium``. :param cells_labels: Passed to ``spatialdata_io.readers.xenium.xenium``. :param nucleus_labels: Passed to ``spatialdata_io.readers.xenium.xenium``. :param transcripts: Passed to ``spatialdata_io.readers.xenium.xenium``. :param morphology_mip: Passed to ``spatialdata_io.readers.xenium.xenium``. :param morphology_focus: Passed to ``spatialdata_io.readers.xenium.xenium``. :param aligned_images: Passed to ``spatialdata_io.readers.xenium.xenium``. :param cells_table: Passed to ``spatialdata_io.readers.xenium.xenium``. :param gex_only: Passed to ``spatialdata_io.readers.xenium.xenium``. :param show_progress: Whether to display progress bars while binning codewords. :returns: SpatialData object augmented with bin-by-codeword count tables at each requested resolution and, when requested, a cell-by-codeword table named ``table_codeword``. :rtype: spatialdata.SpatialData :raises ImportError: If required optional dependencies are not installed. :raises ValueError: If path/layout/arguments are invalid.