spatialdata-io 0.1.2__tar.gz → 0.1.3.post0__tar.gz

spatialdata_io-0.1.3.post0/.github/codecov.yml

@@ -0,0 +1,17 @@
+# Based on pydata/xarray
+codecov:
+    require_ci_to_pass: false
+
+coverage:
+    status:
+        project:
+            default:
+                # Require 1% coverage, i.e., always succeed
+                target: 1
+        patch: false
+        changes: false
+
+comment:
+    layout: "diff, flags, files"
+    behavior: once
+    require_base: false

spatialdata_io-0.1.3.post0/.github/workflows/prepare_test_data.yaml

@@ -0,0 +1,35 @@
+name: Prepare test data
+
+on:
+    workflow_dispatch:
+# uncomment and adjust the branch name if you need to add new datasets to the artifact
+#    push:
+#        branches:
+#            - main
+
+jobs:
+    prepare-data:
+        runs-on: ubuntu-latest
+
+        steps:
+            - uses: actions/checkout@v3
+
+            - name: Download test datasets
+              run: |
+                  mkdir -p ./data
+                  cd ./data
+                  curl -O https://cf.10xgenomics.com/samples/xenium/2.0.0/Xenium_V1_human_Breast_2fov/Xenium_V1_human_Breast_2fov_outs.zip
+                  curl -O https://cf.10xgenomics.com/samples/xenium/2.0.0/Xenium_V1_human_Lung_2fov/Xenium_V1_human_Lung_2fov_outs.zip
+
+            - name: Unzip files
+              run: |
+                  unzip ./data/Xenium_V1_human_Breast_2fov_outs.zip -d ./data/Xenium_V1_human_Breast_2fov_outs
+                  unzip ./data/Xenium_V1_human_Lung_2fov_outs.zip -d ./data/Xenium_V1_human_Lung_2fov_outs
+                  rm ./data/Xenium_V1_human_Breast_2fov_outs.zip
+                  rm ./data/Xenium_V1_human_Lung_2fov_outs.zip
+
+            - name: Upload artifacts
+              uses: actions/upload-artifact@v3
+              with:
+                  name: data
+                  path: ./data

{spatialdata_io-0.1.2 → spatialdata_io-0.1.3.post0}/.github/workflows/test.yaml

@@ -50,6 +50,21 @@ jobs:
             - name: Install dependencies
               run: |
                   pip install --pre -e ".[dev,test]"
+
+            - name: Download artifact of test data
+              if: matrix.python == '3.10'
+              uses: dawidd6/action-download-artifact@v2
+              with:
+                  workflow: prepare_test_data.yaml
+                  name: data
+                  path: ./data
+
+            - name: List the data directory
+              if: matrix.python == '3.10'
+              run: |
+                  ls -l ./data
+                  pwd
+
             - name: Test
               env:
                   MPLBACKEND: agg
@@ -58,7 +73,9 @@ jobs:
               run: |
                   pytest -v --cov --color=yes --cov-report=xml
             - name: Upload coverage to Codecov
-              uses: codecov/codecov-action@v3.1.1
+              uses: codecov/codecov-action@v4
               with:
                   name: coverage
                   verbose: true
+              env:
+                  CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

{spatialdata_io-0.1.2 → spatialdata_io-0.1.3.post0}/.gitignore

@@ -2,6 +2,7 @@
 .DS_Store
 *~
 *.tmp
+temp/
 
 # Compiled files
 __pycache__/
@@ -31,6 +32,9 @@ __pycache__/
 
 # other
 _version.py
-.code-workspace
-temp/
 node_modules/
+.code-workspace
+
+# test datasets (e.g. Xenium ones)
+data/
+tests/data

{spatialdata_io-0.1.2 → spatialdata_io-0.1.3.post0}/.pre-commit-config.yaml

@@ -7,7 +7,7 @@ default_stages:
 minimum_pre_commit_version: 2.16.0
 repos:
     - repo: https://github.com/psf/black
-      rev: 24.3.0
+      rev: 24.4.2
       hooks:
           - id: black
     - repo: https://github.com/pre-commit/mirrors-prettier
@@ -15,7 +15,7 @@ repos:
       hooks:
           - id: prettier
     - repo: https://github.com/asottile/blacken-docs
-      rev: 1.16.0
+      rev: 1.18.0
       hooks:
           - id: blacken-docs
     - repo: https://github.com/PyCQA/isort
@@ -23,7 +23,7 @@ repos:
       hooks:
           - id: isort
     - repo: https://github.com/pre-commit/mirrors-mypy
-      rev: v1.9.0
+      rev: v1.10.1
       hooks:
           - id: mypy
             additional_dependencies: [numpy, types-PyYAML]
@@ -40,7 +40,7 @@ repos:
                 - flake8-bugbear
                 - flake8-blind-except
     - repo: https://github.com/pre-commit/pre-commit-hooks
-      rev: v4.5.0
+      rev: v4.6.0
       hooks:
           - id: detect-private-key
           - id: check-ast
@@ -59,7 +59,7 @@ repos:
                 - --remove-unused-variable
                 - --ignore-init-module-imports
     - repo: https://github.com/PyCQA/flake8
-      rev: 7.0.0
+      rev: 7.1.0
       hooks:
           - id: flake8
             additional_dependencies:
@@ -70,7 +70,7 @@ repos:
                 - flake8-bugbear
                 - flake8-blind-except
     - repo: https://github.com/asottile/pyupgrade
-      rev: v3.15.2
+      rev: v3.16.0
       hooks:
           - id: pyupgrade
             args: [--py3-plus, --py39-plus, --keep-runtime-typing]

{spatialdata_io-0.1.2 → spatialdata_io-0.1.3.post0}/CHANGELOG.md

@@ -8,6 +8,27 @@ and this project adheres to [Semantic Versioning][].
 [keep a changelog]: https://keepachangelog.com/en/1.0.0/
 [semantic versioning]: https://semver.org/spec/v2.0.0.html
 
+## [0.1.4] - xxxx-xx-xx
+
+## [0.1.3] - 2024-07-03
+
+### Added
+
+-   (Xenium) support reading multi-polygon selection files from the Xenium Explorer
+-   (ISS) An experimental loader to load elemental ISS data objects, e.g. raw.tif, label.tif and anndata.h5ad
+-   (Stereo-seq) Added reader @LLehner @timtreis @florianingelfinger #70
+-   (MERSCOPE) Optional rioxarray backend for MERSCOPE data (reads chunks)
+-   (MERSCOPE) Can choose which elements should be loaded
+
+### Fixed
+
+-   (Visium) Fixed issue with joining a SpatialElement with a table due to index values not being unique.
+    obs_names_make_unique is now called internally to enforce unique index values allowing for join operations.
+
+### Changed
+
+-   (MERSCOPE) "global" coordinate system is used as a default instead of "microns"
+
 ## [0.1.2] - 2024-03-30
 
 ### Added

{spatialdata_io-0.1.2 → spatialdata_io-0.1.3.post0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: spatialdata-io
-Version: 0.1.2
+Version: 0.1.3.post0
 Summary: SpatialData IO for common techs
 Project-URL: Documentation, https://spatialdata-io.readthedocs.io/
 Project-URL: Source, https://github.com/scverse/spatialdata-io
@@ -48,7 +48,7 @@ Requires-Dist: pyarrow
 Requires-Dist: readfcs
 Requires-Dist: scanpy
 Requires-Dist: scikit-image
-Requires-Dist: spatialdata
+Requires-Dist: spatialdata>=0.2.1
 Provides-Extra: dev
 Requires-Dist: bump2version; extra == 'dev'
 Requires-Dist: pre-commit; extra == 'dev'
@@ -91,6 +91,7 @@ This package contains reader functions to load common spatial omics formats into
 -   MCMICRO (output data)
 -   NanoString CosMx
 -   Steinbock (output data)
+-   STOmics Stereo-seq
 -   Vizgen MERSCOPE (MERFISH)
 
 ## Getting started

{spatialdata_io-0.1.2 → spatialdata_io-0.1.3.post0}/README.md

@@ -21,6 +21,7 @@ This package contains reader functions to load common spatial omics formats into
 -   MCMICRO (output data)
 -   NanoString CosMx
 -   Steinbock (output data)
+-   STOmics Stereo-seq
 -   Vizgen MERSCOPE (MERFISH)
 
 ## Getting started

{spatialdata_io-0.1.2 → spatialdata_io-0.1.3.post0}/_version.py

@@ -12,5 +12,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.1.2'
-__version_tuple__ = version_tuple = (0, 1, 2)
+__version__ = version = '0.1.3.post0'
+__version_tuple__ = version_tuple = (0, 1, 3)

{spatialdata_io-0.1.2 → spatialdata_io-0.1.3.post0}/docs/api.md

@@ -20,25 +20,34 @@ I/O for the `spatialdata` project.
     dbit
     mcmicro
     merscope
+    seqfish
     steinbock
+    stereoseq
     visium
     visium_hd
     xenium
 ```
 
-### Conversion functions
-
-### Utility functions
+### Experimental readers
 
 ```{eval-rst}
+.. currentmodule:: spatialdata_io.experimental
+
 .. autosummary::
     :toctree: generated
 
-    xenium_aligned_image
-    xenium_explorer_selection
+    iss
 ```
 
-### Experimental readers
+### Conversion functions
+
+```{eval-rst}
+.. currentmodule:: spatialdata_io
+
+.. autosummary::
+    :toctree: generated
+
+```
 
 ### Experimental conversion functions
 
@@ -51,3 +60,15 @@ I/O for the `spatialdata` project.
     from_legacy_anndata
     to_legacy_anndata
 ```
+
+### Utility functions
+
+```{eval-rst}
+.. currentmodule:: spatialdata_io
+
+.. autosummary::
+    :toctree: generated
+
+    xenium_aligned_image
+    xenium_explorer_selection
+```

{spatialdata_io-0.1.2 → spatialdata_io-0.1.3.post0}/pyproject.toml

@@ -25,7 +25,7 @@ dependencies = [
     "anndata",
     "numpy",
     "scanpy",
-    "spatialdata",
+    "spatialdata>=0.2.1",
     "scikit-image",
     "h5py",
     "joblib",

{spatialdata_io-0.1.2 → spatialdata_io-0.1.3.post0}/src/spatialdata_io/__init__.py

@@ -6,7 +6,9 @@ from spatialdata_io.readers.curio import curio
 from spatialdata_io.readers.dbit import dbit
 from spatialdata_io.readers.mcmicro import mcmicro
 from spatialdata_io.readers.merscope import merscope
+from spatialdata_io.readers.seqfish import seqfish
 from spatialdata_io.readers.steinbock import steinbock
+from spatialdata_io.readers.stereoseq import stereoseq
 from spatialdata_io.readers.visium import visium
 from spatialdata_io.readers.visium_hd import visium_hd
 from spatialdata_io.readers.xenium import (
@@ -17,12 +19,14 @@ from spatialdata_io.readers.xenium import (
 
 __all__ = [
     "curio",
+    "seqfish",
     "visium",
     "xenium",
     "codex",
     "cosmx",
     "mcmicro",
     "steinbock",
+    "stereoseq",
     "merscope",
     "xenium_aligned_image",
     "xenium_explorer_selection",

{spatialdata_io-0.1.2 → spatialdata_io-0.1.3.post0}/src/spatialdata_io/_constants/_constants.py

@@ -59,6 +59,36 @@ class CosmxKeys(ModeEnum):
     TARGET_OF_TRANSCRIPT = "target"
 
 
+@unique
+class SeqfishKeys(ModeEnum):
+    """Keys for *Spatial Genomics SeqFISH* formatted dataset."""
+
+    # file extensions
+    CSV_FILE = ".csv"
+    TIFF_FILE = ".tiff"
+    OME_TIFF_FILE = ".ome.tiff"
+    # file identifiers
+    SECTION = "section"
+    TRANSCRIPT_COORDINATES = "TranscriptCoordinates"
+    DAPI = "DAPI"
+    COUNTS_FILE = "CxG"
+    CELL_MASK_FILE = "CellMask"
+    CELL_COORDINATES = "CellCoordinates"
+    # transcripts
+    TRANSCRIPTS_X = "x"
+    TRANSCRIPTS_Y = "y"
+    FEATURE_KEY = "name"
+    INSTANCE_KEY_POINTS = "cell"
+    # cells
+    AREA = "area"
+    CELL_X = "center_x"
+    CELL_Y = "center_y"
+    # metadata
+    SPATIAL_KEY = "spatial"
+    REGION_KEY = "region"
+    INSTANCE_KEY_TABLE = "instance_id"
+
+
 @unique
 class XeniumKeys(ModeEnum):
     """Keys for *10X Genomics Xenium* formatted dataset."""
@@ -121,6 +151,10 @@ class XeniumKeys(ModeEnum):
     NUCLEUS_COUNT = "nucleus_count"
     Z_LEVEL = "z_level"
 
+    EXPLORER_SELECTION_X = "X"
+    EXPLORER_SELECTION_Y = "Y"
+    EXPLORER_SELECTION_KEY = "Selection"
+
 
 @unique
 class VisiumKeys(ModeEnum):
@@ -161,6 +195,79 @@ class SteinbockKeys(ModeEnum):
     LABEL_SUFFIX = ".tiff"
 
 
+@unique
+class StereoseqKeys(ModeEnum):
+    """Keys for *Stereo-seq* formatted dataset."""
+
+    # file extensions
+    GEF_FILE = ".gef"
+    TIF_FILE = ".tif"
+    # directories
+    MERGE = "01.merge"
+    COUNT_DIRECTORY = "02.count"
+    REGISTER = "03.register"
+    TISSUECUT = "04.tissuecut"
+    SPATIALCLUSTER = "05.spatialcluster"
+    SATURATION = "06.saturation"
+    CELLCUT = "041.cellcut"
+    CELLCLUSTER = "051.cellcluster"
+    # file identifiers
+    MASK_TIF = "_mask.tif"
+    REGIST_TIF = "_regist.tif"
+    TISSUE_TIF = "_tissue_cut.tif"
+    CELL_CLUSTER_H5AD = "cell.cluster.h5ad"
+    RAW_GEF = ".raw.gef"
+    CELLBIN_GEF = ".cellbin.gef"
+    TISSUECUT_GEF = ".tissuecut.gef"
+    TISSUE_GEM = ".tissue.gem.gz"
+    # transcripts
+    FEATURE_KEY = "gene"
+    GENE_NAME = "geneName"
+    CELL_COUNT = "cellCount"
+    MAX_MID_COUNT = "maxMIDcount"
+    GENE_EXP = "geneExp"
+    EXPRESSION = "expression"
+    EXON = "exon"
+    GENE_ID = "geneID"
+    GENE_EXP_EXON = "geneExpExon"
+    # cells
+    ID = "id"
+    CELL_ID = "cellID"
+    GENE_COUNT = "geneCount"
+    DNBCOUNT = "dnbCount"
+    CELL_AREA = "area"
+    CELL_TYPE_ID = "cellTypeID"
+    CLUSTER_ID = "clusterID"
+    CELL_BIN = "cellBin"
+    CELL_EXON = "cellExon"
+    CELL_DATASET = "cell"
+    GENE_EXON = "geneExon"
+    CELL_BORDER = "cellBorder"
+    CELL_EXP = "cellExp"
+    CELL_EXP_EXON = "cellExpExon"
+    PADDING_VALUE = 32767
+    # metadata
+    COUNT = "count"
+    EXP_COUNT = "expCount"
+    OFFSET = "offset"
+    COORD_X = "x"
+    COORD_Y = "y"
+    SPATIAL_KEY = "spatial"
+    REGION = "cells"
+    REGION_KEY = "region"
+    INSTANCE_KEY = "instance_id"
+    BLOCK_INDEX = "blockIndex"
+    BLOCK_SIZE = "blockSize"
+    CELL_TYPE_LIST = "cellTypeList"
+    # bin data and metadata
+    BIN1 = "bin1"
+    MIN_X = "minX"
+    MIN_Y = "minY"
+    MAX_X = "maxX"
+    MAX_Y = "maxY"
+    RESOLUTION = "resolution"
+
+
 @unique
 class McmicroKeys(ModeEnum):
     """Keys for *Mcmicro* formatted dataset."""
@@ -238,6 +345,7 @@ class VisiumHDKeys(ModeEnum):
     DEFAULT_BIN = "square_008um"
     BIN_PREFIX = "square_"
     MICROSCOPE_IMAGE = "microscope_image"
+    BINNED_OUTPUTS = "binned_outputs"
 
     # counts and locations files
     FILTERED_COUNTS_FILE = "filtered_feature_bc_matrix.h5"

{spatialdata_io-0.1.2 → spatialdata_io-0.1.3.post0}/src/spatialdata_io/converters/legacy_anndata.py

@@ -173,7 +173,7 @@ def to_legacy_anndata(
         sdata_images = sdata.subset(element_names=list(sdata.images.keys()))
         for image_name, image in sdata_images.images.items():
             sdata_pre_rasterize[image_name] = image
-        bb = get_extent(sdata_images)
+        bb = get_extent(sdata_images, coordinate_system=coordinate_system)
 
         parameters_dict = {"x": "target_width", "y": "target_height", "z": "target_depth"}
         longest_side = max(bb, key=bb.get)

{spatialdata_io-0.1.2 → spatialdata_io-0.1.3.post0}/src/spatialdata_io/experimental/__init__.py

@@ -2,5 +2,6 @@ from spatialdata_io.converters.legacy_anndata import (
     from_legacy_anndata,
     to_legacy_anndata,
 )
+from spatialdata_io.readers.iss import iss
 
-__all__ = ["from_legacy_anndata", "to_legacy_anndata"]
+__all__ = ["from_legacy_anndata", "to_legacy_anndata", "iss"]

{spatialdata_io-0.1.2 → spatialdata_io-0.1.3.post0}/src/spatialdata_io/readers/_utils/_utils.py

@@ -1,6 +1,7 @@
 from __future__ import annotations
 
 import os
+from collections.abc import Mapping
 from pathlib import Path
 from typing import Any, Optional, Union
 
@@ -66,3 +67,20 @@ def _read_counts(
 
     adata.uns["spatial"] = {library_id: {"metadata": {}}}  # can overwrite
     return adata, library_id
+
+
+def _initialize_raster_models_kwargs(
+    image_models_kwargs: Mapping[str, Any], labels_models_kwargs: Mapping[str, Any]
+) -> tuple[dict[str, Any], dict[str, Any]]:
+    image_models_kwargs = dict(image_models_kwargs)
+    if "chunks" not in image_models_kwargs:
+        image_models_kwargs["chunks"] = (1, 4096, 4096)
+    if "scale_factors" not in image_models_kwargs:
+        image_models_kwargs["scale_factors"] = [2, 2, 2, 2]
+
+    labels_models_kwargs = dict(labels_models_kwargs)
+    if "chunks" not in labels_models_kwargs:
+        labels_models_kwargs["chunks"] = (4096, 4096)
+    if "scale_factors" not in labels_models_kwargs:
+        labels_models_kwargs["scale_factors"] = [2, 2, 2, 2]
+    return image_models_kwargs, labels_models_kwargs

{spatialdata_io-0.1.2 → spatialdata_io-0.1.3.post0}/src/spatialdata_io/readers/cosmx.py

@@ -12,7 +12,7 @@ import numpy as np
 import pandas as pd
 import pyarrow as pa
 from anndata import AnnData
-from dask.dataframe.core import DataFrame as DaskDataFrame
+from dask.dataframe import DataFrame as DaskDataFrame
 from dask_image.imread import imread
 from scipy.sparse import csr_matrix
 

{spatialdata_io-0.1.2 → spatialdata_io-0.1.3.post0}/src/spatialdata_io/readers/dbit.py

@@ -37,48 +37,77 @@ def _check_path(
     ----------
     path
         The path of the main directory where to search for the path.
-    path_specific
-        path to the file, if it is not in the main directory.
     pattern
         regex pattern.
     key
         String to match in the path or path_specific path.
+    path_specific
+        path to the file, if it is not in the main directory.
+        If it is given and valid, this is used and 'path' is neglected.
     optional_arg
-        User specify if the file to search is mandatory (optional_arg=True, raise an Error if not found)
-        or optional (optional_arg=False, raise a Warning if not found).
+        User specify if the file to search is:
+            mandatory:  (optional_arg=False, raise an Error if not found)
+            optional:   (optional_arg=True, raise a Warning if not found).
 
     Raises
     ------
     FileNotFoundError
-        The error is raised if no match is found in the given paths and optional_arg=True.
+        Raised if no match is found in the given paths and optional_arg=False.
+    Exception
+        Raised if there are multiple file mathing a pattern.
+    IndexError
+        Raised if no matching file is found.
 
     Returns
     -------
-    tuple(pathlib.PosixPath, bool)
-        return a tuple(pathlib.PosixPath, bool). The bool is a flag that indicate if one of the supplied path arguments points to a file that match the supplied key.
+    (tuple[Union[Path, None], bool])
+        return the file path if valid, or None if not valid, and a bool.
+        The bool is a flag that indicates if one of the supplied path arguments
+        points to a file that matches the supplied key.
+
     """
     flag = False
     file_path = None
-    try:
-        checked_file = [i for i in os.listdir(path) if pattern.match(i)][0]  # this is the filename
-        file_path = Path.joinpath(path, checked_file)
-        flag = True
-    except IndexError:
-        # handle case in which the searched file is not in the same directory as path
-        if path_specific is not None:
-            if os.path.isfile(path_specific):
-                file_path = Path(path_specific)
-                flag = True
-            else:
-                if optional_arg:
-                    logger.warning(f"{path_specific} is not a valid path for {key}. No {key} will be used.")
-                else:
-                    raise FileNotFoundError(f"{path_specific} is not a valid path for a {key} file.")
+    # check if a specific file path is given and is valid.
+    # If yes, it is used. Has priority with respect to the 'path' argument.
+    if path_specific is not None:
+        if os.path.isfile(path_specific):
+            file_path = Path(path_specific)
+            flag = True
         else:
+            # if path_specific is not valid but optional, give warning
             if optional_arg:
-                logger.warning(f"No file containing {key} found in folder {path}. No {key} will be used.")
+                logger.warning(f"{path_specific} is not a valid path for {key}. No {key} will be used.")
+            # if path_specific is not valid but mandatory, raise error
             else:
-                raise FileNotFoundError(f"No file containing {key} found in folder {path}.")
+                raise FileNotFoundError(f"{path_specific} is not a valid path for a {key} file.")
+
+    else:
+        # search for the pattern matching file in path
+        matches = [i for i in os.listdir(path) if pattern.match(i)]
+        if len(matches) > 1:
+            message = f"There are {len(matches)} file matching {key} in {Path(path)}. Specify the correct file path to avoid ambiguities."
+            if optional_arg:
+                logger.warning(message)
+                return file_path, flag
+            else:
+                raise Exception(message)
+        else:
+            # if there is a matching file, use it
+            try:
+                checked_file = matches[0]  # this is the filename
+                file_path = Path.joinpath(path, checked_file)
+                flag = True
+            # if there are no files matching the pattern, raise error
+            except IndexError:
+                message = f"There are no files in {path} matching {key}."
+                if optional_arg:
+                    logger.warning(message)
+                    return file_path, flag
+                else:
+                    raise IndexError(message)
+
+    logger.warning(f"{file_path} is used.")
     return file_path, flag
 
 
@@ -189,7 +218,7 @@ def _xy2edges(xy: list[int], scale: float = 1.0, border: bool = True, border_sca
 
 @inject_docs(vx=DbitKeys)
 def dbit(
-    path: str | Path,
+    path: Optional[str | Path] = None,
     anndata_path: Optional[str] = None,
     barcode_position: Optional[str] = None,
     image_path: Optional[str] = None,
@@ -236,12 +265,14 @@ def dbit(
     -------
     :class:`spatialdata.SpatialData`.
     """
-    path = Path(path)
-    # if path is invalid, raise error
-    if not os.path.isdir(path):
-        raise FileNotFoundError(
-            f"The path you have passed: {path} has not been found. A correct path to the data directory is needed."
-        )
+    if path is not None:
+        path = Path(path)
+        # if path is invalid, raise error
+        if not os.path.isdir(path):
+            raise FileNotFoundError(
+                f"The path you have passed: {path} has not been found. A correct path to the data directory is needed."
+            )
+
     # compile regex pattern to find file name in path, according to _constants.DbitKeys()
     patt_h5ad = re.compile(f".*{DbitKeys.COUNTS_FILE}")
     patt_barcode = re.compile(f".*{DbitKeys.BARCODE_POSITION}.*")
@@ -249,13 +280,13 @@ def dbit(
 
     # search for files paths. Gives priority to files matching the pattern found in path.
     anndata_path_checked = _check_path(
-        path=path, path_specific=anndata_path, pattern=patt_h5ad, key=DbitKeys.COUNTS_FILE
+        path=path, path_specific=anndata_path, pattern=patt_h5ad, key=DbitKeys.COUNTS_FILE  # type: ignore
     )[0]
     barcode_position_checked = _check_path(
-        path=path, path_specific=barcode_position, pattern=patt_barcode, key=DbitKeys.BARCODE_POSITION
+        path=path, path_specific=barcode_position, pattern=patt_barcode, key=DbitKeys.BARCODE_POSITION  # type: ignore
     )[0]
     image_path_checked, hasimage = _check_path(
-        path=path,
+        path=path,  # type: ignore
         path_specific=image_path,
         pattern=patt_lowres,
         key=DbitKeys.IMAGE_LOWRES_FILE,
@@ -324,7 +355,7 @@ def dbit(
     ra = shapely.to_ragged_array([shapely.Polygon(x) for x in f])
     grid = sd.models.ShapesModel.parse(ra[1], geometry=ra[0], offsets=ra[2], index=adata.obs["pixel_id"].copy())
     # create SpatialData object!
-    sdata = sd.SpatialData(table=table_data, shapes={dataset_id: grid})
+    sdata = sd.SpatialData(tables={"table": table_data}, shapes={dataset_id: grid})
     if hasimage:
         imgname = dataset_id + "_image"
         sdata.images[imgname] = image_sd