spatialdata-io 0.1.1__tar.gz → 0.1.3__tar.gz

spatialdata_io-0.1.3/.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/.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-0.1.3/.github/workflows/release.yaml

@@ -0,0 +1,31 @@
+name: Release
+
+on:
+    release:
+        types: [published]
+
+jobs:
+    release:
+        # requires that you have put your twine API key in your
+        # github secrets (see readme for details)
+        runs-on: ubuntu-latest
+        if: contains(github.ref, 'tags')
+        steps:
+            - name: Checkout code
+              uses: actions/checkout@v3
+
+            - name: Set up Python 3.10
+              uses: actions/setup-python@v4
+              with:
+                  python-version: "3.10"
+
+            - name: Install hatch
+              run: pip install hatch
+
+            - name: Build project for distribution
+              run: hatch build
+
+            - name: Publish a Python distribution to PyPI
+              uses: pypa/gh-action-pypi-publish@release/v1
+              with:
+                  password: ${{ secrets.PYPI_API_TOKEN }}

spatialdata_io-0.1.1/.github/workflows/test_and_deploy.yaml → spatialdata_io-0.1.3/.github/workflows/test.yaml

@@ -28,7 +28,7 @@ jobs:
         steps:
             - uses: actions/checkout@v2
             - name: Set up Python ${{ matrix.python }}
-              uses: actions/setup-python@v2
+              uses: actions/setup-python@v4
               with:
                   python-version: ${{ matrix.python }}
 
@@ -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
@@ -58,33 +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
-    deploy:
-        # this will run when you have tagged a commit, starting with "v*"
-        # and requires that you have put your twine API key in your
-        # github secrets (see readme for details)
-        needs: [test]
-        runs-on: ubuntu-latest
-        if: contains(github.ref, 'tags')
-        steps:
-            - name: Checkout code
-              uses: actions/checkout@v3
-
-            - name: Set up Python 3.10
-              uses: actions/setup-python@v4
-              with:
-                  python-version: "3.10"
-
-            - name: Install hatch
-              run: pip install hatch
-
-            - name: Build project for distribution
-              run: hatch build
-
-            - name: Publish a Python distribution to PyPI
-              uses: pypa/gh-action-pypi-publish@release/v1
-              with:
-                  password: ${{ secrets.PYPI_API_TOKEN }}
+              env:
+                  CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

{spatialdata_io-0.1.1 → spatialdata_io-0.1.3}/.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-0.1.1 → spatialdata_io-0.1.3}/.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
@@ -23,7 +23,7 @@ repos:
       hooks:
           - id: isort
     - repo: https://github.com/pre-commit/mirrors-mypy
-      rev: v1.9.0
+      rev: v1.10.0
       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
@@ -70,7 +70,7 @@ repos:
                 - flake8-bugbear
                 - flake8-blind-except
     - repo: https://github.com/asottile/pyupgrade
-      rev: v3.15.1
+      rev: v3.16.0
       hooks:
           - id: pyupgrade
             args: [--py3-plus, --py39-plus, --keep-runtime-typing]

{spatialdata_io-0.1.1 → spatialdata_io-0.1.3}/CHANGELOG.md

@@ -8,7 +8,39 @@ 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
 
-## [0.1.0] - 2024-03-24
+## [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
+
+-   (Visium HD) added reader, coauthored by @LLehner
+
+### Fixed
+
+-   (Xenium) reader for 1.0.1 (paper data) and unknown versions
+-   (Xenium) fix in reading "minimalistic" Xenium datasets #132
+
+## [0.1.1] - 2024-03-24
 
 ### Added
 

{spatialdata_io-0.1.1 → spatialdata_io-0.1.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: spatialdata-io
-Version: 0.1.1
+Version: 0.1.3
 Summary: SpatialData IO for common techs
 Project-URL: Documentation, https://spatialdata-io.readthedocs.io/
 Project-URL: Source, https://github.com/scverse/spatialdata-io
@@ -46,8 +46,9 @@ Requires-Dist: joblib
 Requires-Dist: numpy
 Requires-Dist: pyarrow
 Requires-Dist: readfcs
+Requires-Dist: scanpy
 Requires-Dist: scikit-image
-Requires-Dist: spatialdata
+Requires-Dist: spatialdata>=0.1.2
 Provides-Extra: dev
 Requires-Dist: bump2version; extra == 'dev'
 Requires-Dist: pre-commit; extra == 'dev'
@@ -75,21 +76,23 @@ Description-Content-Type: text/markdown
 [![Documentation][badge-docs]][link-docs]
 [![DOI](https://zenodo.org/badge/544045123.svg)](https://zenodo.org/badge/latestdoi/544045123)
 
-[badge-tests]: https://github.com/scverse/spatialdata-io/actions/workflows/test_and_deploy.yaml/badge.svg
-[link-tests]: https://github.com/scverse/spatialdata-io/actions/workflows/test_and_deploy.yaml
+[badge-tests]: https://github.com/scverse/spatialdata-io/actions/workflows/test.yaml/badge.svg
+[link-tests]: https://github.com/scverse/spatialdata-io/actions/workflows/test.yaml
 [badge-docs]: https://img.shields.io/readthedocs/spatialdata-io
 
 This package contains reader functions to load common spatial omics formats into SpatialData. Currently, we provide support for:
 
--   NanoString CosMx
--   MCMICRO (output data)
--   Steinbock (output data)
 -   10x Genomics Visium
+-   10x Genomics Visium HD
 -   10x Genomics Xenium
--   Curio Seeker
 -   Akoya PhenoCycler (formerly CODEX)
--   Vizgen MERSCOPE (MERFISH)
+-   Curio Seeker
 -   DBiT-seq
+-   MCMICRO (output data)
+-   NanoString CosMx
+-   Steinbock (output data)
+-   STOmics Stereo-seq
+-   Vizgen MERSCOPE (MERFISH)
 
 ## Getting started
 

{spatialdata_io-0.1.1 → spatialdata_io-0.1.3}/README.md

@@ -6,21 +6,23 @@
 [![Documentation][badge-docs]][link-docs]
 [![DOI](https://zenodo.org/badge/544045123.svg)](https://zenodo.org/badge/latestdoi/544045123)
 
-[badge-tests]: https://github.com/scverse/spatialdata-io/actions/workflows/test_and_deploy.yaml/badge.svg
-[link-tests]: https://github.com/scverse/spatialdata-io/actions/workflows/test_and_deploy.yaml
+[badge-tests]: https://github.com/scverse/spatialdata-io/actions/workflows/test.yaml/badge.svg
+[link-tests]: https://github.com/scverse/spatialdata-io/actions/workflows/test.yaml
 [badge-docs]: https://img.shields.io/readthedocs/spatialdata-io
 
 This package contains reader functions to load common spatial omics formats into SpatialData. Currently, we provide support for:
 
--   NanoString CosMx
--   MCMICRO (output data)
--   Steinbock (output data)
 -   10x Genomics Visium
+-   10x Genomics Visium HD
 -   10x Genomics Xenium
--   Curio Seeker
 -   Akoya PhenoCycler (formerly CODEX)
--   Vizgen MERSCOPE (MERFISH)
+-   Curio Seeker
 -   DBiT-seq
+-   MCMICRO (output data)
+-   NanoString CosMx
+-   Steinbock (output data)
+-   STOmics Stereo-seq
+-   Vizgen MERSCOPE (MERFISH)
 
 ## Getting started
 

{spatialdata_io-0.1.1 → spatialdata_io-0.1.3}/_version.py

@@ -12,5 +12,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.1.1'
-__version_tuple__ = version_tuple = (0, 1, 1)
+__version__ = version = '0.1.3'
+__version_tuple__ = version_tuple = (0, 1, 3)

{spatialdata_io-0.1.1 → spatialdata_io-0.1.3}/docs/api.md

@@ -15,29 +15,39 @@ I/O for the `spatialdata` project.
     :toctree: generated
 
     codex
-    curio
     cosmx
+    curio
+    dbit
+    mcmicro
+    merscope
+    seqfish
+    steinbock
+    stereoseq
     visium
+    visium_hd
     xenium
-    steinbock
-    merscope
-    mcmicro
-    dbit
 ```
 
-### 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
 
@@ -50,3 +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-0.1.1 → spatialdata_io-0.1.3}/docs/conf.py

@@ -98,6 +98,7 @@ intersphinx_mapping = {
     "xarray": ("https://docs.xarray.dev/en/stable/", None),
     "datatree": ("https://datatree.readthedocs.io/en/latest/", None),
     "shapely": ("https://shapely.readthedocs.io/en/stable/", None),
+    "imageio": ("https://imageio.readthedocs.io/en/stable/", None),
 }
 
 # List of patterns, relative to source directory, that match files and
@@ -125,6 +126,7 @@ nitpick_ignore = [
     ("py:class", "Path"),
     ("py:class", "AnnData"),
     ("py:class", "SpatialData"),
+    ("py:func", "imageio.imread"),  # maybe this can be fixed
 ]
 
 

{spatialdata_io-0.1.1 → spatialdata_io-0.1.3}/pyproject.toml

@@ -24,7 +24,8 @@ urls.Home-page = "https://github.com/scverse/spatialdata-io"
 dependencies = [
     "anndata",
     "numpy",
-    "spatialdata",
+    "scanpy",
+    "spatialdata>=0.1.2",
     "scikit-image",
     "h5py",
     "joblib",

{spatialdata_io-0.1.1 → spatialdata_io-0.1.3}/src/spatialdata_io/__init__.py

@@ -6,8 +6,11 @@ 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 (
     xenium,
     xenium_aligned_image,
@@ -16,16 +19,19 @@ from spatialdata_io.readers.xenium import (
 
 __all__ = [
     "curio",
+    "seqfish",
     "visium",
     "xenium",
     "codex",
     "cosmx",
     "mcmicro",
     "steinbock",
+    "stereoseq",
     "merscope",
     "xenium_aligned_image",
     "xenium_explorer_selection",
     "dbit",
+    "visium_hd",
 ]
 
 __version__ = version("spatialdata-io")

{spatialdata_io-0.1.1 → spatialdata_io-0.1.3}/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."""
@@ -227,3 +334,61 @@ class DbitKeys(ModeEnum):
     BARCODE_POSITION = "barcode_list"
     # image
     IMAGE_LOWRES_FILE = "tissue_lowres_image.png"
+
+
+@unique
+class VisiumHDKeys(ModeEnum):
+    """Keys for *10X Genomics Visium hd* formatted dataset."""
+
+    # directories
+    SPATIAL = "spatial"
+    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"
+    RAW_COUNTS_FILE = "raw_feature_bc_matrix.h5"
+    TISSUE_POSITIONS_FILE = "tissue_positions.parquet"
+
+    # images
+    IMAGE_HIRES_FILE = "spatial/tissue_hires_image.png"
+    IMAGE_LOWRES_FILE = "spatial/tissue_lowres_image.png"
+    IMAGE_CYTASSIST = "spatial/cytassist_image.tiff"
+
+    # scalefactors
+    SCALEFACTORS_FILE = "scalefactors_json.json"
+
+    # scalefactors keys
+    SCALEFACTORS_HIRES = "tissue_hires_scalef"
+    SCALEFACTORS_LOWRES = "tissue_lowres_scalef"
+    SCALEFACTORS_SPOT_DIAMETER_FULLRES = "spot_diameter_fullres"
+    SCALEFACTORS_BIN_SIZE_UM = "bin_size_um"
+    SCALEFACTORS_MICRONS_PER_PIXEL = "microns_per_pixel"
+
+    # locations keys
+    LOCATIONS_X = "pxl_col_in_fullres"
+    LOCATIONS_Y = "pxl_row_in_fullres"
+    BARCODE = "barcode"
+    IN_TISSUE = "in_tissue"
+    ARRAY_ROW = "array_row"
+    ARRAY_COL = "array_col"
+
+    # table keys
+    REGION_KEY = "region"
+    INSTANCE_KEY = "location_id"
+
+    # feature slice file (it contains transformation matrices in the metadata)
+    FEATURE_SLICE_FILE = "feature_slice.h5"
+
+    # METADATA_KEYS
+    METADATA_JSON = "metadata_json"
+    HD_LAYOUT_JSON = "hd_layout_json"
+    TRANSFORM = "transform"
+    TRANSFORM_MATRICES = "transform_matrices"
+    CYTASSIST_COLROW_TO_SPOT_COLROW = ("cytassist_colrow_to_spot_colrow",)
+    SPOT_COLROW_TO_CYTASSIST_COLROW = ("spot_colrow_to_cytassist_colrow",)
+    MICROSCOPE_COLROW_TO_SPOT_COLROW = ("microscope_colrow_to_spot_colrow",)
+    SPOT_COLROW_TO_MICROSCOPE_COLROW = ("spot_colrow_to_microscope_colrow",)
+    FILE_FORMAT = "file_format"

{spatialdata_io-0.1.1 → spatialdata_io-0.1.3}/src/spatialdata_io/converters/legacy_anndata.py

@@ -8,7 +8,7 @@ from spatialdata import (
     SpatialData,
     get_centroids,
     get_extent,
-    join_sdata_spatialelement_table,
+    join_spatialelement_table,
     to_circles,
 )
 from spatialdata._core.operations._utils import transform_to_data_extent
@@ -149,8 +149,8 @@ def to_legacy_anndata(
     shapes = to_circles(element)
     circles_sdata = SpatialData(tables={table_name: table}, shapes={region_name: shapes})
 
-    joined_elements, new_table = join_sdata_spatialelement_table(
-        sdata=circles_sdata, spatial_element_name=region_name, table_name=table_name, how="inner", match_rows="left"
+    joined_elements, new_table = join_spatialelement_table(
+        sdata=circles_sdata, spatial_element_names=region_name, table_name=table_name, how="inner", match_rows="left"
     )
 
     # the table after the filtering must not be empty
@@ -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)