spatialdata-io 0.1.0rc0__tar.gz → 0.1.2__tar.gz

spatialdata_io-0.1.2/.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-0.1.0rc0/.github/workflows/test_and_deploy.yaml → spatialdata_io-0.1.2/.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 }}
 
@@ -62,29 +62,3 @@ jobs:
               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 }}

{spatialdata_io-0.1.0rc0 → spatialdata_io-0.1.2}/.pre-commit-config.yaml

@@ -70,7 +70,7 @@ repos:
                 - flake8-bugbear
                 - flake8-blind-except
     - repo: https://github.com/asottile/pyupgrade
-      rev: v3.15.1
+      rev: v3.15.2
       hooks:
           - id: pyupgrade
             args: [--py3-plus, --py39-plus, --keep-runtime-typing]

{spatialdata_io-0.1.0rc0 → spatialdata_io-0.1.2}/CHANGELOG.md

@@ -8,23 +8,36 @@ 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
+## [0.1.2] - 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
 
--   (MCMICRO) support for TMAs (such as the data of exemplar-002)
 -   (Xenium) support for post-xenium aligned images (IF, HE)
 -   (Xenium) reader for the selection coordinates file from the Xenium Explorer
+-   (Xenium) support for the new Xenium 2.0.0 (multimodal segmentation)
+-   (Xenium) reading multiscale labels from cells.zarr.zip
+-   (MCMICRO) support for TMAs (such as the data of exemplar-002)
 -   (DBiT-seq) reader
 -   converter functions `experimental.to_legacy_anndata()` and `experimental.from_legacy_anndata()`
 -   (Visium) support for raw reads (capture locations not under tissue)
 
 ### Fixed
 
--   (MERSCOPE) don't try to load unexisting elements #87
--   (Visium) fixed axes ordering
 -   (Xenium) fixed index (fail on write)
 -   (Xenium) renamed cells_as_shapes to cells_as_circles; set default to True
+-   (MERSCOPE) don't try to load unexisting elements #87
+-   (Visium) fixed axes ordering
 
 ## [0.0.9] - 2023-11-06
 

{spatialdata_io-0.1.0rc0 → spatialdata_io-0.1.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: spatialdata-io
-Version: 0.1.0rc0
+Version: 0.1.2
 Summary: SpatialData IO for common techs
 Project-URL: Documentation, https://spatialdata-io.readthedocs.io/
 Project-URL: Source, https://github.com/scverse/spatialdata-io
@@ -46,6 +46,7 @@ Requires-Dist: joblib
 Requires-Dist: numpy
 Requires-Dist: pyarrow
 Requires-Dist: readfcs
+Requires-Dist: scanpy
 Requires-Dist: scikit-image
 Requires-Dist: spatialdata
 Provides-Extra: dev
@@ -75,21 +76,22 @@ 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)
+-   Vizgen MERSCOPE (MERFISH)
 
 ## Getting started
 

{spatialdata_io-0.1.0rc0 → spatialdata_io-0.1.2}/README.md

@@ -6,21 +6,22 @@
 [![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)
+-   Vizgen MERSCOPE (MERFISH)
 
 ## Getting started
 

{spatialdata_io-0.1.0rc0 → spatialdata_io-0.1.2}/_version.py

@@ -12,5 +12,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.1.0rc0'
-__version_tuple__ = version_tuple = (0, 1, 0)
+__version__ = version = '0.1.2'
+__version_tuple__ = version_tuple = (0, 1, 2)

{spatialdata_io-0.1.0rc0 → spatialdata_io-0.1.2}/docs/api.md

@@ -15,14 +15,15 @@ I/O for the `spatialdata` project.
     :toctree: generated
 
     codex
-    curio
     cosmx
+    curio
+    dbit
+    mcmicro
+    merscope
+    steinbock
     visium
+    visium_hd
     xenium
-    steinbock
-    merscope
-    mcmicro
-    dbit
 ```
 
 ### Conversion functions

{spatialdata_io-0.1.0rc0 → spatialdata_io-0.1.2}/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-0.1.0rc0 → spatialdata_io-0.1.2}/pyproject.toml

@@ -24,6 +24,7 @@ urls.Home-page = "https://github.com/scverse/spatialdata-io"
 dependencies = [
     "anndata",
     "numpy",
+    "scanpy",
     "spatialdata",
     "scikit-image",
     "h5py",

{spatialdata_io-0.1.0rc0 → spatialdata_io-0.1.2}/src/spatialdata_io/__init__.py

@@ -8,6 +8,7 @@ from spatialdata_io.readers.mcmicro import mcmicro
 from spatialdata_io.readers.merscope import merscope
 from spatialdata_io.readers.steinbock import steinbock
 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,
@@ -26,6 +27,7 @@ __all__ = [
     "xenium_aligned_image",
     "xenium_explorer_selection",
     "dbit",
+    "visium_hd",
 ]
 
 __version__ = version("spatialdata-io")

{spatialdata_io-0.1.0rc0 → spatialdata_io-0.1.2}/src/spatialdata_io/_constants/_constants.py

@@ -93,8 +93,17 @@ class XeniumKeys(ModeEnum):
     CELL_NUCLEUS_AREA = "nucleus_area"
 
     # morphology images
+    # before version 2.0.0
     MORPHOLOGY_MIP_FILE = "morphology_mip.ome.tif"
     MORPHOLOGY_FOCUS_FILE = "morphology_focus.ome.tif"
+    # from version 2.0.0
+    MORPHOLOGY_FOCUS_DIR = "morphology_focus"
+    MORPHOLOGY_FOCUS_CHANNEL_IMAGE = "morphology_focus_{:04}.ome.tif"
+    # from analysis_summary.html > Image QC of https://www.10xgenomics.com/datasets/preview-data-ffpe-human-lung-cancer-with-xenium-multimodal-cell-segmentation-1-standard
+    MORPHOLOGY_FOCUS_CHANNEL_0 = "DAPI"  # nuclear
+    MORPHOLOGY_FOCUS_CHANNEL_1 = "ATP1A1/CD45/E-Cadherin"  # boundary
+    MORPHOLOGY_FOCUS_CHANNEL_2 = "18S"  # interior - RNA
+    MORPHOLOGY_FOCUS_CHANNEL_3 = "AlphaSMA/Vimentin"  # interior - protein
 
     # post-xenium images
     ALIGNED_IF_IMAGE_SUFFIX = "if_image.ome.tif"
@@ -104,6 +113,14 @@ class XeniumKeys(ModeEnum):
     ALIGNMENT_FILE_SUFFIX_TO_REMOVE = ".ome.tif"
     ALIGNMENT_FILE_SUFFIX_TO_ADD = "alignment.csv"
 
+    # specs keys
+    ANALYSIS_SW_VERSION = "analysis_sw_version"
+
+    # zarr file with labels file and cell summary keys
+    CELLS_ZARR = "cells.zarr.zip"
+    NUCLEUS_COUNT = "nucleus_count"
+    Z_LEVEL = "z_level"
+
 
 @unique
 class VisiumKeys(ModeEnum):
@@ -210,3 +227,60 @@ 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"
+
+    # 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-0.1.0rc0 → spatialdata_io-0.1.2}/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