Merge pull request #130 from scverse/visium_hd

Visium HD support
scverse · Mar 29, 2024 · f33092b · f33092b
2 parents 77bd666 + b5b5742
commit f33092b
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -10,6 +10,10 @@ and this project adheres to [Semantic Versioning][].
 
 ## [0.1.2] - xxxx-xx-xx
 
+### Added
+
+-   (Visium HD) added reader, coauthored by @LLehner
+
 ### Fixed
 
 -   (Xenium) reader for 1.0.1 (paper data) and unknown versions

diff --git a/README.md b/README.md
@@ -12,15 +12,16 @@
 
 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
 

diff --git a/docs/api.md b/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

diff --git a/src/spatialdata_io/__init__.py b/src/spatialdata_io/__init__.py
@@ -8,6 +8,7 @@
 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 @@
     "xenium_aligned_image",
     "xenium_explorer_selection",
     "dbit",
+    "visium_hd",
 ]
 
 __version__ = version("spatialdata-io")
diff --git a/src/spatialdata_io/_constants/_constants.py b/src/spatialdata_io/_constants/_constants.py
@@ -227,3 +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"
diff --git a/src/spatialdata_io/converters/legacy_anndata.py b/src/spatialdata_io/converters/legacy_anndata.py
@@ -8,7 +8,7 @@
     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