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Feat: Support for Visium HD cell segmentation in Space Ranger 4.0 #328

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Feat: Support for Visium HD cell segmentation in Space Ranger 4.0 #328

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b1e6d06
feat: suppor for spaceranger4.0
stephenwilliams22 Sep 24, 2025
a6d7e9f
make nuc segmentation and cut dup code
stephenwilliams22 Oct 2, 2025
31379c8
use only in_nucleus
stephenwilliams22 Oct 2, 2025
34ac722
make local functions
stephenwilliams22 Oct 2, 2025
b7848fa
ruff
stephenwilliams22 Oct 6, 2025
ae43fe7
typing
stephenwilliams22 Oct 6, 2025
31c76fd
nuc seg cli
stephenwilliams22 Oct 7, 2025
9134c94
tests
stephenwilliams22 Oct 8, 2025
42028ce
add vignette
stephenwilliams22 Oct 10, 2025
b269d32
update BARCODE_MAPPINGS_PATH and calc centroids
stephenwilliams22 Oct 10, 2025
0e891ec
delete vignette. moved to new PR
stephenwilliams22 Oct 13, 2025
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4 changes: 4 additions & 0 deletions src/spatialdata_io/__main__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -417,6 +417,8 @@ def visium_hd_wrapper(
output: str,
dataset_id: str | None = None,
filtered_counts_file: bool = True,
load_segmentations_only: bool = True,
load_nucleus_segmentations: bool = False,
bin_size: int | list[int] | None = None,
bins_as_squares: bool = True,
fullres_image_file: str | Path | None = None,
Expand All @@ -428,6 +430,8 @@ def visium_hd_wrapper(
path=input,
dataset_id=dataset_id,
filtered_counts_file=filtered_counts_file,
load_segmentations_only=load_segmentations_only,
load_nucleus_segmentations=load_nucleus_segmentations,
bin_size=bin_size,
bins_as_squares=bins_as_squares,
fullres_image_file=fullres_image_file,
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9 changes: 9 additions & 0 deletions src/spatialdata_io/_constants/_constants.py
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Expand Up @@ -353,11 +353,16 @@ class VisiumHDKeys(ModeEnum):
BIN_PREFIX = "square_"
MICROSCOPE_IMAGE = "microscope_image"
BINNED_OUTPUTS = "binned_outputs"
SEGMENTATION_OUTPUTS = "segmented_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"
BARCODE_MAPPINGS_FILE = "barcode_mappings.parquet"
FILTERED_CELL_COUNTS_FILE = "filtered_feature_cell_matrix.h5"
CELL_SEGMENTATION_GEOJSON_PATH = "cell_segmentations.geojson"
NUCLEUS_SEGMENTATION_GEOJSON_PATH = "nucleus_segmentations.geojson"

# images
IMAGE_HIRES_FILE = "tissue_hires_image.png"
Expand Down Expand Up @@ -399,3 +404,7 @@ class VisiumHDKeys(ModeEnum):
MICROSCOPE_COLROW_TO_SPOT_COLROW = ("microscope_colrow_to_spot_colrow",)
SPOT_COLROW_TO_MICROSCOPE_COLROW = ("spot_colrow_to_microscope_colrow",)
FILE_FORMAT = "file_format"

# Cell Segmentation keys
CELL_SEG_KEY_HD = 'cell_segmentations'
NUCLEUS_SEG_KEY_HD = 'nucleus_segmentations'
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