Wire save_spatialdata flag into ISTSegmentationWriter and CLI

Adds --save-spatialdata and --boundary-method CLI flags (under the
existing I/O group) and threads them through ISTSegmentationWriter
to emit a SpatialData zarr store next to the AnnData output. Adds
the 'spatialdata' optional dependency. Integration shape taken
from PR #37 commit f99b3fb by @enric-bazz, narrowed to the output
path only (no loader, no 3D, no QV filter, no logging refactor).

Original-author: enric-bazz <enrico.bazzacco02@outlook.it>

Author: enric-bazz

pyproject.toml

@@ -29,6 +29,11 @@ dependencies = [
     "tifffile"
 ]
 
+[project.optional-dependencies]
+spatialdata = [
+    "spatialdata>=0.7.2",
+]
+
 [build-system]
 requires = ["hatchling"]
 build-backend = "hatchling.build"

src/segger/cli/segment.py

@@ -306,7 +306,17 @@ def segment(
         "save_anndata",
         group=group_io,
     )] = registry.get_default("save_anndata"),
-    
+
+    save_spatialdata: Annotated[bool, registry.get_parameter(
+        "save_spatialdata",
+        group=group_io,
+    )] = registry.get_default("save_spatialdata"),
+
+    boundary_method: Annotated[
+        Literal["convex_hull", "skip"],
+        registry.get_parameter("boundary_method", group=group_io),
+    ] = registry.get_default("boundary_method"),
+
     debug: Annotated[bool, Parameter(
         help="Whether to save additional debug information (trainer, predictions).",
     )] = "none",
@@ -395,6 +405,8 @@ def segment(
     writer = ISTSegmentationWriter(
         output_directory,
         save_anndata=save_anndata,
+        save_spatialdata=save_spatialdata,
+        boundary_method=boundary_method,
         debug=debug,
     )
     trainer = Trainer(

src/segger/data/writer.py

@@ -28,12 +28,16 @@ def __init__(
             self,
             output_directory: Path,
             save_anndata: bool = True,
+            save_spatialdata: bool = False,
+            boundary_method: str = "convex_hull",
             debug: bool = False
         ):
         # "write" callback at the end of prediction epoch
         super().__init__(write_interval="epoch")
         self.output_directory = Path(output_directory)
         self.save_anndata = save_anndata
+        self.save_spatialdata = save_spatialdata
+        self.boundary_method = boundary_method
 
         # setup debugging
         self.debug = debug
@@ -83,6 +87,19 @@ def write_on_epoch_end(
         if self.save_anndata:
             self.write_anndata(trainer, segmentation)
 
+        # write spatialdata zarr
+        if self.save_spatialdata:
+            logger.debug("Writing SpatialData output...")
+            from ..export.spatialdata_writer import SpatialDataWriter
+            SpatialDataWriter(
+                boundary_method=self.boundary_method,
+            ).write(
+                predictions=segmentation,
+                output_dir=self.output_directory,
+                transcripts=trainer.datamodule.tx,
+                output_name="segger_segmentation.zarr",
+            )
+
     def write_anndata(
             self,
             trainer: Trainer,