From 95786d170e12f9eb0d7ff31c034d432a8c4d5e2e Mon Sep 17 00:00:00 2001
From: tobiaspk <krauset@mskcc.org>
Date: Tue, 25 Aug 2026 14:57:02 -0400
Subject: [PATCH 01/19] Initial spatialdata interface

---
 src/segger/cli/export.py | 68 +++++++++++++++++++++++++++++++++-------
 1 file changed, 56 insertions(+), 12 deletions(-)

diff --git a/src/segger/cli/export.py b/src/segger/cli/export.py
index 7d0b6a8..6092c37 100644
--- a/src/segger/cli/export.py
+++ b/src/segger/cli/export.py
@@ -2,7 +2,9 @@
 
 One command writes the chosen SpatialData elements: ``anndata`` the cell by gene table
 (``adata.h5ad``), ``transcripts`` the assigned transcripts/points (``transcripts.parquet``),
-and ``boundaries`` one polygon per cell/shapes (``cell_boundaries.parquet``). Default: anndata + boundaries.
+``boundaries`` one polygon per cell/shapes (``cell_boundaries.parquet``), and ``spatialdata``
+which copies an existing SpatialData store (``--sdata``) into the output directory and adds
+the transcripts, cell boundaries, and table elements to the copy. Default: anndata + boundaries.
 """
 
 from __future__ import annotations
@@ -15,12 +17,21 @@
 _group_io = Group(name="I/O", sort_key=0)
 _group_opts = Group(name="Options", sort_key=1)
 
-_Element = Literal["anndata", "transcripts", "boundaries"]
+_Element = Literal["anndata", "transcripts", "boundaries", "spatialdata"]
 _DEFAULT_ELEMENTS = ("anndata", "boundaries")
 
 _Seg = Annotated[Path, Parameter(alias="-s", group=_group_io, validator=validators.Path(exists=True, dir_okay=False))]
 _Source = Annotated[Path, Parameter(alias="-i", group=_group_io, validator=validators.Path(exists=True, dir_okay=True))]
 _Out = Annotated[Path, Parameter(alias="-o", group=_group_io)]
+_Sdata = Annotated[
+    Optional[Path],
+    Parameter(
+        alias="--sdata",
+        group=_group_io,
+        validator=validators.Path(exists=True, dir_okay=True),
+        help="Existing SpatialData Zarr store to copy into the output directory and add elements to (required for 'spatialdata').",
+    ),
+]
 
 _IncludeAll = Annotated[
     bool,
@@ -94,11 +105,33 @@ def _load_assigned(
     return assigned
 
 
+def _write_to_sdata(sdata_path: Path, output_directory: Path, assigned: "pl.DataFrame", gdf: "gpd.GeoDataFrame", adata: "AnnData") -> Path:
+    """Copy the source SpatialData store into the output directory, then add segger's elements to the copy."""
+    import shutil
+    import spatialdata
+    from spatialdata.models import PointsModel, ShapesModel, TableModel
+
+    dest = output_directory / sdata_path.name
+    if dest.exists():
+        raise FileExistsError(f"{dest} already exists; aborting to avoid overwriting an existing SpatialData store.")
+    shutil.copytree(sdata_path, dest)
+
+    sdata = spatialdata.read_zarr(dest)
+    sdata["transcripts"] = PointsModel.parse(
+        assigned.to_pandas(), coordinates={"x": "x", "y": "y"}, feature_key="feature_name", instance_key="segger_cell_id"
+    )
+    sdata["cell_boundaries"] = ShapesModel.parse(gdf)
+    sdata["table"] = TableModel.parse(adata)
+    sdata.write_element(["transcripts", "cell_boundaries", "table"], overwrite=True)
+    return dest
+
+
 def export(
     *elements: Annotated[_Element, Parameter(help="Elements to write (default: anndata boundaries).")],
     segmentation_path: _Seg,
     source_path: _Source,
     output_directory: _Out,
+    sdata_path: _Sdata = None,
     method: Annotated[
         Literal["delaunay", "convex_hull"],
         Parameter(group=_group_opts, help="Cell-polygon method for boundaries."),
@@ -110,27 +143,38 @@ def export(
     min_similarity: _MinSim = None,
     min_transcripts: _MinTx = 10,
 ):
-    """Write a segger segmentation as scverse SpatialData elements (anndata, transcripts, boundaries)."""
+    """Write a segger segmentation as scverse SpatialData elements (anndata, transcripts, boundaries, spatialdata)."""
     selected = elements or _DEFAULT_ELEMENTS
+    if "spatialdata" in selected and sdata_path is None:
+        raise ValueError("--sdata is required when exporting 'spatialdata'.")
+
     assigned = _load_assigned(segmentation_path, source_path, include_all_transcripts, min_similarity, min_transcripts)
     output_directory.mkdir(parents=True, exist_ok=True)
 
+    # compute outputs
     gdf = None
-    if "boundaries" in selected:
+    if "boundaries" in selected or "spatialdata" in selected:
         from ..export import generate_boundaries
-
         gdf = generate_boundaries(assigned, cell_id="segger_cell_id", method=method, smoothing=chaikin_iterations)
-        gdf.to_parquet(output_directory / "cell_boundaries.parquet")
-        print(f"Wrote {len(gdf)} {method} cell boundaries: {output_directory / 'cell_boundaries.parquet'}")
 
-    if "anndata" in selected:
+    adata = None
+    if "anndata" in selected or "spatialdata" in selected:
         from ..export import build_anndata
-
-        # Use the exported polygon areas so obs["area"] matches the boundaries; omitted otherwise.
         adata = build_anndata(assigned, cell_id="segger_cell_id", area=gdf.geometry.area if gdf is not None else None)
-        adata.write_h5ad(output_directory / "adata.h5ad")
-        print(f"Wrote AnnData ({adata.n_obs} cells x {adata.n_vars} genes): {output_directory / 'adata.h5ad'}")
 
+    # save outputs
     if "transcripts" in selected:
         assigned.write_parquet(output_directory / "transcripts.parquet")
         print(f"Wrote {assigned.height} assigned transcripts: {output_directory / 'transcripts.parquet'}")
+
+    if "boundaries" in selected:
+        gdf.to_parquet(output_directory / "cell_boundaries.parquet")
+        print(f"Wrote {len(gdf)} {method} cell boundaries: {output_directory / 'cell_boundaries.parquet'}")
+
+    if "anndata" in selected:
+        adata.write_h5ad(output_directory / "adata.h5ad")
+        print(f"Wrote AnnData ({adata.n_obs} cells x {adata.n_vars} genes): {output_directory / 'adata.h5ad'}")
+
+    if "spatialdata" in selected:
+        dest = _write_to_sdata(sdata_path, output_directory, assigned, gdf, adata)
+        print(f"Added transcripts, cell_boundaries and table to {dest}")

From 3fb3775f6cd37b7d21ae880117c5783e5dd6f946 Mon Sep 17 00:00:00 2001
From: tobiaspk <krauset@mskcc.org>
Date: Tue, 25 Aug 2026 15:00:19 -0400
Subject: [PATCH 02/19] Use new 'filtered' column and remove faulty
 min_similarity validators

---
 src/segger/cli/export.py | 16 +++++-----------
 1 file changed, 5 insertions(+), 11 deletions(-)

diff --git a/src/segger/cli/export.py b/src/segger/cli/export.py
index 6092c37..751e76b 100644
--- a/src/segger/cli/export.py
+++ b/src/segger/cli/export.py
@@ -41,8 +41,7 @@
     Optional[float],
     Parameter(
         group=_group_opts,
-        validator=validators.Number(gte=0, lte=1),
-        help="Fixed similarity threshold (0-1), overriding the per-gene threshold from segmentation.",
+        help="Custom required similarity threshold, overriding the per-gene threshold from segmentation.",
     ),
 ]
 _MinTx = Annotated[
@@ -79,18 +78,13 @@ def _load_assigned(
     pred_cols = [c for c in (std.row_index, "segger_cell_id", "segger_similarity", "similarity_threshold") if c in seg.columns]
     merged = tx.join(seg.select(pred_cols), on=std.row_index, how="left")
 
-    has_assignment = pl.col("segger_cell_id").is_not_null()
     if include_all_transcripts:
-        keep = has_assignment
+        keep = pl.col("segger_cell_id").is_not_null()
     elif min_similarity is not None:
-        if "segger_similarity" not in merged.columns:
-            raise ValueError("--min-similarity needs a 'segger_similarity' column in the segmentation file.")
-        keep = has_assignment & (pl.col("segger_similarity") >= min_similarity)
-    elif {"segger_similarity", "similarity_threshold"} <= set(merged.columns):
-        keep = has_assignment & (pl.col("segger_similarity") >= pl.col("similarity_threshold"))
+        keep = pl.col("segger_cell_id").is_not_null() & (pl.col("segger_similarity") >= min_similarity)
     else:
-        keep = has_assignment
-
+        keep = pl.col("filtered")
+    
     assigned = merged.filter(keep).select(
         pl.col(std.row_index),
         pl.col("segger_cell_id").cast(pl.String),

From 29c2011250d17003650983df0c92b1426a9edec4 Mon Sep 17 00:00:00 2001
From: tobiaspk <krauset@mskcc.org>
Date: Tue, 25 Aug 2026 15:12:14 -0400
Subject: [PATCH 03/19] Make -i/source_path optional; fall back to joining
 source transcripts for legacy segmentation outputs

---
 src/segger/cli/export.py | 45 ++++++++++++++++++++++++++++------------
 1 file changed, 32 insertions(+), 13 deletions(-)

diff --git a/src/segger/cli/export.py b/src/segger/cli/export.py
index 751e76b..f8c9aab 100644
--- a/src/segger/cli/export.py
+++ b/src/segger/cli/export.py
@@ -21,7 +21,15 @@
 _DEFAULT_ELEMENTS = ("anndata", "boundaries")
 
 _Seg = Annotated[Path, Parameter(alias="-s", group=_group_io, validator=validators.Path(exists=True, dir_okay=False))]
-_Source = Annotated[Path, Parameter(alias="-i", group=_group_io, validator=validators.Path(exists=True, dir_okay=True))]
+_Source = Annotated[
+    Optional[Path],
+    Parameter(
+        alias="-i",
+        group=_group_io,
+        validator=validators.Path(exists=True, dir_okay=True),
+        help="Source transcripts directory; only needed for segmentation outputs written before x/y/feature_name were included inline.",
+    ),
+]
 _Out = Annotated[Path, Parameter(alias="-o", group=_group_io)]
 _Sdata = Annotated[
     Optional[Path],
@@ -54,37 +62,48 @@
 ]
 
 
+def _legacy_join(seg: "pl.DataFrame", source_path: Optional[Path], std) -> "pl.DataFrame":
+    """Join x/y/feature_name onto a segmentation output written before they were included inline."""
+    if source_path is None:
+        raise ValueError("This segmentation output predates inline x/y/feature_name; pass -i/--source-path to join them from the source transcripts.")
+    import polars as pl
+
+    from ..io import get_preprocessor
+
+    tx = get_preprocessor(source_path).transcripts
+    tx = tx.collect() if isinstance(tx, pl.LazyFrame) else tx
+    pred_cols = [c for c in (std.row_index, "segger_cell_id", "segger_similarity", "similarity_threshold") if c in seg.columns]
+    return tx.join(seg.select(pred_cols), on=std.row_index, how="left")
+
+
 def _load_assigned(
     segmentation_path: Path,
-    source_path: Path,
+    source_path: Optional[Path],
     include_all_transcripts: bool,
     min_similarity: Optional[float],
     min_transcripts: int = 10,
 ) -> "pl.DataFrame":
-    """Join predictions onto source transcripts; return the kept tx (row_index/segger_cell_id/feature_name/x/y)."""
+    """Return the kept assigned tx (row_index/segger_cell_id/feature_name/x/y)."""
     import polars as pl
 
-    from ..io import StandardTranscriptFields, get_preprocessor
+    from ..io import StandardTranscriptFields
 
     std = StandardTranscriptFields()
     seg = pl.read_parquet(segmentation_path)
     if "segger_cell_id" not in seg.columns:
         raise ValueError(f"No 'segger_cell_id' column in {segmentation_path}.")
 
-    tx = get_preprocessor(source_path).transcripts
-    if isinstance(tx, pl.LazyFrame):
-        tx = tx.collect()
-
-    pred_cols = [c for c in (std.row_index, "segger_cell_id", "segger_similarity", "similarity_threshold") if c in seg.columns]
-    merged = tx.join(seg.select(pred_cols), on=std.row_index, how="left")
+    merged = seg if {std.x, std.y, std.feature} <= set(seg.columns) else _legacy_join(seg, source_path, std)
 
     if include_all_transcripts:
         keep = pl.col("segger_cell_id").is_not_null()
     elif min_similarity is not None:
         keep = pl.col("segger_cell_id").is_not_null() & (pl.col("segger_similarity") >= min_similarity)
-    else:
+    elif "filtered" in merged.columns:
         keep = pl.col("filtered")
-    
+    else:
+        keep = pl.col("segger_cell_id").is_not_null() & (pl.col("segger_similarity") >= pl.col("similarity_threshold"))
+
     assigned = merged.filter(keep).select(
         pl.col(std.row_index),
         pl.col("segger_cell_id").cast(pl.String),
@@ -123,8 +142,8 @@ def _write_to_sdata(sdata_path: Path, output_directory: Path, assigned: "pl.Data
 def export(
     *elements: Annotated[_Element, Parameter(help="Elements to write (default: anndata boundaries).")],
     segmentation_path: _Seg,
-    source_path: _Source,
     output_directory: _Out,
+    source_path: _Source = None,
     sdata_path: _Sdata = None,
     method: Annotated[
         Literal["delaunay", "convex_hull"],

From 4ea4f502c7ba19a8cb0e86739a1eaad71806d23b Mon Sep 17 00:00:00 2001
From: tobiaspk <krauset@mskcc.org>
Date: Tue, 25 Aug 2026 15:16:41 -0400
Subject: [PATCH 04/19] Add example usage to export docstring

---
 src/segger/cli/export.py | 18 ++++++++++++------
 1 file changed, 12 insertions(+), 6 deletions(-)

diff --git a/src/segger/cli/export.py b/src/segger/cli/export.py
index f8c9aab..f11a3f0 100644
--- a/src/segger/cli/export.py
+++ b/src/segger/cli/export.py
@@ -1,10 +1,16 @@
 """``segger export``: write a segger segmentation as scverse-compatible files.
 
-One command writes the chosen SpatialData elements: ``anndata`` the cell by gene table
-(``adata.h5ad``), ``transcripts`` the assigned transcripts/points (``transcripts.parquet``),
-``boundaries`` one polygon per cell/shapes (``cell_boundaries.parquet``), and ``spatialdata``
-which copies an existing SpatialData store (``--sdata``) into the output directory and adds
-the transcripts, cell boundaries, and table elements to the copy. Default: anndata + boundaries.
+Example usage:
+    # save anndata and boundaries
+    segger export anndata \
+      -s $PATH_OUTPUT/segger_segmentation.parquet \
+      -o $PATH_OUTPUT/adata_export
+
+    # save spatialdata - sdata object must exist already, this will copy it
+    segger export spatialdata \
+      -s $PATH_OUTPUT/segger_segmentation.parquet \
+      -o $PATH_OUTPUT/sdata_export \
+      --sdata $PATH_INPUT/sdata.zarr
 """
 
 from __future__ import annotations
@@ -27,7 +33,7 @@
         alias="-i",
         group=_group_io,
         validator=validators.Path(exists=True, dir_okay=True),
-        help="Source transcripts directory; only needed for segmentation outputs written before x/y/feature_name were included inline.",
+        help="Source transcripts directory. Only needed for segger v0.2.0 (before x/y/feature_name were included in outputs).",
     ),
 ]
 _Out = Annotated[Path, Parameter(alias="-o", group=_group_io)]

From 5e71342111e9be7508f6c7ab1031efa143f9f6ab Mon Sep 17 00:00:00 2001
From: tobiaspk <krauset@mskcc.org>
Date: Tue, 25 Aug 2026 15:20:07 -0400
Subject: [PATCH 05/19] Log copy/write start for spatialdata export; check
 destination existence upfront

---
 src/segger/cli/export.py | 22 ++++++++++++++--------
 1 file changed, 14 insertions(+), 8 deletions(-)

diff --git a/src/segger/cli/export.py b/src/segger/cli/export.py
index f11a3f0..9ba47f0 100644
--- a/src/segger/cli/export.py
+++ b/src/segger/cli/export.py
@@ -124,15 +124,13 @@ def _load_assigned(
     return assigned
 
 
-def _write_to_sdata(sdata_path: Path, output_directory: Path, assigned: "pl.DataFrame", gdf: "gpd.GeoDataFrame", adata: "AnnData") -> Path:
-    """Copy the source SpatialData store into the output directory, then add segger's elements to the copy."""
+def _write_to_sdata(sdata_path: Path, dest: Path, assigned: "pl.DataFrame", gdf: "gpd.GeoDataFrame", adata: "AnnData") -> Path:
+    """Copy the source SpatialData store to ``dest``, then add segger's elements to the copy."""
     import shutil
     import spatialdata
     from spatialdata.models import PointsModel, ShapesModel, TableModel
 
-    dest = output_directory / sdata_path.name
-    if dest.exists():
-        raise FileExistsError(f"{dest} already exists; aborting to avoid overwriting an existing SpatialData store.")
+    print(f"Copying {sdata_path} to {dest}...")
     shutil.copytree(sdata_path, dest)
 
     sdata = spatialdata.read_zarr(dest)
@@ -141,6 +139,8 @@ def _write_to_sdata(sdata_path: Path, output_directory: Path, assigned: "pl.Data
     )
     sdata["cell_boundaries"] = ShapesModel.parse(gdf)
     sdata["table"] = TableModel.parse(adata)
+
+    print(f"Writing transcripts, cell_boundaries and table to {dest}...")
     sdata.write_element(["transcripts", "cell_boundaries", "table"], overwrite=True)
     return dest
 
@@ -164,8 +164,14 @@ def export(
 ):
     """Write a segger segmentation as scverse SpatialData elements (anndata, transcripts, boundaries, spatialdata)."""
     selected = elements or _DEFAULT_ELEMENTS
-    if "spatialdata" in selected and sdata_path is None:
-        raise ValueError("--sdata is required when exporting 'spatialdata'.")
+
+    sdata_dest = None
+    if "spatialdata" in selected:
+        if sdata_path is None:
+            raise ValueError("--sdata is required when exporting 'spatialdata'.")
+        sdata_dest = output_directory / sdata_path.name
+        if sdata_dest.exists():
+            raise FileExistsError(f"{sdata_dest} already exists; aborting to avoid overwriting an existing SpatialData store.")
 
     assigned = _load_assigned(segmentation_path, source_path, include_all_transcripts, min_similarity, min_transcripts)
     output_directory.mkdir(parents=True, exist_ok=True)
@@ -195,5 +201,5 @@ def export(
         print(f"Wrote AnnData ({adata.n_obs} cells x {adata.n_vars} genes): {output_directory / 'adata.h5ad'}")
 
     if "spatialdata" in selected:
-        dest = _write_to_sdata(sdata_path, output_directory, assigned, gdf, adata)
+        dest = _write_to_sdata(sdata_path, sdata_dest, assigned, gdf, adata)
         print(f"Added transcripts, cell_boundaries and table to {dest}")

From 785fd35cd99eb0310915ff5bbfb213a592d0ff22 Mon Sep 17 00:00:00 2001
From: tobiaspk <krauset@mskcc.org>
Date: Tue, 25 Aug 2026 17:06:36 -0400
Subject: [PATCH 06/19] Check spatialdata package is importable before
 exporting the 'spatialdata' element

---
 src/segger/cli/export.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/src/segger/cli/export.py b/src/segger/cli/export.py
index 9ba47f0..19c27d7 100644
--- a/src/segger/cli/export.py
+++ b/src/segger/cli/export.py
@@ -167,6 +167,10 @@ def export(
 
     sdata_dest = None
     if "spatialdata" in selected:
+        import importlib.util
+
+        if importlib.util.find_spec("spatialdata") is None:
+            raise ImportError("The 'spatialdata' element needs the spatialdata package: pip install segger[spatialdata]")
         if sdata_path is None:
             raise ValueError("--sdata is required when exporting 'spatialdata'.")
         sdata_dest = output_directory / sdata_path.name

From 35b7acf36b5bd64c535db7dc4b5ff5d96be6c6e5 Mon Sep 17 00:00:00 2001
From: tobiaspk <krauset@mskcc.org>
Date: Wed, 26 Aug 2026 14:18:29 -0400
Subject: [PATCH 07/19] add spatialdata dependency

---
 pixi.lock                | 622 +++++++++++++++++++++++++++++++++++++--
 pixi.toml                |   3 +-
 src/segger/cli/export.py |   2 +-
 3 files changed, 603 insertions(+), 24 deletions(-)

diff --git a/pixi.lock b/pixi.lock
index 6900a66..cddf7d0 100644
--- a/pixi.lock
+++ b/pixi.lock
@@ -40,17 +40,22 @@ environments:
       - conda: https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_h366c992_103.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/tzdata-2025c-hc9c84f9_1.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.7-hb78ec9c_6.conda
+      - pypi: https://files.pythonhosted.org/packages/6d/f4/5a7d76dc844d3ff8ed1f1a043158aa393794aebb787d3e2f8c0fe87f674f/aiobotocore-3.8.0-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/0f/15/5bf3b99495fb160b63f95972b81750f18f7f4e02ad051373b669d17d44f2/aiohappyeyeballs-2.6.1-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/a1/7e/6815aab7d3a56610891c76ef79095677b8b5be6646aaf00f69b221765021/aiohttp-3.13.3-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl
+      - pypi: https://files.pythonhosted.org/packages/10/a1/510b0a7fadc6f43a6ce50152e69dbd86415240835868bb0bd9b5b88b1e06/aioitertools-0.13.0-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/fb/76/641ae371508676492379f16e2fa48f4e2c11741bd63c48be4b12a6b09cba/aiosignal-1.4.0-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/4c/f4/4d0193dc5bab3af74e9560a8b45830d88ac707467d15ceff7e3df17adc41/anndata-0.12.10-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/a0/d3/54cd560804a8c2b898824778e86c13c2a14600bc83532a9c4f69f2f469c3/array_api_compat-1.14.0-py3-none-any.whl
+      - pypi: https://files.pythonhosted.org/packages/2d/6a/885bc91484e1aa8f618f6f0228d76d0e67000b0fdd6090673b777e311913/asciitree-0.3.3.tar.gz
       - pypi: https://files.pythonhosted.org/packages/3a/2a/7cc015f5b9f5db42b7d48157e23356022889fc354a2813c15934b7cb5c0e/attrs-25.4.0-py3-none-any.whl
+      - pypi: https://files.pythonhosted.org/packages/0e/f2/4bd8f2f419088feb3ce55f0ca91040ff902f402edfd197450b20a2e1d533/botocore-1.43.46-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/06/f3/39cf3367b8107baa44f861dc802cbf16263c945b62d8265d36034fc07bea/cachetools-7.0.5-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/9a/3c/c17fb3ca2d9c3acff52e30b309f538586f9f5b9c9cf454f3845fc9af4881/certifi-2026.2.25-py3-none-any.whl
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+  - myst-nb ; extra == 'docs'
+  - sphinx-autobuild ; extra == 'docs'
+  - sphinx-autodoc-typehints ; extra == 'docs'
+  - sphinx-book-theme>=1.0.0 ; extra == 'docs'
+  - sphinx-copybutton ; extra == 'docs'
+  - sphinx-design ; extra == 'docs'
+  - sphinx-pytest ; extra == 'docs'
+  - sphinx>=4.5 ; extra == 'docs'
+  - sphinxcontrib-bibtex>=1.0.0 ; extra == 'docs'
+  - napari-spatialdata[all] ; extra == 'extra'
+  - spatialdata-io ; extra == 'extra'
+  - spatialdata-plot ; extra == 'extra'
+  - pytest ; extra == 'test'
+  - pytest-cov ; extra == 'test'
+  - pytest-mock ; extra == 'test'
+  - torch ; extra == 'test'
+  - torch ; extra == 'torch'
+  requires_python: '>=3.10,<3.13'
 - pypi: https://files.pythonhosted.org/packages/40/c6/9ae8e9b0721e9b6eb5f340c3a0ce8cd7cce4f66e03dd81f80d60f111987f/statsmodels-0.14.6-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl
   name: statsmodels
   version: 0.14.6
@@ -3377,7 +3832,7 @@ packages:
   version: 1.1.0
   sha256: 15ccc861ac51c53696de0a5d6d4607f99c210739caf987b5d2054f3efed429d8
   requires_python: '>=3.9'
-- pypi: https://download.pytorch.org/whl/cu121/torch-2.5.1%2Bcu121-cp311-cp311-linux_x86_64.whl
+- pypi: https://download-r2.pytorch.org/whl/cu121/torch-2.5.1%2Bcu121-cp311-cp311-linux_x86_64.whl
   name: torch
   version: 2.5.1+cu121
   sha256: c8ab8c92eab928a93c483f83ca8c63f13dafc10fc93ad90ed2dcb7c82ea50410
@@ -3633,7 +4088,7 @@ packages:
   - kornia>=0.6.7 ; extra == 'dev'
   - statsmodels>0.13.5 ; extra == 'dev'
   requires_python: '>=3.10'
-- pypi: https://download.pytorch.org/whl/cu121/torchvision-0.20.1%2Bcu121-cp311-cp311-linux_x86_64.whl
+- pypi: https://download-r2.pytorch.org/whl/cu121/torchvision-0.20.1%2Bcu121-cp311-cp311-linux_x86_64.whl
   name: torchvision
   version: 0.20.1+cu121
   sha256: 237609a3551c2b68f32bcd3f3875dca93836010d83922ef2f3bd3a7540caee58
@@ -3680,7 +4135,7 @@ packages:
   - pytest ; extra == 'testing'
   - scikit-learn ; extra == 'testing'
   requires_python: '>=3.8'
-- pypi: https://download.pytorch.org/whl/triton-3.1.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
+- pypi: https://download-r2.pytorch.org/whl/triton-3.1.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
   name: triton
   version: 3.1.0
   sha256: 0f34f6e7885d1bf0eaaf7ba875a5f0ce6f3c13ba98f9503651c1e6dc6757ed5c
@@ -3698,10 +4153,6 @@ packages:
   - matplotlib ; extra == 'tutorials'
   - pandas ; extra == 'tutorials'
   - tabulate ; extra == 'tutorials'
-- pypi: https://download.pytorch.org/whl/typing_extensions-4.15.0-py3-none-any.whl
-  name: typing-extensions
-  version: 4.15.0
-  requires_python: '>=3.9'
 - pypi: https://files.pythonhosted.org/packages/18/67/36e9267722cc04a6b9f15c7f3441c2363321a3ea07da7ae0c0707beb2a9c/typing_extensions-4.15.0-py3-none-any.whl
   name: typing-extensions
   version: 4.15.0
@@ -3790,6 +4241,111 @@ packages:
   - pysocks>=1.5.6,!=1.5.7,<2.0 ; extra == 'socks'
   - backports-zstd>=1.0.0 ; python_full_version < '3.14' and extra == 'zstd'
   requires_python: '>=3.9'
+- pypi: https://files.pythonhosted.org/packages/71/71/4cd2151a236f44a6e2dd4ed8011838d7ba0be3d656c8bafdfc65a2ed1917/wrapt-2.3.0-cp311-cp311-manylinux1_x86_64.manylinux_2_28_x86_64.manylinux_2_5_x86_64.whl
+  name: wrapt
+  version: 2.3.0
+  sha256: fc648a335d7e01adb3640b25f02fd0ea05886cf04d0af7f4ee902bc7b5e466e8
+  requires_dist:
+  - pytest ; extra == 'dev'
+  - setuptools ; extra == 'dev'
+  requires_python: '>=3.9'
+- pypi: https://files.pythonhosted.org/packages/40/ed/1c4631ad5909487ea8907cd326d9855c2207d790e3936e77bda48173b8be/xarray-2024.11.0-py3-none-any.whl
+  name: xarray
+  version: 2024.11.0
+  sha256: 6ee94f63ddcbdd0cf3909d1177f78cdac756640279c0e32ae36819a89cdaba37
+  requires_dist:
+  - numpy>=1.24
+  - packaging>=23.2
+  - pandas>=2.1
+  - scipy ; extra == 'accel'
+  - bottleneck ; extra == 'accel'
+  - numbagg ; extra == 'accel'
+  - numba>=0.54 ; extra == 'accel'
+  - flox ; extra == 'accel'
+  - opt-einsum ; extra == 'accel'
+  - xarray[accel,etc,io,parallel,viz] ; extra == 'complete'
+  - hypothesis ; extra == 'dev'
+  - jinja2 ; extra == 'dev'
+  - mypy ; extra == 'dev'
+  - pre-commit ; extra == 'dev'
+  - pytest ; extra == 'dev'
+  - pytest-cov ; extra == 'dev'
+  - pytest-env ; extra == 'dev'
+  - pytest-xdist ; extra == 'dev'
+  - pytest-timeout ; extra == 'dev'
+  - ruff ; extra == 'dev'
+  - sphinx ; extra == 'dev'
+  - sphinx-autosummary-accessors ; extra == 'dev'
+  - xarray[complete] ; extra == 'dev'
+  - netcdf4 ; extra == 'io'
+  - h5netcdf ; extra == 'io'
+  - scipy ; extra == 'io'
+  - pydap ; python_full_version < '3.10' and extra == 'io'
+  - zarr ; extra == 'io'
+  - fsspec ; extra == 'io'
+  - cftime ; extra == 'io'
+  - pooch ; extra == 'io'
+  - sparse ; extra == 'etc'
+  - dask[complete] ; extra == 'parallel'
+  - cartopy ; extra == 'viz'
+  - matplotlib ; extra == 'viz'
+  - nc-time-axis ; extra == 'viz'
+  - seaborn ; extra == 'viz'
+  requires_python: '>=3.10'
+- pypi: https://files.pythonhosted.org/packages/aa/7b/9adbd82e2b7b8571da23856a890324b42cfbc38ae0ceac2177e5256f7216/xarray_dataclasses-1.9.1-py3-none-any.whl
+  name: xarray-dataclasses
+  version: 1.9.1
+  sha256: 3590556ef795ebbb33908b484a58311192d880cbb511666fe4c354569c3c468f
+  requires_dist:
+  - numpy>=1.22,<1.25 ; python_full_version == '3.8.*'
+  - numpy>=1.22,<3.0 ; python_full_version >= '3.9' and python_full_version < '3.14'
+  - typing-extensions>=4.0,<5.0
+  - xarray>=2022.3,<2023.2 ; python_full_version == '3.8.*'
+  - xarray>=2022.3,<2025.0 ; python_full_version >= '3.9' and python_full_version < '3.14'
+  requires_python: '>=3.8,<3.14'
+- pypi: https://files.pythonhosted.org/packages/a9/6d/f585a27b380ee987619b5617c0ca672a71a4345b67cfedbb6299750ce845/xarray_schema-0.0.3-py3-none-any.whl
+  name: xarray-schema
+  version: 0.0.3
+  sha256: aa6f856626b2e100213ba290407797464608b2555bb8e0b26093a97fe1ba38ce
+  requires_dist:
+  - xarray>=0.16
+  - numpy>=1.21
+  requires_python: '>=3.8'
+- pypi: https://files.pythonhosted.org/packages/61/ee/9d0bb9f1bbaf347efe2ca6ad7bae259d6ed9e7a2b4441bd16b88723145a1/xarray_spatial-0.5.3-py3-none-any.whl
+  name: xarray-spatial
+  version: 0.5.3
+  sha256: 84f5a3e07a1ac3212bcfff3c4677daa3c529a533f1493eb555f8e498b7d9746e
+  requires_dist:
+  - datashader>=0.15.0
+  - numba
+  - xarray
+  - numpy
+  - dask[dataframe] ; extra == 'doc'
+  - geopandas ; extra == 'doc'
+  - jinja2>=2.11 ; extra == 'doc'
+  - ipykernel ; extra == 'doc'
+  - matplotlib ; extra == 'doc'
+  - nbsphinx ; extra == 'doc'
+  - numpydoc ; extra == 'doc'
+  - pandoc ; extra == 'doc'
+  - pydata-sphinx-theme ; extra == 'doc'
+  - sphinx ; extra == 'doc'
+  - sphinx-panels ; extra == 'doc'
+  - sphinx-rtd-theme ; extra == 'doc'
+  - awkward>=1.4 ; extra == 'optional'
+  - geopandas ; extra == 'optional'
+  - shapely ; extra == 'optional'
+  - spatialpandas ; extra == 'optional'
+  - rtxpy ; extra == 'optional'
+  - flake8 ; extra == 'tests'
+  - isort ; extra == 'tests'
+  - noise>=1.2.2 ; extra == 'tests'
+  - dask ; extra == 'tests'
+  - pyarrow ; extra == 'tests'
+  - pytest ; extra == 'tests'
+  - pytest-cov ; extra == 'tests'
+  - scipy ; extra == 'tests'
+  requires_python: '>=3.8'
 - pypi: https://files.pythonhosted.org/packages/a5/86/cf2c0321dc3940a7aa73076f4fd677a0fb3e405cb297ead7d864fd90847e/xxhash-3.6.0-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl
   name: xxhash
   version: 3.6.0
@@ -3804,6 +4360,28 @@ packages:
   - multidict>=4.0
   - propcache>=0.2.1
   requires_python: '>=3.10'
+- pypi: https://files.pythonhosted.org/packages/5e/d8/9ffd8c237b3559945bb52103cf0eed64ea098f7b7f573f8d2962ef27b4b2/zarr-2.18.7-py3-none-any.whl
+  name: zarr
+  version: 2.18.7
+  sha256: ac3dc4033e9ae4e9d7b5e27c97ea3eaf1003cc0a07f010bd83d5134bf8c4b223
+  requires_dist:
+  - asciitree
+  - numpy>=1.24
+  - fasteners ; sys_platform != 'emscripten'
+  - numcodecs>=0.10.0,!=0.14.0,!=0.14.1,<0.16
+  - notebook ; extra == 'jupyter'
+  - ipytree>=0.2.2 ; extra == 'jupyter'
+  - ipywidgets>=8.0.0 ; extra == 'jupyter'
+  - sphinx ; extra == 'docs'
+  - sphinx-automodapi ; extra == 'docs'
+  - sphinx-design ; extra == 'docs'
+  - sphinx-issues ; extra == 'docs'
+  - sphinx-copybutton ; extra == 'docs'
+  - pydata-sphinx-theme ; extra == 'docs'
+  - numpydoc ; extra == 'docs'
+  - numcodecs[msgpack]!=0.14.0,!=0.14.1,<0.16 ; extra == 'docs'
+  - pytest-doctestplus ; extra == 'docs'
+  requires_python: '>=3.11'
 - pypi: https://files.pythonhosted.org/packages/44/15/bb13b4913ef95ad5448490821eee4671d0e67673342e4d4070854e5fe081/zarr-3.1.5-py3-none-any.whl
   name: zarr
   version: 3.1.5
diff --git a/pixi.toml b/pixi.toml
index b27ccad..73fc6f5 100644
--- a/pixi.toml
+++ b/pixi.toml
@@ -37,9 +37,10 @@ cudf-cu12 = "==24.10.*"
 cuml-cu12 = "==24.10.*"
 cugraph-cu12 = "==24.10.*"
 cupy-cuda12x = ">=12.2,<13.0"
+spatialdata = ">=0.4.0, <0.5"
 
 [tool.uv.extra-build-dependencies]
 torch-scatter = ["torch"]
 
 [environments]
-cuda121 = ["cuda121"]
\ No newline at end of file
+cuda121 = ["cuda121"]
diff --git a/src/segger/cli/export.py b/src/segger/cli/export.py
index 19c27d7..3ec26e2 100644
--- a/src/segger/cli/export.py
+++ b/src/segger/cli/export.py
@@ -170,7 +170,7 @@ def export(
         import importlib.util
 
         if importlib.util.find_spec("spatialdata") is None:
-            raise ImportError("The 'spatialdata' element needs the spatialdata package: pip install segger[spatialdata]")
+            raise ImportError("The 'spatialdata' element needs the spatialdata package. Make sure spatialdata is installed in your environment, for example with `pip install spatialdata`.")
         if sdata_path is None:
             raise ValueError("--sdata is required when exporting 'spatialdata'.")
         sdata_dest = output_directory / sdata_path.name

From 18bcc509fb673662d404830a46055cb4f8074754 Mon Sep 17 00:00:00 2001
From: tobiaspk <krauset@mskcc.org>
Date: Wed, 26 Aug 2026 14:41:49 -0400
Subject: [PATCH 08/19] Parallelize cell boundary generation across CPUs

Runs cell_boundary for each cell in a ProcessPoolExecutor sized to the
SLURM-allocated CPU count instead of a single-threaded loop.
---
 src/segger/export/boundary.py | 26 +++++++++++++++++++++-----
 1 file changed, 21 insertions(+), 5 deletions(-)

diff --git a/src/segger/export/boundary.py b/src/segger/export/boundary.py
index 65ea72b..2a30466 100644
--- a/src/segger/export/boundary.py
+++ b/src/segger/export/boundary.py
@@ -7,6 +7,8 @@
 
 from __future__ import annotations
 
+import os
+from concurrent.futures import ProcessPoolExecutor
 from typing import Literal, Optional, Union
 
 import geopandas as gpd
@@ -184,6 +186,13 @@ def cell_boundary(
     return poly
 
 
+def _build_one_boundary(inputs: tuple) -> tuple:
+    """Run ``cell_boundary`` for one cell; returns (cell_id, n_transcripts, geometry)."""
+    cid, pts, method, smoothing, connectivity = inputs
+    geom = cell_boundary(pts, method=method, smoothing=smoothing, connectivity=connectivity)
+    return str(cid), len(pts), geom
+
+
 def generate_boundaries(
     transcripts: Union[pl.DataFrame, pd.DataFrame],
     cell_id: str = "cell_id",
@@ -203,11 +212,18 @@ def generate_boundaries(
         n_groups = grouped.ngroups
         groups = ((cid, g[[x, y]].to_numpy()) for cid, g in grouped)
 
-    ids, n_tx, geoms = [], [], []
-    for cid, pts in tqdm(groups, total=n_groups, desc="Building cell boundaries"):
-        ids.append(str(cid))
-        n_tx.append(len(pts))
-        geoms.append(cell_boundary(pts, method=method, smoothing=smoothing, connectivity=connectivity))
+    inputs = [(cid, pts, method, smoothing, connectivity) for cid, pts in groups]
+
+    n_workers = len(os.sched_getaffinity(0))
+    with ProcessPoolExecutor(max_workers=n_workers) as pool:
+        results = list(
+            tqdm(
+                pool.map(_build_one_boundary, inputs, chunksize=10),
+                total=n_groups,
+                desc="Building cell boundaries",
+            )
+        )
+    ids, n_tx, geoms = zip(*results) if results else ((), (), ())
 
     # Output the SpatialData instance key as "cell_id" regardless of the input column name. Keep it as
     # a column too: geoparquet drops a named index, and it must match the table instance key to join.

From dc9c7d5334002dc1a0cc8c9cd44e5887d6131947 Mon Sep 17 00:00:00 2001
From: Tobiaspk <tobiaspk1@gmail.com>
Date: Thu, 27 Aug 2026 11:38:29 -0400
Subject: [PATCH 09/19] Add setuptools dependency to cuda121 env

spatialdata's xarray_schema dependency imports pkg_resources, which
comes from setuptools; not otherwise pulled in by the resolved env.
---
 pixi.lock | 17 +++++++++--------
 pixi.toml |  1 +
 2 files changed, 10 insertions(+), 8 deletions(-)

diff --git a/pixi.lock b/pixi.lock
index cddf7d0..d84af50 100644
--- a/pixi.lock
+++ b/pixi.lock
@@ -175,7 +175,7 @@ environments:
       - pypi: https://files.pythonhosted.org/packages/09/7d/af933f0f6e0767995b4e2d705a0665e454d1c19402aa7e895de3951ebb04/scipy-1.17.1-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl
       - pypi: https://files.pythonhosted.org/packages/83/11/00d3c3dfc25ad54e731d91449895a79e4bf2384dc3ac01809010ba88f6d5/seaborn-0.13.2-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/44/7c/64d18f2374e19ba9bee52dee885ec81f808a1863ed0995495b83319b88bc/session_info2-0.4-py3-none-any.whl
-      - pypi: https://files.pythonhosted.org/packages/95/9c/c510029fc6ef33a6275cd2c5d3cecd6613dfd6aa401d57c54f1c18852ccf/setuptools-84.0.0-py3-none-any.whl
+      - pypi: https://files.pythonhosted.org/packages/e1/e3/c164c88b2e5ce7b24d667b9bd83589cf4f3520d97cad01534cd3c4f55fdb/setuptools-81.0.0-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/13/02/58b0b8d9c17c93ab6340edd8b7308c0c5a5b81f94ce65705819b7416dba5/shapely-2.1.2-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.whl
       - pypi: https://files.pythonhosted.org/packages/b7/ce/149a00dd41f10bc29e5921b496af8b574d8413afcd5e30dfa0ed46c2cc5e/six-1.17.0-py2.py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/e8/ae/fa6cd331b364ad2bbc31652d025f5747d89cbb75576733dfdf8efe3e4d62/slicerator-1.1.0-py3-none-any.whl
@@ -3577,10 +3577,10 @@ packages:
   - pytest-subprocess ; extra == 'test'
   - testing-common-database ; extra == 'test'
   requires_python: '>=3.10'
-- pypi: https://files.pythonhosted.org/packages/95/9c/c510029fc6ef33a6275cd2c5d3cecd6613dfd6aa401d57c54f1c18852ccf/setuptools-84.0.0-py3-none-any.whl
+- pypi: https://files.pythonhosted.org/packages/e1/e3/c164c88b2e5ce7b24d667b9bd83589cf4f3520d97cad01534cd3c4f55fdb/setuptools-81.0.0-py3-none-any.whl
   name: setuptools
-  version: 84.0.0
-  sha256: 51a52592b3b99e102b609654876bd65f19f999935166d1352678931132b0c670
+  version: 81.0.0
+  sha256: fdd925d5c5d9f62e4b74b30d6dd7828ce236fd6ed998a08d81de62ce5a6310d6
   requires_dist:
   - pytest>=6,!=8.1.* ; extra == 'test'
   - virtualenv>=13.0.0 ; extra == 'test'
@@ -3621,18 +3621,19 @@ packages:
   - importlib-metadata>=6 ; python_full_version < '3.10' and extra == 'core'
   - tomli>=2.0.1 ; python_full_version < '3.11' and extra == 'core'
   - wheel>=0.43.0 ; extra == 'core'
+  - platformdirs>=4.2.2 ; extra == 'core'
   - jaraco-functools>=4 ; extra == 'core'
   - more-itertools ; extra == 'core'
-  - pytest-checkdocs>=2.14 ; extra == 'check'
+  - pytest-checkdocs>=2.4 ; extra == 'check'
   - pytest-ruff>=0.2.1 ; sys_platform != 'cygwin' and extra == 'check'
   - ruff>=0.13.0 ; sys_platform != 'cygwin' and extra == 'check'
   - pytest-cov ; extra == 'cover'
-  - pytest-enabler>=3.4 ; extra == 'enabler'
-  - pytest-mypy>=1.0.1 ; platform_python_implementation != 'PyPy' and extra == 'type'
+  - pytest-enabler>=2.2 ; extra == 'enabler'
+  - pytest-mypy ; extra == 'type'
   - mypy==1.18.* ; extra == 'type'
   - importlib-metadata>=7.0.2 ; python_full_version < '3.10' and extra == 'type'
   - jaraco-develop>=7.21 ; sys_platform != 'cygwin' and extra == 'type'
-  requires_python: '>=3.10'
+  requires_python: '>=3.9'
 - pypi: https://files.pythonhosted.org/packages/13/02/58b0b8d9c17c93ab6340edd8b7308c0c5a5b81f94ce65705819b7416dba5/shapely-2.1.2-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.whl
   name: shapely
   version: 2.1.2
diff --git a/pixi.toml b/pixi.toml
index 73fc6f5..7d048d2 100644
--- a/pixi.toml
+++ b/pixi.toml
@@ -38,6 +38,7 @@ cuml-cu12 = "==24.10.*"
 cugraph-cu12 = "==24.10.*"
 cupy-cuda12x = ">=12.2,<13.0"
 spatialdata = ">=0.4.0, <0.5"
+setuptools = ">=81.0.0, <82"
 
 [tool.uv.extra-build-dependencies]
 torch-scatter = ["torch"]

From d48625a5e49ae2134b287e2c01d8d2858bd7c1ce Mon Sep 17 00:00:00 2001
From: Tobiaspk <tobiaspk1@gmail.com>
Date: Thu, 27 Aug 2026 11:38:34 -0400
Subject: [PATCH 10/19] Fix parallel boundary generation: list unpacking and
 worker count

zip(*results) produced tuples, which geopandas' set_geometry mistakes
for a column-name lookup instead of geometry values, dumping every
polygon into the error message. Convert to lists. Also leave one CPU
free instead of using every allocated core.
---
 src/segger/export/boundary.py | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/src/segger/export/boundary.py b/src/segger/export/boundary.py
index 2a30466..3307d90 100644
--- a/src/segger/export/boundary.py
+++ b/src/segger/export/boundary.py
@@ -214,7 +214,7 @@ def generate_boundaries(
 
     inputs = [(cid, pts, method, smoothing, connectivity) for cid, pts in groups]
 
-    n_workers = len(os.sched_getaffinity(0))
+    n_workers = max(len(os.sched_getaffinity(0)) - 1, 1)
     with ProcessPoolExecutor(max_workers=n_workers) as pool:
         results = list(
             tqdm(
@@ -223,10 +223,9 @@ def generate_boundaries(
                 desc="Building cell boundaries",
             )
         )
-    ids, n_tx, geoms = zip(*results) if results else ((), (), ())
+    ids, n_tx, geoms = map(list, zip(*results)) if results else ([], [], [])
 
-    # Output the SpatialData instance key as "cell_id" regardless of the input column name. Keep it as
-    # a column too: geoparquet drops a named index, and it must match the table instance key to join.
+    # Output the SpatialData instance key as "cell_id" regardless of the input column name.
     gdf = gpd.GeoDataFrame(
         {"cell_id": ids, "n_transcripts": n_tx}, geometry=geoms, index=pd.Index(ids, name="cell_id")
     )

From d1ec959e045e873c42bf8023cb6a4411685c1776 Mon Sep 17 00:00:00 2001
From: Tobiaspk <tobiaspk1@gmail.com>
Date: Thu, 27 Aug 2026 11:38:40 -0400
Subject: [PATCH 11/19] Write spatialdata export elements in place, avoid
 dask-expr crash

- Disable dask's query-planning backend at the top of segger/__init__.py:
  cudf is imported unconditionally by every CLI subcommand and pulls in
  dask.dataframe before export code ever runs, so setting the config
  lazily inside the export path was too late.
- _write_to_sdata now adds elements directly to the given --sdata store
  instead of copytree-ing it into the output directory first; avoids
  the 'cannot overwrite' error from the raw Xenium sdata's transcripts/
  cell_boundaries/table already occupying those element names.
- Fail fast: check the target element names don't already exist before
  doing any of the (expensive) segmentation/boundary work.
- Add --spatialdata-element-prefix (default '_segger') to name segger's
  elements distinctly from the source sdata's own.
- -o/--output-directory is now optional, only required for the
  anndata/transcripts/boundaries elements.
---
 src/segger/__init__.py   |  5 +++
 src/segger/cli/export.py | 79 +++++++++++++++++++++++++++-------------
 2 files changed, 58 insertions(+), 26 deletions(-)

diff --git a/src/segger/__init__.py b/src/segger/__init__.py
index 67cb121..a4ef99d 100644
--- a/src/segger/__init__.py
+++ b/src/segger/__init__.py
@@ -1,6 +1,11 @@
 import logging
 import os
 from pathlib import Path
+
+import dask
+
+dask.config.set({"dataframe.query-planning": False})  # spatialdata doesn't yet support dask-expr; must be set before cudf pulls in dask.dataframe
+
 import cupy as cp
 import torch
 import rmm
diff --git a/src/segger/cli/export.py b/src/segger/cli/export.py
index 3ec26e2..807649b 100644
--- a/src/segger/cli/export.py
+++ b/src/segger/cli/export.py
@@ -6,10 +6,9 @@
       -s $PATH_OUTPUT/segger_segmentation.parquet \
       -o $PATH_OUTPUT/adata_export
 
-    # save spatialdata - sdata object must exist already, this will copy it
+    # save spatialdata - adds elements directly to an existing sdata object, no -o needed
     segger export spatialdata \
       -s $PATH_OUTPUT/segger_segmentation.parquet \
-      -o $PATH_OUTPUT/sdata_export \
       --sdata $PATH_INPUT/sdata.zarr
 """
 
@@ -36,14 +35,17 @@
         help="Source transcripts directory. Only needed for segger v0.2.0 (before x/y/feature_name were included in outputs).",
     ),
 ]
-_Out = Annotated[Path, Parameter(alias="-o", group=_group_io)]
+_Out = Annotated[
+    Optional[Path],
+    Parameter(alias="-o", group=_group_io, help="Required unless the only element being exported is 'spatialdata'."),
+]
 _Sdata = Annotated[
     Optional[Path],
     Parameter(
         alias="--sdata",
         group=_group_io,
         validator=validators.Path(exists=True, dir_okay=True),
-        help="Existing SpatialData Zarr store to copy into the output directory and add elements to (required for 'spatialdata').",
+        help="Existing SpatialData Zarr store to add elements to in place (required for 'spatialdata').",
     ),
 ]
 
@@ -66,6 +68,14 @@
         help="Minimum number of assigned transcripts a cell must have to be included.",
     ),
 ]
+_SpatialdataElementPrefix = Annotated[
+    str,
+    Parameter(
+        group=_group_opts,
+        help="Appended to spatialdata element names, e.g. '_segger' -> 'transcripts_segger' "
+        "(avoids colliding with an existing same-named element, e.g. from the raw Xenium sdata).",
+    ),
+]
 
 
 def _legacy_join(seg: "pl.DataFrame", source_path: Optional[Path], std) -> "pl.DataFrame":
@@ -124,31 +134,42 @@ def _load_assigned(
     return assigned
 
 
-def _write_to_sdata(sdata_path: Path, dest: Path, assigned: "pl.DataFrame", gdf: "gpd.GeoDataFrame", adata: "AnnData") -> Path:
-    """Copy the source SpatialData store to ``dest``, then add segger's elements to the copy."""
-    import shutil
+def _sdata_element_names(spatialdata_element_prefix: str) -> list:
+    return [
+        f"transcripts{spatialdata_element_prefix}",
+        f"cell_boundaries{spatialdata_element_prefix}",
+        f"table{spatialdata_element_prefix}"
+    ]
+
+def _check_sdata_writable(sdata_path: Path, spatialdata_element_prefix: str) -> None:
+    """Fail fast if any target element name already exists, before doing any of the actual work."""
+    kinds = ("points", "shapes", "tables")
+    for kind, name in zip(kinds, _sdata_element_names(spatialdata_element_prefix)):
+        if (sdata_path / kind / name).exists():
+            raise FileExistsError(f"{sdata_path / kind / name} already exists; pick a different --spatialdata-element-prefix.")
+
+
+def _write_to_sdata(sdata_path: Path, assigned: "pl.DataFrame", gdf: "gpd.GeoDataFrame", adata: "AnnData", spatialdata_element_prefix: str = "") -> None:
+    """Add segger's elements directly to the existing SpatialData store at ``sdata_path``."""
     import spatialdata
     from spatialdata.models import PointsModel, ShapesModel, TableModel
 
-    print(f"Copying {sdata_path} to {dest}...")
-    shutil.copytree(sdata_path, dest)
-
-    sdata = spatialdata.read_zarr(dest)
-    sdata["transcripts"] = PointsModel.parse(
+    names = _sdata_element_names(spatialdata_element_prefix)
+    sdata = spatialdata.read_zarr(sdata_path)
+    sdata[names[0]] = PointsModel.parse(
         assigned.to_pandas(), coordinates={"x": "x", "y": "y"}, feature_key="feature_name", instance_key="segger_cell_id"
     )
-    sdata["cell_boundaries"] = ShapesModel.parse(gdf)
-    sdata["table"] = TableModel.parse(adata)
+    sdata[names[1]] = ShapesModel.parse(gdf)
+    sdata[names[2]] = TableModel.parse(adata)
 
-    print(f"Writing transcripts, cell_boundaries and table to {dest}...")
-    sdata.write_element(["transcripts", "cell_boundaries", "table"], overwrite=True)
-    return dest
+    print(f"Writing {', '.join(names)} to {sdata_path}...")
+    sdata.write_element(names, overwrite=True)
 
 
 def export(
     *elements: Annotated[_Element, Parameter(help="Elements to write (default: anndata boundaries).")],
     segmentation_path: _Seg,
-    output_directory: _Out,
+    output_directory: _Out = None,
     source_path: _Source = None,
     sdata_path: _Sdata = None,
     method: Annotated[
@@ -161,11 +182,11 @@ def export(
     include_all_transcripts: _IncludeAll = False,
     min_similarity: _MinSim = None,
     min_transcripts: _MinTx = 10,
+    spatialdata_element_prefix: _SpatialdataElementPrefix = "_segger",
 ):
     """Write a segger segmentation as scverse SpatialData elements (anndata, transcripts, boundaries, spatialdata)."""
     selected = elements or _DEFAULT_ELEMENTS
 
-    sdata_dest = None
     if "spatialdata" in selected:
         import importlib.util
 
@@ -173,12 +194,13 @@ def export(
             raise ImportError("The 'spatialdata' element needs the spatialdata package. Make sure spatialdata is installed in your environment, for example with `pip install spatialdata`.")
         if sdata_path is None:
             raise ValueError("--sdata is required when exporting 'spatialdata'.")
-        sdata_dest = output_directory / sdata_path.name
-        if sdata_dest.exists():
-            raise FileExistsError(f"{sdata_dest} already exists; aborting to avoid overwriting an existing SpatialData store.")
+        _check_sdata_writable(sdata_path, spatialdata_element_prefix)
+    if set(selected) - {"spatialdata"} and output_directory is None:
+        raise ValueError("-o/--output-directory is required unless the only element being exported is 'spatialdata'.")
 
     assigned = _load_assigned(segmentation_path, source_path, include_all_transcripts, min_similarity, min_transcripts)
-    output_directory.mkdir(parents=True, exist_ok=True)
+    if output_directory is not None:
+        output_directory.mkdir(parents=True, exist_ok=True)
 
     # compute outputs
     gdf = None
@@ -189,7 +211,12 @@ def export(
     adata = None
     if "anndata" in selected or "spatialdata" in selected:
         from ..export import build_anndata
-        adata = build_anndata(assigned, cell_id="segger_cell_id", area=gdf.geometry.area if gdf is not None else None)
+        adata = build_anndata(
+            assigned,
+            cell_id="segger_cell_id",
+            area=gdf.geometry.area if gdf is not None else None,
+            region=f"cell_boundaries{spatialdata_element_prefix}",
+        )
 
     # save outputs
     if "transcripts" in selected:
@@ -205,5 +232,5 @@ def export(
         print(f"Wrote AnnData ({adata.n_obs} cells x {adata.n_vars} genes): {output_directory / 'adata.h5ad'}")
 
     if "spatialdata" in selected:
-        dest = _write_to_sdata(sdata_path, sdata_dest, assigned, gdf, adata)
-        print(f"Added transcripts, cell_boundaries and table to {dest}")
+        _write_to_sdata(sdata_path, assigned, gdf, adata, spatialdata_element_prefix=spatialdata_element_prefix)
+        print(f"Added {', '.join(_sdata_element_names(spatialdata_element_prefix))} to {sdata_path}")

From b0e198c767095a115509c619cc4375f2ac3008ce Mon Sep 17 00:00:00 2001
From: Tobiaspk <tobiaspk1@gmail.com>
Date: Fri, 28 Aug 2026 12:19:43 -0400
Subject: [PATCH 12/19] Thread an optional z coordinate through export and
 training writers

Points and table centroids include z when present; no-op until a reader emits it.
Spatialdata writes now fail on a name collision instead of overwriting.

Co-authored-by: Elyas Heidari <55977725+EliHei2@users.noreply.github.com>
Co-authored-by: enric-bazz <enrico.bazzacco02@outlook.it>
---
 src/segger/cli/export.py            | 17 +++++++++++++----
 src/segger/data/writer.py           | 12 +++++++-----
 src/segger/export/anndata_writer.py | 13 +++++++++----
 src/segger/io/fields.py             |  1 +
 4 files changed, 30 insertions(+), 13 deletions(-)

diff --git a/src/segger/cli/export.py b/src/segger/cli/export.py
index 807649b..7fd4388 100644
--- a/src/segger/cli/export.py
+++ b/src/segger/cli/export.py
@@ -120,12 +120,15 @@ def _load_assigned(
     else:
         keep = pl.col("segger_cell_id").is_not_null() & (pl.col("segger_similarity") >= pl.col("similarity_threshold"))
 
+    coord_cols = [pl.col(std.x).alias("x"), pl.col(std.y).alias("y")]
+    if std.z in merged.columns:
+        coord_cols.append(pl.col(std.z).alias("z"))
+
     assigned = merged.filter(keep).select(
         pl.col(std.row_index),
         pl.col("segger_cell_id").cast(pl.String),
         pl.col(std.feature).alias("feature_name"),
-        pl.col(std.x).alias("x"),
-        pl.col(std.y).alias("y"),
+        *coord_cols,
     )
 
     if min_transcripts > 0:
@@ -144,6 +147,7 @@ def _sdata_element_names(spatialdata_element_prefix: str) -> list:
 def _check_sdata_writable(sdata_path: Path, spatialdata_element_prefix: str) -> None:
     """Fail fast if any target element name already exists, before doing any of the actual work."""
     kinds = ("points", "shapes", "tables")
+    # TODO: Load sdata, instead of assuming that files exist
     for kind, name in zip(kinds, _sdata_element_names(spatialdata_element_prefix)):
         if (sdata_path / kind / name).exists():
             raise FileExistsError(f"{sdata_path / kind / name} already exists; pick a different --spatialdata-element-prefix.")
@@ -156,14 +160,18 @@ def _write_to_sdata(sdata_path: Path, assigned: "pl.DataFrame", gdf: "gpd.GeoDat
 
     names = _sdata_element_names(spatialdata_element_prefix)
     sdata = spatialdata.read_zarr(sdata_path)
+    coordinates = {"x": "x", "y": "y"}
+    if "z" in assigned.columns:
+        coordinates["z"] = "z"
+    # TODO: Consider using the transformations from the base elements!
     sdata[names[0]] = PointsModel.parse(
-        assigned.to_pandas(), coordinates={"x": "x", "y": "y"}, feature_key="feature_name", instance_key="segger_cell_id"
+        assigned.to_pandas(), coordinates=coordinates, feature_key="feature_name", instance_key="segger_cell_id"
     )
     sdata[names[1]] = ShapesModel.parse(gdf)
     sdata[names[2]] = TableModel.parse(adata)
 
     print(f"Writing {', '.join(names)} to {sdata_path}...")
-    sdata.write_element(names, overwrite=True)
+    sdata.write_element(names, overwrite=False)
 
 
 def export(
@@ -214,6 +222,7 @@ def export(
         adata = build_anndata(
             assigned,
             cell_id="segger_cell_id",
+            z="z",
             area=gdf.geometry.area if gdf is not None else None,
             region=f"cell_boundaries{spatialdata_element_prefix}",
         )
diff --git a/src/segger/data/writer.py b/src/segger/data/writer.py
index dfc1139..7f62be5 100644
--- a/src/segger/data/writer.py
+++ b/src/segger/data/writer.py
@@ -110,6 +110,10 @@ def write_anndata(
         tx_fields = TrainingTranscriptFields()
 
         tx = trainer.datamodule.tx
+        coordinate_columns = [tx_fields.x, tx_fields.y]
+        if tx_fields.z in tx.columns:
+            coordinate_columns.append(tx_fields.z)
+
         transcripts = (
             segmentation
             .filter(
@@ -118,8 +122,7 @@ def write_anndata(
             .join(
                 tx.select([
                     tx_fields.row_index,
-                    tx_fields.x,
-                    tx_fields.y,
+                    *coordinate_columns,
                     tx_fields.feature,
                 ]),
                 on=tx_fields.row_index,
@@ -132,8 +135,7 @@ def write_anndata(
                 "segger_cell_id",
                 "segger_similarity",
                 "similarity_threshold",
-                tx_fields.x,
-                tx_fields.y,
+                *coordinate_columns,
             ])
         )
 
@@ -142,7 +144,7 @@ def write_anndata(
             feature_column="segger_gene",
             cell_id_column="segger_cell_id",
             score_column="segger_similarity",
-            coordinate_columns=[tx_fields.x, tx_fields.y],
+            coordinate_columns=coordinate_columns,
         )
         adata.write_h5ad(self.output_directory / 'segger_anndata.h5ad')
 
diff --git a/src/segger/export/anndata_writer.py b/src/segger/export/anndata_writer.py
index b957e56..a8921bc 100644
--- a/src/segger/export/anndata_writer.py
+++ b/src/segger/export/anndata_writer.py
@@ -15,19 +15,24 @@ def build_anndata(
     feature: str = "feature_name",
     x: str = "x",
     y: str = "y",
+    z: Optional[str] = None,
     region: str = "cell_boundaries",
     area: Optional[pd.Series] = None,
 ) -> AnnData:
     """Cell x gene table built on :func:`anndata_from_transcripts`, with the SpatialData link added.
 
-    ``obs`` is indexed by the cell id; centroids land in ``obsm["spatial"]`` and the table-to-shapes
-    link in ``uns["spatialdata_attrs"]``. ``area`` (a per-cell Series, e.g. the exported boundary
-    polygon areas) is written to ``obs["area"]`` when given.
+    ``obs`` is indexed by cell id, with centroids in ``obsm["spatial"]`` (3D if ``z`` is given and
+    present) and the table-to-shapes link in ``uns["spatialdata_attrs"]``. ``area``, when given, is
+    written to ``obs["area"]``.
     """
     from ..data.utils.anndata import anndata_from_transcripts
 
+    coordinate_columns = [x, y]
+    if z is not None and z in assigned.columns:
+        coordinate_columns.append(z)
+
     adata = anndata_from_transcripts(
-        assigned, feature_column=feature, cell_id_column=cell_id, coordinate_columns=[x, y]
+        assigned, feature_column=feature, cell_id_column=cell_id, coordinate_columns=coordinate_columns
     )
     if "X_spatial" in adata.obsm:
         adata.obsm["spatial"] = adata.obsm.pop("X_spatial")
diff --git a/src/segger/io/fields.py b/src/segger/io/fields.py
index 8dc30a9..315965c 100644
--- a/src/segger/io/fields.py
+++ b/src/segger/io/fields.py
@@ -107,6 +107,7 @@ class StandardTranscriptFields:
     row_index: str = 'row_index'
     x: str = 'x'
     y: str = 'y'
+    z: str = 'z'
     feature: str = 'feature_name'
     cell_id: str = 'cell_id'
     compartment: str = 'cell_compartment'

From 6515b6e5ab63f15409dede3ba1cb1c838e89a2c9 Mon Sep 17 00:00:00 2001
From: Tobiaspk <tobiaspk1@gmail.com>
Date: Mon, 31 Aug 2026 14:59:02 -0400
Subject: [PATCH 13/19] Append segger columns to existing transcripts element
 instead of a new one

Per PR #80 discussion: transcripts_segger duplicated the sdata transcripts
table and dropped unassigned/control transcripts. Now left-joins segger's
columns (segger_cell_id, segger_similarity, segger_similarity_threshold,
segger_converged, segger_filtered) onto the existing points element in
place, with unassigned transcripts left null and a new segger_unused flag
for rows segger never saw at all.
---
 src/segger/cli/export.py | 145 +++++++++++++++++++++++++++++++--------
 1 file changed, 115 insertions(+), 30 deletions(-)

diff --git a/src/segger/cli/export.py b/src/segger/cli/export.py
index 7fd4388..b32f1a0 100644
--- a/src/segger/cli/export.py
+++ b/src/segger/cli/export.py
@@ -72,10 +72,17 @@
     str,
     Parameter(
         group=_group_opts,
-        help="Appended to spatialdata element names, e.g. '_segger' -> 'transcripts_segger' "
+        help="Appended to the new spatialdata element names, e.g. '_segger' -> 'cell_boundaries_segger' "
         "(avoids colliding with an existing same-named element, e.g. from the raw Xenium sdata).",
     ),
 ]
+_TranscriptsElement = Annotated[
+    str,
+    Parameter(
+        group=_group_opts,
+        help="Name of the existing points element in --sdata to append segger's columns to.",
+    ),
+]
 
 
 def _legacy_join(seg: "pl.DataFrame", source_path: Optional[Path], std) -> "pl.DataFrame":
@@ -92,9 +99,22 @@ def _legacy_join(seg: "pl.DataFrame", source_path: Optional[Path], std) -> "pl.D
     return tx.join(seg.select(pred_cols), on=std.row_index, how="left")
 
 
+def _load_merged(segmentation_path: Path, source_path: Optional[Path]) -> "pl.DataFrame":
+    """Full segmentation output (every transcript segger considered), joined with x/y/feature_name when not already inline."""
+    import polars as pl
+
+    from ..io import StandardTranscriptFields
+
+    std = StandardTranscriptFields()
+    seg = pl.read_parquet(segmentation_path)
+    if "segger_cell_id" not in seg.columns:
+        raise ValueError(f"No 'segger_cell_id' column in {segmentation_path}.")
+
+    return seg if {std.x, std.y, std.feature} <= set(seg.columns) else _legacy_join(seg, source_path, std)
+
+
 def _load_assigned(
-    segmentation_path: Path,
-    source_path: Optional[Path],
+    merged: "pl.DataFrame",
     include_all_transcripts: bool,
     min_similarity: Optional[float],
     min_transcripts: int = 10,
@@ -105,11 +125,6 @@ def _load_assigned(
     from ..io import StandardTranscriptFields
 
     std = StandardTranscriptFields()
-    seg = pl.read_parquet(segmentation_path)
-    if "segger_cell_id" not in seg.columns:
-        raise ValueError(f"No 'segger_cell_id' column in {segmentation_path}.")
-
-    merged = seg if {std.x, std.y, std.feature} <= set(seg.columns) else _legacy_join(seg, source_path, std)
 
     if include_all_transcripts:
         keep = pl.col("segger_cell_id").is_not_null()
@@ -139,38 +154,96 @@ def _load_assigned(
 
 def _sdata_element_names(spatialdata_element_prefix: str) -> list:
     return [
-        f"transcripts{spatialdata_element_prefix}",
         f"cell_boundaries{spatialdata_element_prefix}",
         f"table{spatialdata_element_prefix}"
     ]
 
-def _check_sdata_writable(sdata_path: Path, spatialdata_element_prefix: str) -> None:
-    """Fail fast if any target element name already exists, before doing any of the actual work."""
-    kinds = ("points", "shapes", "tables")
-    # TODO: Load sdata, instead of assuming that files exist
-    for kind, name in zip(kinds, _sdata_element_names(spatialdata_element_prefix)):
-        if (sdata_path / kind / name).exists():
-            raise FileExistsError(f"{sdata_path / kind / name} already exists; pick a different --spatialdata-element-prefix.")
+def _check_sdata_writable(sdata, transcripts_element: str, spatialdata_element_prefix: str) -> None:
+    """Fail fast if the transcripts element is missing, or any target element name already exists."""
+    if transcripts_element not in sdata.points:
+        raise KeyError(f"{transcripts_element!r} not found in sdata.points; pass --transcripts-element to point at the right one.")
+    cell_boundaries_name, table_name = _sdata_element_names(spatialdata_element_prefix)
+    if cell_boundaries_name in sdata.shapes:
+        raise FileExistsError(f"{cell_boundaries_name!r} already exists in sdata.shapes; pick a different --spatialdata-element-prefix.")
+    if table_name in sdata.tables:
+        raise FileExistsError(f"{table_name!r} already exists in sdata.tables; pick a different --spatialdata-element-prefix.")
 
 
-def _write_to_sdata(sdata_path: Path, assigned: "pl.DataFrame", gdf: "gpd.GeoDataFrame", adata: "AnnData", spatialdata_element_prefix: str = "") -> None:
-    """Add segger's elements directly to the existing SpatialData store at ``sdata_path``."""
-    import spatialdata
+_SEGGER_COLUMN_RENAMES = {
+    "similarity_threshold": "segger_similarity_threshold",
+    "converged": "segger_converged",
+    "filtered": "segger_filtered",
+}
+
+
+def _segger_transcript_columns(merged: "pl.DataFrame", row_index: str) -> "pl.DataFrame":
+    """Segger's per-transcript outputs, renamed for joining onto an existing transcripts table."""
+    import polars as pl
+
+    present = [c for c in _SEGGER_COLUMN_RENAMES if c in merged.columns]
+    return (
+        merged.select(row_index, "segger_cell_id", "segger_similarity", *present)
+        .rename({c: _SEGGER_COLUMN_RENAMES[c] for c in present})
+        .with_columns(pl.col("segger_cell_id").cast(pl.String))
+    )
+
+
+def _append_segger_to_transcripts(sdata, merged: "pl.DataFrame", std, transcripts_element: str) -> "pl.DataFrame":
+    """Left-join segger's outputs onto the sdata store's existing transcripts table.
+
+    Assumes ``std.row_index`` was assigned over the same rows, in the same order, as the existing
+    transcripts table (true when segger's preprocessor read the same source file spatialdata was
+    built from). Rows absent from ``merged`` -- e.g. control probes or low-quality transcripts
+    dropped before segger ever saw them -- are flagged ``segger_unused``; the rest get segger's own
+    columns, including a null ``segger_cell_id`` for anything segger didn't assign.
+    """
+    import polars as pl
+
+    existing = sdata.points[transcripts_element]
+    existing = existing.compute() if hasattr(existing, "compute") else existing
+    tx = pl.from_pandas(existing).with_row_index(name=std.row_index)
+
+    seg_cols = _segger_transcript_columns(merged, std.row_index).with_columns(pl.lit(True).alias("_segger_seen"))
+    return (
+        tx.join(seg_cols, on=std.row_index, how="left")
+        .with_columns(pl.col("_segger_seen").is_null().alias("segger_unused"))
+        .drop(std.row_index, "_segger_seen")
+    )
+
+
+def _write_to_sdata(
+    sdata,
+    merged: "pl.DataFrame",
+    gdf: "gpd.GeoDataFrame",
+    adata: "AnnData",
+    spatialdata_element_prefix: str = "",
+    transcripts_element: str = "transcripts",
+) -> None:
+    """Append segger's columns to the existing transcripts element, and add its boundaries/table elements to the given SpatialData store."""
     from spatialdata.models import PointsModel, ShapesModel, TableModel
 
+    from ..io import StandardTranscriptFields
+
+    std = StandardTranscriptFields()
     names = _sdata_element_names(spatialdata_element_prefix)
-    sdata = spatialdata.read_zarr(sdata_path)
+
+    attrs = sdata.points[transcripts_element].attrs.get("spatialdata_attrs", {})
+    joined = _append_segger_to_transcripts(sdata, merged, std, transcripts_element)
     coordinates = {"x": "x", "y": "y"}
-    if "z" in assigned.columns:
+    if "z" in joined.columns:
         coordinates["z"] = "z"
     # TODO: Consider using the transformations from the base elements!
-    sdata[names[0]] = PointsModel.parse(
-        assigned.to_pandas(), coordinates=coordinates, feature_key="feature_name", instance_key="segger_cell_id"
+    sdata[transcripts_element] = PointsModel.parse(
+        joined.to_pandas(),
+        coordinates=coordinates,
+        feature_key=attrs.get("feature_key"),
+        instance_key=attrs.get("instance_key"),
     )
-    sdata[names[1]] = ShapesModel.parse(gdf)
-    sdata[names[2]] = TableModel.parse(adata)
+    sdata[names[0]] = ShapesModel.parse(gdf)
+    sdata[names[1]] = TableModel.parse(adata)
 
-    print(f"Writing {', '.join(names)} to {sdata_path}...")
+    print(f"Writing {transcripts_element}, {', '.join(names)} to {sdata.path}...")
+    sdata.write_element([transcripts_element], overwrite=True)
     sdata.write_element(names, overwrite=False)
 
 
@@ -191,10 +264,12 @@ def export(
     min_similarity: _MinSim = None,
     min_transcripts: _MinTx = 10,
     spatialdata_element_prefix: _SpatialdataElementPrefix = "_segger",
+    transcripts_element: _TranscriptsElement = "transcripts",
 ):
     """Write a segger segmentation as scverse SpatialData elements (anndata, transcripts, boundaries, spatialdata)."""
     selected = elements or _DEFAULT_ELEMENTS
 
+    sdata = None
     if "spatialdata" in selected:
         import importlib.util
 
@@ -202,11 +277,15 @@ def export(
             raise ImportError("The 'spatialdata' element needs the spatialdata package. Make sure spatialdata is installed in your environment, for example with `pip install spatialdata`.")
         if sdata_path is None:
             raise ValueError("--sdata is required when exporting 'spatialdata'.")
-        _check_sdata_writable(sdata_path, spatialdata_element_prefix)
+        import spatialdata as _spatialdata
+
+        sdata = _spatialdata.read_zarr(sdata_path)
+        _check_sdata_writable(sdata, transcripts_element, spatialdata_element_prefix)
     if set(selected) - {"spatialdata"} and output_directory is None:
         raise ValueError("-o/--output-directory is required unless the only element being exported is 'spatialdata'.")
 
-    assigned = _load_assigned(segmentation_path, source_path, include_all_transcripts, min_similarity, min_transcripts)
+    merged = _load_merged(segmentation_path, source_path)
+    assigned = _load_assigned(merged, include_all_transcripts, min_similarity, min_transcripts)
     if output_directory is not None:
         output_directory.mkdir(parents=True, exist_ok=True)
 
@@ -241,5 +320,11 @@ def export(
         print(f"Wrote AnnData ({adata.n_obs} cells x {adata.n_vars} genes): {output_directory / 'adata.h5ad'}")
 
     if "spatialdata" in selected:
-        _write_to_sdata(sdata_path, assigned, gdf, adata, spatialdata_element_prefix=spatialdata_element_prefix)
-        print(f"Added {', '.join(_sdata_element_names(spatialdata_element_prefix))} to {sdata_path}")
+        _write_to_sdata(
+            sdata,
+            merged,
+            gdf,
+            adata,
+            spatialdata_element_prefix=spatialdata_element_prefix,
+            transcripts_element=transcripts_element,
+        )

From a1e223b92d085ae8fac17077500ab8e187b92406 Mon Sep 17 00:00:00 2001
From: Tobiaspk <tobiaspk1@gmail.com>
Date: Mon, 31 Aug 2026 15:57:20 -0400
Subject: [PATCH 14/19] Simplify export.py to rely on the 'filtered' column
 directly

Rework transcripts loading around a single load_transcripts() that trusts
segger's own 'filtered' flag instead of recomputing similarity thresholds
client-side, and rename the sdata element options to explicit
--sdata-transcripts-name/--sdata-cell-boundaries-name/--sdata-table-name.
Fix two gaps that would have broken the spatialdata path: load_transcripts
now returns the full per-transcript frame alongside the assigned subset
(needed to append segger's columns onto the sdata transcripts table), and
_merge_sdata_transcripts keeps row_index through its select so the join
onto the sdata table doesn't fail.
---
 src/segger/cli/export.py | 251 +++++++++++++++++----------------------
 1 file changed, 108 insertions(+), 143 deletions(-)

diff --git a/src/segger/cli/export.py b/src/segger/cli/export.py
index b32f1a0..1ff3fdc 100644
--- a/src/segger/cli/export.py
+++ b/src/segger/cli/export.py
@@ -16,9 +16,11 @@
 
 from pathlib import Path
 from typing import Annotated, Literal, Optional
-
 from cyclopts import Parameter, Group, validators
 
+import polars as pl
+from ..io import StandardTranscriptFields
+
 _group_io = Group(name="I/O", sort_key=0)
 _group_opts = Group(name="Options", sort_key=1)
 
@@ -51,200 +53,159 @@
 
 _IncludeAll = Annotated[
     bool,
-    Parameter(group=_group_opts, help="Keep every cell-assigned transcript, ignoring the similarity threshold."),
-]
-_MinSim = Annotated[
-    Optional[float],
-    Parameter(
-        group=_group_opts,
-        help="Custom required similarity threshold, overriding the per-gene threshold from segmentation.",
-    ),
+    Parameter(group=_group_opts, help="Keep every transcript in the segmentation output, not just the ones segger's 'filtered' flag marked as kept."),
 ]
-_MinTx = Annotated[
-    int,
+_SdataTranscriptsName = Annotated[
+    str,
     Parameter(
         group=_group_opts,
-        validator=validators.Number(gte=0),
-        help="Minimum number of assigned transcripts a cell must have to be included.",
+        help="Name of the existing points element in --sdata to append segger's columns to.",
     ),
 ]
-_SpatialdataElementPrefix = Annotated[
+_SdataCellBoundariesName = Annotated[
     str,
     Parameter(
         group=_group_opts,
-        help="Appended to the new spatialdata element names, e.g. '_segger' -> 'cell_boundaries_segger' "
+        help="Name of the shapes element segger's cell boundaries are written to "
         "(avoids colliding with an existing same-named element, e.g. from the raw Xenium sdata).",
     ),
 ]
-_TranscriptsElement = Annotated[
+_SdataTableName = Annotated[
     str,
     Parameter(
         group=_group_opts,
-        help="Name of the existing points element in --sdata to append segger's columns to.",
+        help="Name of the table element segger's AnnData is written to.",
     ),
 ]
 
 
-def _legacy_join(seg: "pl.DataFrame", source_path: Optional[Path], std) -> "pl.DataFrame":
-    """Join x/y/feature_name onto a segmentation output written before they were included inline."""
-    if source_path is None:
-        raise ValueError("This segmentation output predates inline x/y/feature_name; pass -i/--source-path to join them from the source transcripts.")
-    import polars as pl
-
-    from ..io import get_preprocessor
-
-    tx = get_preprocessor(source_path).transcripts
-    tx = tx.collect() if isinstance(tx, pl.LazyFrame) else tx
-    pred_cols = [c for c in (std.row_index, "segger_cell_id", "segger_similarity", "similarity_threshold") if c in seg.columns]
-    return tx.join(seg.select(pred_cols), on=std.row_index, how="left")
-
-
-def _load_merged(segmentation_path: Path, source_path: Optional[Path]) -> "pl.DataFrame":
-    """Full segmentation output (every transcript segger considered), joined with x/y/feature_name when not already inline."""
-    import polars as pl
-
-    from ..io import StandardTranscriptFields
-
-    std = StandardTranscriptFields()
-    seg = pl.read_parquet(segmentation_path)
-    if "segger_cell_id" not in seg.columns:
-        raise ValueError(f"No 'segger_cell_id' column in {segmentation_path}.")
-
-    return seg if {std.x, std.y, std.feature} <= set(seg.columns) else _legacy_join(seg, source_path, std)
-
-
-def _load_assigned(
-    merged: "pl.DataFrame",
+# -- LOAD TRANSCRIPTS --
+def load_transcripts(
+    segmentation_path: Path,
     include_all_transcripts: bool,
-    min_similarity: Optional[float],
-    min_transcripts: int = 10,
-) -> "pl.DataFrame":
-    """Return the kept assigned tx (row_index/segger_cell_id/feature_name/x/y)."""
-    import polars as pl
-
-    from ..io import StandardTranscriptFields
+    source_path: Path = None,
+):
+    # read transcripts
+    tx = pl.read_parquet(segmentation_path)
 
+    # check if legacy result (before v0.2.0)
     std = StandardTranscriptFields()
+    if not {std.x, std.y, std.feature, "filtered"} <= set(tx.columns):
+        tx = _legacy_join(tx, source_path=source_path, std=std)
 
-    if include_all_transcripts:
-        keep = pl.col("segger_cell_id").is_not_null()
-    elif min_similarity is not None:
-        keep = pl.col("segger_cell_id").is_not_null() & (pl.col("segger_similarity") >= min_similarity)
-    elif "filtered" in merged.columns:
-        keep = pl.col("filtered")
-    else:
-        keep = pl.col("segger_cell_id").is_not_null() & (pl.col("segger_similarity") >= pl.col("similarity_threshold"))
-
+    # subset
     coord_cols = [pl.col(std.x).alias("x"), pl.col(std.y).alias("y")]
-    if std.z in merged.columns:
+    if std.z in tx.columns:
         coord_cols.append(pl.col(std.z).alias("z"))
 
-    assigned = merged.filter(keep).select(
+    # filter
+    kept = tx.filter(pl.col("filtered")) if not include_all_transcripts else tx
+
+    # select
+    assigned = kept.select(
         pl.col(std.row_index),
         pl.col("segger_cell_id").cast(pl.String),
         pl.col(std.feature).alias("feature_name"),
         *coord_cols,
     )
 
-    if min_transcripts > 0:
-        assigned = assigned.filter(pl.len().over("segger_cell_id") >= min_transcripts)
-
-    return assigned
+    return assigned, tx
 
 
-def _sdata_element_names(spatialdata_element_prefix: str) -> list:
-    return [
-        f"cell_boundaries{spatialdata_element_prefix}",
-        f"table{spatialdata_element_prefix}"
-    ]
+def _legacy_join(tx: "pl.DataFrame", source_path: Optional[Path], std) -> "pl.DataFrame":
+    """Join x/y/feature_name onto a segmentation output written before they were included inline."""
+    if source_path is None:
+        raise ValueError("This segmentation output predates inline x/y/feature_name; pass -i/--source-path to join them from the source transcripts.")
 
-def _check_sdata_writable(sdata, transcripts_element: str, spatialdata_element_prefix: str) -> None:
+    from ..io import get_preprocessor
+    
+    # load and merge
+    tx_all = get_preprocessor(source_path).transcripts
+    pred_cols = [c for c in (std.row_index, "segger_cell_id", "segger_similarity", "similarity_threshold") if c in tx.columns]
+    tx = tx.select(pred_cols).join(tx_all, on=std.row_index, how="left")
+
+    # add "filtered"
+    tx = tx.with_columns((
+        (pl.col("segger_cell_id").is_not_null()) & (pl.col("segger_similarity") >= pl.col("similarity_threshold"))
+    ).alias("filtered"))
+    
+    return tx
+
+# -- Spatial Data Support
+def _check_sdata_elements(
+        sdata,
+        element_names: dict,
+    ) -> None:
     """Fail fast if the transcripts element is missing, or any target element name already exists."""
-    if transcripts_element not in sdata.points:
-        raise KeyError(f"{transcripts_element!r} not found in sdata.points; pass --transcripts-element to point at the right one.")
-    cell_boundaries_name, table_name = _sdata_element_names(spatialdata_element_prefix)
-    if cell_boundaries_name in sdata.shapes:
-        raise FileExistsError(f"{cell_boundaries_name!r} already exists in sdata.shapes; pick a different --spatialdata-element-prefix.")
-    if table_name in sdata.tables:
-        raise FileExistsError(f"{table_name!r} already exists in sdata.tables; pick a different --spatialdata-element-prefix.")
-
+    if element_names["transcripts"] not in sdata.points:
+        raise KeyError(f"{element_names['transcripts']!r} not found in sdata.points; pass --sdata-transcripts-name to point at the right one.")
+    if element_names["cell_boundaries"] in sdata.shapes:
+        raise FileExistsError(f"{element_names['cell_boundaries']!r} already exists in sdata.shapes; pass --sdata-cell-boundaries-name to specify a different name.")
+    if element_names["table"] in sdata.tables:
+        raise FileExistsError(f"{element_names['table']!r} already exists in sdata.tables; pass --sdata-table-name to specify a different name.")
 
-_SEGGER_COLUMN_RENAMES = {
-    "similarity_threshold": "segger_similarity_threshold",
-    "converged": "segger_converged",
-    "filtered": "segger_filtered",
-}
 
 
-def _segger_transcript_columns(merged: "pl.DataFrame", row_index: str) -> "pl.DataFrame":
+def _merge_sdata_transcripts(sdata_tx: "pl.DataFrame", tx: "pl.DataFrame", row_index: str) -> "pl.DataFrame":
     """Segger's per-transcript outputs, renamed for joining onto an existing transcripts table."""
-    import polars as pl
-
-    present = [c for c in _SEGGER_COLUMN_RENAMES if c in merged.columns]
-    return (
-        merged.select(row_index, "segger_cell_id", "segger_similarity", *present)
-        .rename({c: _SEGGER_COLUMN_RENAMES[c] for c in present})
-        .with_columns(pl.col("segger_cell_id").cast(pl.String))
-    )
-
-
-def _append_segger_to_transcripts(sdata, merged: "pl.DataFrame", std, transcripts_element: str) -> "pl.DataFrame":
-    """Left-join segger's outputs onto the sdata store's existing transcripts table.
-
-    Assumes ``std.row_index`` was assigned over the same rows, in the same order, as the existing
-    transcripts table (true when segger's preprocessor read the same source file spatialdata was
-    built from). Rows absent from ``merged`` -- e.g. control probes or low-quality transcripts
-    dropped before segger ever saw them -- are flagged ``segger_unused``; the rest get segger's own
-    columns, including a null ``segger_cell_id`` for anything segger didn't assign.
-    """
-    import polars as pl
-
-    existing = sdata.points[transcripts_element]
-    existing = existing.compute() if hasattr(existing, "compute") else existing
-    tx = pl.from_pandas(existing).with_row_index(name=std.row_index)
-
-    seg_cols = _segger_transcript_columns(merged, std.row_index).with_columns(pl.lit(True).alias("_segger_seen"))
-    return (
-        tx.join(seg_cols, on=std.row_index, how="left")
-        .with_columns(pl.col("_segger_seen").is_null().alias("segger_unused"))
-        .drop(std.row_index, "_segger_seen")
-    )
 
+    # rename; these names are hardcoded. make sure to update this if any name should change going forward
+    map_columns = {
+        "segger_cell_id": "segger_cell_id",
+        "segger_similarity": "segger_similarity",
+        "similarity_threshold": "segger_similarity_threshold",
+        "converged": "segger_converged",
+        "filtered": "segger_filtered",
+    }
+    tx = tx \
+        .rename(map_columns) \
+        .select(row_index, *map_columns.values()) \
+
+    # sdata_tx is already passed in as a DataFrame
+    if hasattr(sdata_tx, "compute"):
+        sdata_tx = sdata_tx.compute()
+    sdata_tx = pl.from_pandas(sdata_tx).with_row_index(name=row_index)
+
+    # merge
+    sdata_tx = sdata_tx \
+        .join(tx, on=row_index, how="left") \
+        .with_columns(pl.col("segger_filtered").is_not_null().alias("segger_seen")) \
+
+    return sdata_tx
 
 def _write_to_sdata(
     sdata,
-    merged: "pl.DataFrame",
+    tx: "pl.DataFrame",
     gdf: "gpd.GeoDataFrame",
     adata: "AnnData",
-    spatialdata_element_prefix: str = "",
     transcripts_element: str = "transcripts",
+    cell_boundaries_element: str = "cell_boundaries_segger",
+    table_element: str = "table_segger",
 ) -> None:
     """Append segger's columns to the existing transcripts element, and add its boundaries/table elements to the given SpatialData store."""
     from spatialdata.models import PointsModel, ShapesModel, TableModel
 
-    from ..io import StandardTranscriptFields
-
     std = StandardTranscriptFields()
-    names = _sdata_element_names(spatialdata_element_prefix)
 
     attrs = sdata.points[transcripts_element].attrs.get("spatialdata_attrs", {})
-    joined = _append_segger_to_transcripts(sdata, merged, std, transcripts_element)
+    tx = _merge_sdata_transcripts(sdata.points[transcripts_element], tx, "row_index")
+
     coordinates = {"x": "x", "y": "y"}
-    if "z" in joined.columns:
+    if "z" in tx.columns:
         coordinates["z"] = "z"
     # TODO: Consider using the transformations from the base elements!
     sdata[transcripts_element] = PointsModel.parse(
-        joined.to_pandas(),
+        tx.to_pandas(),
         coordinates=coordinates,
         feature_key=attrs.get("feature_key"),
         instance_key=attrs.get("instance_key"),
     )
-    sdata[names[0]] = ShapesModel.parse(gdf)
-    sdata[names[1]] = TableModel.parse(adata)
+    sdata[cell_boundaries_element] = ShapesModel.parse(gdf)
+    sdata[table_element] = TableModel.parse(adata)
 
-    print(f"Writing {transcripts_element}, {', '.join(names)} to {sdata.path}...")
+    print(f"Writing {transcripts_element}, {cell_boundaries_element}, {table_element} to {sdata.path}...")
     sdata.write_element([transcripts_element], overwrite=True)
-    sdata.write_element(names, overwrite=False)
+    sdata.write_element([cell_boundaries_element, table_element], overwrite=False)
 
 
 def export(
@@ -261,10 +222,9 @@ def export(
         int, Parameter(group=_group_opts, help="Chaikin corner-cutting iterations to round boundaries (0 disables).")
     ] = 0,
     include_all_transcripts: _IncludeAll = False,
-    min_similarity: _MinSim = None,
-    min_transcripts: _MinTx = 10,
-    spatialdata_element_prefix: _SpatialdataElementPrefix = "_segger",
-    transcripts_element: _TranscriptsElement = "transcripts",
+    sdata_transcripts_name: _SdataTranscriptsName = "transcripts",
+    sdata_cell_boundaries_name: _SdataCellBoundariesName = "cell_boundaries_segger",
+    sdata_table_name: _SdataTableName = "table_segger",
 ):
     """Write a segger segmentation as scverse SpatialData elements (anndata, transcripts, boundaries, spatialdata)."""
     selected = elements or _DEFAULT_ELEMENTS
@@ -280,12 +240,16 @@ def export(
         import spatialdata as _spatialdata
 
         sdata = _spatialdata.read_zarr(sdata_path)
-        _check_sdata_writable(sdata, transcripts_element, spatialdata_element_prefix)
+        _check_sdata_elements(sdata, {
+            "transcripts": sdata_transcripts_name,
+            "cell_boundaries": sdata_cell_boundaries_name,
+            "table": sdata_table_name,
+        })
+
     if set(selected) - {"spatialdata"} and output_directory is None:
         raise ValueError("-o/--output-directory is required unless the only element being exported is 'spatialdata'.")
 
-    merged = _load_merged(segmentation_path, source_path)
-    assigned = _load_assigned(merged, include_all_transcripts, min_similarity, min_transcripts)
+    assigned, tx = load_transcripts(segmentation_path, include_all_transcripts, source_path)
     if output_directory is not None:
         output_directory.mkdir(parents=True, exist_ok=True)
 
@@ -303,7 +267,7 @@ def export(
             cell_id="segger_cell_id",
             z="z",
             area=gdf.geometry.area if gdf is not None else None,
-            region=f"cell_boundaries{spatialdata_element_prefix}",
+            region=sdata_cell_boundaries_name,
         )
 
     # save outputs
@@ -322,9 +286,10 @@ def export(
     if "spatialdata" in selected:
         _write_to_sdata(
             sdata,
-            merged,
+            tx,
             gdf,
             adata,
-            spatialdata_element_prefix=spatialdata_element_prefix,
-            transcripts_element=transcripts_element,
+            transcripts_element=sdata_transcripts_name,
+            cell_boundaries_element=sdata_cell_boundaries_name,
+            table_element=sdata_table_name,
         )

From 7ec59c1af60abab13d9ce7d32845102fdea0e2e6 Mon Sep 17 00:00:00 2001
From: Tobiaspk <tobiaspk1@gmail.com>
Date: Mon, 31 Aug 2026 16:02:02 -0400
Subject: [PATCH 15/19] Take element names as separate args in
 _check_sdata_elements

Matches _write_to_sdata's signature style instead of a dict.
---
 src/segger/cli/export.py | 32 +++++++++++++-------------------
 1 file changed, 13 insertions(+), 19 deletions(-)

diff --git a/src/segger/cli/export.py b/src/segger/cli/export.py
index 1ff3fdc..c6bb851 100644
--- a/src/segger/cli/export.py
+++ b/src/segger/cli/export.py
@@ -134,15 +134,17 @@ def _legacy_join(tx: "pl.DataFrame", source_path: Optional[Path], std) -> "pl.Da
 # -- Spatial Data Support
 def _check_sdata_elements(
         sdata,
-        element_names: dict,
+        transcripts_element: str,
+        cell_boundaries_element: str,
+        table_element: str,
     ) -> None:
     """Fail fast if the transcripts element is missing, or any target element name already exists."""
-    if element_names["transcripts"] not in sdata.points:
-        raise KeyError(f"{element_names['transcripts']!r} not found in sdata.points; pass --sdata-transcripts-name to point at the right one.")
-    if element_names["cell_boundaries"] in sdata.shapes:
-        raise FileExistsError(f"{element_names['cell_boundaries']!r} already exists in sdata.shapes; pass --sdata-cell-boundaries-name to specify a different name.")
-    if element_names["table"] in sdata.tables:
-        raise FileExistsError(f"{element_names['table']!r} already exists in sdata.tables; pass --sdata-table-name to specify a different name.")
+    if transcripts_element not in sdata.points:
+        raise KeyError(f"{transcripts_element!r} not found in sdata.points; pass --sdata-transcripts-name to point at the right one.")
+    if cell_boundaries_element in sdata.shapes:
+        raise FileExistsError(f"{cell_boundaries_element!r} already exists in sdata.shapes; pass --sdata-cell-boundaries-name to specify a different name.")
+    if table_element in sdata.tables:
+        raise FileExistsError(f"{table_element!r} already exists in sdata.tables; pass --sdata-table-name to specify a different name.")
 
 
 
@@ -231,20 +233,12 @@ def export(
 
     sdata = None
     if "spatialdata" in selected:
-        import importlib.util
-
-        if importlib.util.find_spec("spatialdata") is None:
-            raise ImportError("The 'spatialdata' element needs the spatialdata package. Make sure spatialdata is installed in your environment, for example with `pip install spatialdata`.")
         if sdata_path is None:
             raise ValueError("--sdata is required when exporting 'spatialdata'.")
-        import spatialdata as _spatialdata
-
-        sdata = _spatialdata.read_zarr(sdata_path)
-        _check_sdata_elements(sdata, {
-            "transcripts": sdata_transcripts_name,
-            "cell_boundaries": sdata_cell_boundaries_name,
-            "table": sdata_table_name,
-        })
+        import spatialdata as sd
+
+        sdata = sd.read_zarr(sdata_path)
+        _check_sdata_elements(sdata, sdata_transcripts_name, sdata_cell_boundaries_name, sdata_table_name)
 
     if set(selected) - {"spatialdata"} and output_directory is None:
         raise ValueError("-o/--output-directory is required unless the only element being exported is 'spatialdata'.")

From 047716e907ec7bd7391c4157c5e4de38ead6b4f5 Mon Sep 17 00:00:00 2001
From: Tobiaspk <tobiaspk1@gmail.com>
Date: Mon, 31 Aug 2026 17:34:15 -0400
Subject: [PATCH 16/19] Propagate base-element transformations in spatialdata
 export, merge lazily in dask

PointsModel/ShapesModel.parse default to an Identity transform on 'global' when
none is passed, silently dropping whatever scale/affine the base transcripts
element carried. _write_to_sdata now reads it via get_transformation() and
passes it through to both the rewritten transcripts and the new boundaries.

_merge_sdata_transcripts no longer round-trips the base transcripts through
pandas/polars/pandas; it merges lazily in dask (broadcast join, cumsum-built
row_index) and is only materialized once, right before write_element()
overwrites the on-disk store in place (required, since write_element refuses
to overwrite a path a live dask graph still reads from).

include_all_transcripts now defaults to True.
---
 src/segger/cli/export.py | 51 +++++++++++++++++++++++-----------------
 1 file changed, 30 insertions(+), 21 deletions(-)

diff --git a/src/segger/cli/export.py b/src/segger/cli/export.py
index c6bb851..4d82297 100644
--- a/src/segger/cli/export.py
+++ b/src/segger/cli/export.py
@@ -128,6 +128,12 @@ def _legacy_join(tx: "pl.DataFrame", source_path: Optional[Path], std) -> "pl.Da
     tx = tx.with_columns((
         (pl.col("segger_cell_id").is_not_null()) & (pl.col("segger_similarity") >= pl.col("similarity_threshold"))
     ).alias("filtered"))
+
+    # if "converged" exists, also require this to be true
+    if "converged" in tx.columns:
+        tx = tx.with_columns(
+            (pl.col("filtered") & pl.col("converged")).alias("filtered")
+        )
     
     return tx
 
@@ -148,8 +154,8 @@ def _check_sdata_elements(
 
 
 
-def _merge_sdata_transcripts(sdata_tx: "pl.DataFrame", tx: "pl.DataFrame", row_index: str) -> "pl.DataFrame":
-    """Segger's per-transcript outputs, renamed for joining onto an existing transcripts table."""
+def _merge_sdata_transcripts(sdata_tx: "dd.DataFrame", tx: "pl.DataFrame", row_index: str) -> "dd.DataFrame":
+    """Segger's per-transcript outputs, joined onto the existing (dask-backed) transcripts table. Stays lazy throughout."""
 
     # rename; these names are hardcoded. make sure to update this if any name should change going forward
     map_columns = {
@@ -159,19 +165,15 @@ def _merge_sdata_transcripts(sdata_tx: "pl.DataFrame", tx: "pl.DataFrame", row_i
         "converged": "segger_converged",
         "filtered": "segger_filtered",
     }
-    tx = tx \
-        .rename(map_columns) \
-        .select(row_index, *map_columns.values()) \
+    tx = tx.rename(map_columns).select(row_index, *map_columns.values()).to_pandas()
 
-    # sdata_tx is already passed in as a DataFrame
-    if hasattr(sdata_tx, "compute"):
-        sdata_tx = sdata_tx.compute()
-    sdata_tx = pl.from_pandas(sdata_tx).with_row_index(name=row_index)
+    # sdata_tx has no row_index column; construct it
+    sdata_tx = sdata_tx.assign(**{row_index: 1})
+    sdata_tx[row_index] = sdata_tx[row_index].cumsum() - 1
 
-    # merge
-    sdata_tx = sdata_tx \
-        .join(tx, on=row_index, how="left") \
-        .with_columns(pl.col("segger_filtered").is_not_null().alias("segger_seen")) \
+    # merge (tx is small enough to broadcast onto every partition; no shuffle needed)
+    sdata_tx = sdata_tx.merge(tx, on=row_index, how="left")
+    sdata_tx["segger_seen"] = sdata_tx["segger_filtered"].notnull()
 
     return sdata_tx
 
@@ -186,23 +188,30 @@ def _write_to_sdata(
 ) -> None:
     """Append segger's columns to the existing transcripts element, and add its boundaries/table elements to the given SpatialData store."""
     from spatialdata.models import PointsModel, ShapesModel, TableModel
+    from spatialdata.transformations import get_transformation
 
-    std = StandardTranscriptFields()
+    # get current transcripts
+    base_transcripts = sdata.points[transcripts_element]
+    attrs = base_transcripts.attrs.get("spatialdata_attrs", {})
+    transformations = get_transformation(base_transcripts, get_all=True)
 
-    attrs = sdata.points[transcripts_element].attrs.get("spatialdata_attrs", {})
-    tx = _merge_sdata_transcripts(sdata.points[transcripts_element], tx, "row_index")
+    # add segger info; merge stays lazy in dask, but must be materialized before overwriting
+    # transcripts_element on disk below, since it still lazily reads from that same store.
+    tx = _merge_sdata_transcripts(base_transcripts, tx, "row_index").compute().reset_index(drop=True)
 
     coordinates = {"x": "x", "y": "y"}
     if "z" in tx.columns:
         coordinates["z"] = "z"
-    # TODO: Consider using the transformations from the base elements!
+
+    # add model
     sdata[transcripts_element] = PointsModel.parse(
-        tx.to_pandas(),
+        tx,
         coordinates=coordinates,
         feature_key=attrs.get("feature_key"),
         instance_key=attrs.get("instance_key"),
+        transformations=transformations,
     )
-    sdata[cell_boundaries_element] = ShapesModel.parse(gdf)
+    sdata[cell_boundaries_element] = ShapesModel.parse(gdf, transformations=transformations)
     sdata[table_element] = TableModel.parse(adata)
 
     print(f"Writing {transcripts_element}, {cell_boundaries_element}, {table_element} to {sdata.path}...")
@@ -223,7 +232,7 @@ def export(
     chaikin_iterations: Annotated[
         int, Parameter(group=_group_opts, help="Chaikin corner-cutting iterations to round boundaries (0 disables).")
     ] = 0,
-    include_all_transcripts: _IncludeAll = False,
+    include_all_transcripts: _IncludeAll = True,
     sdata_transcripts_name: _SdataTranscriptsName = "transcripts",
     sdata_cell_boundaries_name: _SdataCellBoundariesName = "cell_boundaries_segger",
     sdata_table_name: _SdataTableName = "table_segger",
@@ -236,13 +245,13 @@ def export(
         if sdata_path is None:
             raise ValueError("--sdata is required when exporting 'spatialdata'.")
         import spatialdata as sd
-
         sdata = sd.read_zarr(sdata_path)
         _check_sdata_elements(sdata, sdata_transcripts_name, sdata_cell_boundaries_name, sdata_table_name)
 
     if set(selected) - {"spatialdata"} and output_directory is None:
         raise ValueError("-o/--output-directory is required unless the only element being exported is 'spatialdata'.")
 
+    # load tx
     assigned, tx = load_transcripts(segmentation_path, include_all_transcripts, source_path)
     if output_directory is not None:
         output_directory.mkdir(parents=True, exist_ok=True)

From cf3f58ec1b092ca3f90de175a72a319c800a1454 Mon Sep 17 00:00:00 2001
From: Tobiaspk <tobiaspk1@gmail.com>
Date: Tue, 1 Sep 2026 11:47:38 -0400
Subject: [PATCH 17/19] Fix in-place spatialdata overwrite and drop row_index
 from transcripts

write_element(overwrite=True) always fails for an element inside its own
store (discussion #520). Back up transcripts, detach in-memory handles,
then delete-then-write. Also drop the row_index join key from output.
---
 src/segger/cli/export.py | 45 ++++++++++++++++++++++++++++++++--------
 1 file changed, 36 insertions(+), 9 deletions(-)

diff --git a/src/segger/cli/export.py b/src/segger/cli/export.py
index 4d82297..b5e03b9 100644
--- a/src/segger/cli/export.py
+++ b/src/segger/cli/export.py
@@ -175,6 +175,9 @@ def _merge_sdata_transcripts(sdata_tx: "dd.DataFrame", tx: "pl.DataFrame", row_i
     sdata_tx = sdata_tx.merge(tx, on=row_index, how="left")
     sdata_tx["segger_seen"] = sdata_tx["segger_filtered"].notnull()
 
+    # row_index is only a join key; drop it from the output
+    sdata_tx = sdata_tx.drop(columns=[row_index])
+
     return sdata_tx
 
 def _write_to_sdata(
@@ -195,28 +198,52 @@ def _write_to_sdata(
     attrs = base_transcripts.attrs.get("spatialdata_attrs", {})
     transformations = get_transformation(base_transcripts, get_all=True)
 
-    # add segger info; merge stays lazy in dask, but must be materialized before overwriting
-    # transcripts_element on disk below, since it still lazily reads from that same store.
+    # new element fully in memory, required for overwriting
     tx = _merge_sdata_transcripts(base_transcripts, tx, "row_index").compute().reset_index(drop=True)
 
     coordinates = {"x": "x", "y": "y"}
     if "z" in tx.columns:
         coordinates["z"] = "z"
 
-    # add model
-    sdata[transcripts_element] = PointsModel.parse(
+    # build the new (in-memory, unbacked) elements
+    new_transcripts = PointsModel.parse(
         tx,
         coordinates=coordinates,
         feature_key=attrs.get("feature_key"),
         instance_key=attrs.get("instance_key"),
         transformations=transformations,
     )
-    sdata[cell_boundaries_element] = ShapesModel.parse(gdf, transformations=transformations)
-    sdata[table_element] = TableModel.parse(adata)
-
+    new_boundaries = ShapesModel.parse(gdf, transformations=transformations)
+    new_table = TableModel.parse(adata)
+
+    # SpatialData can't overwrite (#520). Do 1) backup, 2) drop in-memory handles, 3) delete original, 4) write new elements, 5) drop backup
+    # 1 backup
+    backup_element = f"{transcripts_element}_backup"
+    sdata[backup_element] = base_transcripts
+    sdata.write_element([backup_element])
+
+    # 2 detach in-memory
+    del sdata.points[backup_element]
+    sdata[transcripts_element] = new_transcripts
+    sdata[cell_boundaries_element] = new_boundaries
+    sdata[table_element] = new_table
+
+    # 3 4 delete and write
     print(f"Writing {transcripts_element}, {cell_boundaries_element}, {table_element} to {sdata.path}...")
-    sdata.write_element([transcripts_element], overwrite=True)
-    sdata.write_element([cell_boundaries_element, table_element], overwrite=False)
+    try:
+        sdata.delete_element_from_disk(transcripts_element)
+        sdata.write_element([transcripts_element, cell_boundaries_element, table_element])
+    except Exception:
+        print(
+            f"Write failed. The original {transcripts_element!r} is preserved on disk as "
+            f"{backup_element!r}; restore it from there."
+        )
+        raise
+    else:
+        # delete backup
+        sdata.delete_element_from_disk(backup_element)
+        if sdata.has_consolidated_metadata():
+            sdata.write_consolidated_metadata()
 
 
 def export(

From b09195c87839696f664515085876660fac76ad7c Mon Sep 17 00:00:00 2001
From: Tobiaspk <tobiaspk1@gmail.com>
Date: Tue, 1 Sep 2026 11:59:00 -0400
Subject: [PATCH 18/19] Add --min-counts filter and align export table to
 boundaries

Drop cells below min_counts from the table/anndata, and keep only cells
that produced a boundary polygon so the table annotates only real shapes
(no dangling SpatialData annotations). Require min_counts >= 3 for
spatialdata, since boundaries need >= 3 transcripts.
---
 src/segger/cli/export.py            | 16 ++++++++++++++++
 src/segger/export/anndata_writer.py |  4 ++++
 2 files changed, 20 insertions(+)

diff --git a/src/segger/cli/export.py b/src/segger/cli/export.py
index b5e03b9..e8f7e58 100644
--- a/src/segger/cli/export.py
+++ b/src/segger/cli/export.py
@@ -77,6 +77,14 @@
         help="Name of the table element segger's AnnData is written to.",
     ),
 ]
+_MinCounts = Annotated[
+    int,
+    Parameter(
+        group=_group_opts,
+        help="Drop cells with fewer than this many assigned transcripts from the table/anndata "
+        "(must be >= 3 for spatialdata, since boundaries need >= 3 points).",
+    ),
+]
 
 
 # -- LOAD TRANSCRIPTS --
@@ -263,12 +271,16 @@ def export(
     sdata_transcripts_name: _SdataTranscriptsName = "transcripts",
     sdata_cell_boundaries_name: _SdataCellBoundariesName = "cell_boundaries_segger",
     sdata_table_name: _SdataTableName = "table_segger",
+    min_counts: _MinCounts = 10,
 ):
     """Write a segger segmentation as scverse SpatialData elements (anndata, transcripts, boundaries, spatialdata)."""
     selected = elements or _DEFAULT_ELEMENTS
 
     sdata = None
     if "spatialdata" in selected:
+        if min_counts < 3:
+            # cell boundaries need >= 3 transcripts to form a polygon; a lower table cutoff leaves cells without one
+            raise ValueError("--min-counts must be >= 3 for spatialdata: boundaries need >= 3 transcripts to form a polygon.")
         if sdata_path is None:
             raise ValueError("--sdata is required when exporting 'spatialdata'.")
         import spatialdata as sd
@@ -298,7 +310,11 @@ def export(
             z="z",
             area=gdf.geometry.area if gdf is not None else None,
             region=sdata_cell_boundaries_name,
+            min_counts=min_counts,
         )
+        # keep only cells that produced a boundary polygon, so the table annotates only real shapes
+        if gdf is not None:
+            adata = adata[adata.obs_names.isin(gdf.index)].copy()
 
     # save outputs
     if "transcripts" in selected:
diff --git a/src/segger/export/anndata_writer.py b/src/segger/export/anndata_writer.py
index a8921bc..e9d3989 100644
--- a/src/segger/export/anndata_writer.py
+++ b/src/segger/export/anndata_writer.py
@@ -18,6 +18,7 @@ def build_anndata(
     z: Optional[str] = None,
     region: str = "cell_boundaries",
     area: Optional[pd.Series] = None,
+    min_counts: int = 1,
 ) -> AnnData:
     """Cell x gene table built on :func:`anndata_from_transcripts`, with the SpatialData link added.
 
@@ -42,6 +43,9 @@ def build_anndata(
     if area is not None:
         adata.obs["area"] = pd.Series(area).reindex(adata.obs_names).to_numpy()
 
+    if min_counts > 1:
+        adata = adata[adata.obs["n_transcripts"] >= min_counts].copy()
+
     # SpatialData link: region/instance_key obs columns plus the attrs that join table to shapes.
     adata.obs["region"] = pd.Categorical([region] * adata.n_obs, categories=[region])
     adata.obs["cell_id"] = adata.obs_names.to_numpy()

From 2c83537346ffe25383976dc5c034e772ec54b4cf Mon Sep 17 00:00:00 2001
From: Tobiaspk <tobiaspk1@gmail.com>
Date: Fri, 11 Sep 2026 10:17:24 -0400
Subject: [PATCH 19/19] fix: drop pre-existing segger columns before merging
 transcripts

Re-running export against transcripts that already have segger_*
columns caused merge() to silently suffix them with _x/_y instead of
overwriting, corrupting the segger_seen/segger_filtered computation.
---
 src/segger/cli/export.py | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/src/segger/cli/export.py b/src/segger/cli/export.py
index e8f7e58..8bbdfdf 100644
--- a/src/segger/cli/export.py
+++ b/src/segger/cli/export.py
@@ -173,12 +173,17 @@ def _merge_sdata_transcripts(sdata_tx: "dd.DataFrame", tx: "pl.DataFrame", row_i
         "converged": "segger_converged",
         "filtered": "segger_filtered",
     }
+
+    # rename
     tx = tx.rename(map_columns).select(row_index, *map_columns.values()).to_pandas()
 
     # sdata_tx has no row_index column; construct it
     sdata_tx = sdata_tx.assign(**{row_index: 1})
     sdata_tx[row_index] = sdata_tx[row_index].cumsum() - 1
 
+    # delete existing (overwrite is not exactly silent - export would stop if boundaries or table already exists)
+    sdata_tx = sdata_tx.drop(columns=[col for col in map_columns.values() if col in sdata_tx.columns])
+
     # merge (tx is small enough to broadcast onto every partition; no shuffle needed)
     sdata_tx = sdata_tx.merge(tx, on=row_index, how="left")
     sdata_tx["segger_seen"] = sdata_tx["segger_filtered"].notnull()