napari-ome-arrow 0.0.3__tar.gz → 0.0.5__tar.gz

{napari_ome_arrow-0.0.3 → napari_ome_arrow-0.0.5}/.github/workflows/run-tests.yml

@@ -52,5 +52,12 @@ jobs:
         with:
           qt: true
           wm: herbstluftwm
+      - name: Install test dependencies
+        run: >
+          uv sync --frozen
+          --python ${{ matrix.python_version }}
+          --extra all
+          --extra pyside6
+          --extra vortex
       - name: Run pytest
         run: uv run --python ${{ matrix.python_version }} --frozen pytest

{napari_ome_arrow-0.0.3 → napari_ome_arrow-0.0.5}/.pre-commit-config.yaml

@@ -9,7 +9,7 @@ repos:
     -   id: check-yaml
     -   id: detect-private-key
 -   repo: https://github.com/tox-dev/pyproject-fmt
-    rev: "v2.11.1"
+    rev: "v2.12.1"
     hooks:
     -   id: pyproject-fmt
 -   repo: https://github.com/citation-file-format/cffconvert
@@ -34,17 +34,17 @@ repos:
         additional_dependencies:
         -   mdformat-gfm
 -   repo: https://github.com/adrienverge/yamllint
-    rev: v1.37.1
+    rev: v1.38.0
     hooks:
     -   id: yamllint
         exclude: pre-commit-config.yaml
 -   repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: "v0.14.7"
+    rev: "v0.15.0"
     hooks:
     -   id: ruff-format
     -   id: ruff-check
 -   repo: https://github.com/rhysd/actionlint
-    rev: v1.7.9
+    rev: v1.7.10
     hooks:
     -   id: actionlint
 -   repo: https://gitlab.com/vojko.pribudic.foss/pre-commit-update

{napari_ome_arrow-0.0.3 → napari_ome_arrow-0.0.5}/CITATION.cff

@@ -2,7 +2,7 @@
 # Visit https://bit.ly/cffinit to generate yours today!
 ---
 cff-version: 1.2.0
-title: ome_arrow
+title: napari_ome_arrow
 message: >-
   If you use this software, please cite it using the
   metadata from the CITATION.cff file.
@@ -25,10 +25,14 @@ authors:
     orcid: 'https://orcid.org/0000-0002-0503-9348'
 repository-code: "https://github.com/wayscience/ome-arrow"
 abstract: >-
-  Using OME specifications with Apache Arrow for fast, queryable, and language agnostic bioimage data.
+  A Napari plugin for OME-Arrow and OME-Parquet bioimage data
 keywords:
   - python
 license: BSD-3-Clause
+identifiers:
+  - description: Zenodo software DOI
+    type: doi
+    value: 10.5281/zenodo.17613571
 references:
   - authors:
       - name: "ExampleHuman CellProfiler Data Team"
@@ -125,3 +129,29 @@ references:
       JUMP (cpg0000-jump-pilot) was used to help demonstrate napari-ome-arrow's
       ability to parse various image data (specifically, plate BR00117006).
       https://github.com/broadinstitute/cellpainting-gallery
+  - type: article
+    authors:
+      - family-names: Blin
+        given-names: Guillaume
+      - family-names: Sadurska
+        given-names: Dominika
+      - family-names: Portero Migueles
+        given-names: Rafael
+      - family-names: Chen
+        given-names: Ni
+      - family-names: Watson
+        given-names: James A.
+      - family-names: Lowell
+        given-names: Sally
+    title: "Nessys: A new set of tools for the automated detection of nuclei within intact tissues and dense 3D cultures"
+    journal: PLoS Biology
+    volume: "17"
+    issue: "8"
+    pages: e3000388
+    year: 2019
+    doi: "10.1371/journal.pbio.3000388"
+    url: "https://doi.org/10.1371/journal.pbio.3000388"
+    notes: >
+      This work used the file "6001240_labels.zarr" from the DISCEPTS imaging
+      dataset, available through the Image Data Resource (IDR) under accession
+      number idr0062.

{napari_ome_arrow-0.0.3/src/napari_ome_arrow.egg-info → napari_ome_arrow-0.0.5}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: napari-ome-arrow
-Version: 0.0.3
+Version: 0.0.5
 Summary: A Napari plugin for OME-Arrow and OME-Parquet bioimage data
 License: 
         Copyright (c) 2025, Dave Bunten
@@ -51,7 +51,7 @@ Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: magicgui
 Requires-Dist: numpy
-Requires-Dist: ome-arrow>=0.0.2
+Requires-Dist: ome-arrow>=0.0.3
 Requires-Dist: qtpy>=2.4
 Requires-Dist: scikit-image
 Provides-Extra: all
@@ -65,6 +65,8 @@ Provides-Extra: pyside6
 Requires-Dist: napari[pyside6]; extra == "pyside6"
 Requires-Dist: pyside6>=6.6; extra == "pyside6"
 Requires-Dist: qtpy>=2.4; extra == "pyside6"
+Provides-Extra: vortex
+Requires-Dist: vortex-data; extra == "vortex"
 Dynamic: license-file
 
 # napari-ome-arrow
@@ -74,6 +76,7 @@ Dynamic: license-file
 [![Python Version](https://img.shields.io/pypi/pyversions/napari-ome-arrow.svg?color=green)](https://python.org)
 [![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/napari-ome-arrow)](https://napari-hub.org/plugins/napari-ome-arrow)
 [![npe2](https://img.shields.io/badge/plugin-npe2-blue?link=https://napari.org/stable/plugins/index.html)](https://napari.org/stable/plugins/index.html)
+[![Software DOI badge](https://zenodo.org/badge/DOI/10.5281/zenodo.17613571.svg)](https://doi.org/10.5281/zenodo.17613571)
 
 `napari-ome-arrow` is a minimal plugin for [napari](https://napari.org) that opens image data through the [OME-Arrow](https://github.com/wayscience/ome-arrow) toolkit.
 
@@ -82,6 +85,7 @@ It provides a single, explicit pathway for loading OME-style bioimage data:
 - **OME-TIFF** (`.ome.tif`, `.ome.tiff`, `.tif`, `.tiff`)
 - **OME-Zarr** (`.ome.zarr`, `.zarr` stores and URLs)
 - **OME-Parquet** (`.ome.parquet`, `.parquet`, `.pq`)
+- **OME-Vortex** (`.ome.vortex`, `.vortex`)
 - **Bio-Formats–style stack patterns** (paths containing `<`, `>`, or `*`)
 - A simple **`.npy` fallback** for quick testing / ad-hoc arrays
 
@@ -126,8 +130,11 @@ It provides a single, explicit pathway for loading OME-style bioimage data:
   - respects `NAPARI_OME_ARROW_LAYER_TYPE`, and
   - defaults to `"image"` if the variable is not set.
 
-- ✅ **Grid view for multi-row OME-Parquet**
-  When a Parquet file contains multiple OME-Arrow rows, each row is loaded as its own layer and the viewer is switched to napari’s grid mode. Set `NAPARI_OME_ARROW_PARQUET_COLUMN` to pick which image column to visualize.
+- ✅ **Grid view for multi-row OME-Parquet / OME-Vortex**
+  When a Parquet or Vortex file contains multiple OME-Arrow rows, each row is loaded as its own layer and the viewer is switched to napari’s grid mode. Set `NAPARI_OME_ARROW_PARQUET_COLUMN` or `NAPARI_OME_ARROW_VORTEX_COLUMN` to pick which image column to visualize.
+
+- ✅ **Stack scale prompt + override**
+  When loading image stacks (stack patterns), napari prompts for voxel spacing only if no scale metadata or `NAPARI_OME_ARROW_STACK_SCALE` override is present and a Qt UI is available (headless runs skip the prompt). To avoid the prompt, set `NAPARI_OME_ARROW_STACK_SCALE` using `Z,Y,X` or `T,C,Z,Y,X`.
 
 ______________________________________________________________________
 
@@ -153,13 +160,19 @@ To install latest development version :
 pip install git+https://github.com/wayscience/napari-ome-arrow.git
 ```
 
+To enable OME-Vortex support via OME-Arrow, install the optional extra:
+
+```bash
+pip install "napari-ome-arrow[vortex]"
+```
+
 ## Usage
 
 ### From the napari GUI
 
 1. Install the plugin (see above).
 1. Start napari.
-1. Drag and drop an OME-TIFF, OME-Zarr, OME-Parquet file, or stack pattern into the viewer.
+1. Drag and drop an OME-TIFF, OME-Zarr, OME-Parquet, OME-Vortex file, a stack pattern, or a multi-select stack (e.g. `img_000.tif` ... `img_123.tif`) into the viewer.
 1. When prompted, choose **Image** or **Labels**.
 
 The plugin will:
@@ -167,6 +180,7 @@ The plugin will:
 - load the data through `OMEArrow`,
 - map channels and axes appropriately, and
 - automatically switch to 3D if there is a Z-stack.
+- When multiple files look like a numbered stack, treat them as a single stack rather than independent layers.
 
 ### From the command line
 
@@ -183,6 +197,12 @@ NAPARI_OME_ARROW_LAYER_TYPE=labels napari my_labels.ome.parquet
 NAPARI_OME_ARROW_LAYER_TYPE=image \\
 NAPARI_OME_ARROW_PARQUET_COLUMN=Image_FileName_OrigDNA_OMEArrow_ORIG \\
 napari tests/data/cytodataframe/BR00117006.ome.parquet
+
+# Prefill stack voxel spacing for stack patterns (Z,Y,X or T,C,Z,Y,X)
+NAPARI_OME_ARROW_STACK_SCALE=1.0,0.108,0.108 napari "stack/z<000-120>.tif"
+
+# Prefill stack voxel spacing for multi-file stacks (use a pattern or glob on CLI)
+NAPARI_OME_ARROW_STACK_SCALE=1.0,0.108,0.108 napari "stack/img_<000-120>.tif"
 ```
 
 ## Contributing

{napari_ome_arrow-0.0.3 → napari_ome_arrow-0.0.5}/README.md

@@ -5,6 +5,7 @@
 [![Python Version](https://img.shields.io/pypi/pyversions/napari-ome-arrow.svg?color=green)](https://python.org)
 [![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/napari-ome-arrow)](https://napari-hub.org/plugins/napari-ome-arrow)
 [![npe2](https://img.shields.io/badge/plugin-npe2-blue?link=https://napari.org/stable/plugins/index.html)](https://napari.org/stable/plugins/index.html)
+[![Software DOI badge](https://zenodo.org/badge/DOI/10.5281/zenodo.17613571.svg)](https://doi.org/10.5281/zenodo.17613571)
 
 `napari-ome-arrow` is a minimal plugin for [napari](https://napari.org) that opens image data through the [OME-Arrow](https://github.com/wayscience/ome-arrow) toolkit.
 
@@ -13,6 +14,7 @@ It provides a single, explicit pathway for loading OME-style bioimage data:
 - **OME-TIFF** (`.ome.tif`, `.ome.tiff`, `.tif`, `.tiff`)
 - **OME-Zarr** (`.ome.zarr`, `.zarr` stores and URLs)
 - **OME-Parquet** (`.ome.parquet`, `.parquet`, `.pq`)
+- **OME-Vortex** (`.ome.vortex`, `.vortex`)
 - **Bio-Formats–style stack patterns** (paths containing `<`, `>`, or `*`)
 - A simple **`.npy` fallback** for quick testing / ad-hoc arrays
 
@@ -57,8 +59,11 @@ It provides a single, explicit pathway for loading OME-style bioimage data:
   - respects `NAPARI_OME_ARROW_LAYER_TYPE`, and
   - defaults to `"image"` if the variable is not set.
 
-- ✅ **Grid view for multi-row OME-Parquet**
-  When a Parquet file contains multiple OME-Arrow rows, each row is loaded as its own layer and the viewer is switched to napari’s grid mode. Set `NAPARI_OME_ARROW_PARQUET_COLUMN` to pick which image column to visualize.
+- ✅ **Grid view for multi-row OME-Parquet / OME-Vortex**
+  When a Parquet or Vortex file contains multiple OME-Arrow rows, each row is loaded as its own layer and the viewer is switched to napari’s grid mode. Set `NAPARI_OME_ARROW_PARQUET_COLUMN` or `NAPARI_OME_ARROW_VORTEX_COLUMN` to pick which image column to visualize.
+
+- ✅ **Stack scale prompt + override**
+  When loading image stacks (stack patterns), napari prompts for voxel spacing only if no scale metadata or `NAPARI_OME_ARROW_STACK_SCALE` override is present and a Qt UI is available (headless runs skip the prompt). To avoid the prompt, set `NAPARI_OME_ARROW_STACK_SCALE` using `Z,Y,X` or `T,C,Z,Y,X`.
 
 ______________________________________________________________________
 
@@ -84,13 +89,19 @@ To install latest development version :
 pip install git+https://github.com/wayscience/napari-ome-arrow.git
 ```
 
+To enable OME-Vortex support via OME-Arrow, install the optional extra:
+
+```bash
+pip install "napari-ome-arrow[vortex]"
+```
+
 ## Usage
 
 ### From the napari GUI
 
 1. Install the plugin (see above).
 1. Start napari.
-1. Drag and drop an OME-TIFF, OME-Zarr, OME-Parquet file, or stack pattern into the viewer.
+1. Drag and drop an OME-TIFF, OME-Zarr, OME-Parquet, OME-Vortex file, a stack pattern, or a multi-select stack (e.g. `img_000.tif` ... `img_123.tif`) into the viewer.
 1. When prompted, choose **Image** or **Labels**.
 
 The plugin will:
@@ -98,6 +109,7 @@ The plugin will:
 - load the data through `OMEArrow`,
 - map channels and axes appropriately, and
 - automatically switch to 3D if there is a Z-stack.
+- When multiple files look like a numbered stack, treat them as a single stack rather than independent layers.
 
 ### From the command line
 
@@ -114,6 +126,12 @@ NAPARI_OME_ARROW_LAYER_TYPE=labels napari my_labels.ome.parquet
 NAPARI_OME_ARROW_LAYER_TYPE=image \\
 NAPARI_OME_ARROW_PARQUET_COLUMN=Image_FileName_OrigDNA_OMEArrow_ORIG \\
 napari tests/data/cytodataframe/BR00117006.ome.parquet
+
+# Prefill stack voxel spacing for stack patterns (Z,Y,X or T,C,Z,Y,X)
+NAPARI_OME_ARROW_STACK_SCALE=1.0,0.108,0.108 napari "stack/z<000-120>.tif"
+
+# Prefill stack voxel spacing for multi-file stacks (use a pattern or glob on CLI)
+NAPARI_OME_ARROW_STACK_SCALE=1.0,0.108,0.108 napari "stack/img_<000-120>.tif"
 ```
 
 ## Contributing

{napari_ome_arrow-0.0.3 → napari_ome_arrow-0.0.5}/pyproject.toml

@@ -29,7 +29,7 @@ dynamic = [ "version" ]
 dependencies = [
   "magicgui",
   "numpy",
-  "ome-arrow>=0.0.2",
+  "ome-arrow>=0.0.3",
   "qtpy>=2.4",
   "scikit-image",
 ]
@@ -39,6 +39,7 @@ optional-dependencies.all = [ "napari", "qtpy>=2.4" ]
 optional-dependencies.pyqt6 = [ "napari[pyqt6]", "pyqt6>=6.6", "qtpy>=2.4" ]
 # Let users choose their Qt backend explicitly:
 optional-dependencies.pyside6 = [ "napari[pyside6]", "pyside6>=6.6", "qtpy>=2.4" ]
+optional-dependencies.vortex = [ "vortex-data" ]
 urls."Bug Tracker" = "https://github.com/wayscience/napari-ome-arrow/issues"
 urls."Documentation" = "https://github.com/wayscience/napari-ome-arrow#README.md"
 urls."Source Code" = "https://github.com/wayscience/napari-ome-arrow"
@@ -58,13 +59,13 @@ dev = [
 [tool.setuptools]
 include-package-data = true
 
+[tool.setuptools.package-data]
+"*" = [ "*.yaml" ]
+
 [tool.setuptools.packages.find]
 where = [ "src" ]
 exclude = [ "*.tests", "*.tests.*", "tests*" ]
 
-[tool.setuptools.package-data]
-"*" = [ "*.yaml" ]
-
 [tool.setuptools_scm]
 write_to = "src/napari_ome_arrow/_version.py"
 fallback_version = "0.0.1+nogit"

napari_ome_arrow-0.0.5/src/napari_ome_arrow/_reader.py

@@ -0,0 +1,340 @@
+"""
+Minimal napari reader for OME-Arrow sources (stack patterns, OME-Zarr, OME-Parquet,
+OME-Vortex, OME-TIFF) plus a fallback .npy example.
+
+Behavior:
+    * If NAPARI_OME_ARROW_LAYER_TYPE is set to "image" or "labels",
+      that choice is used.
+    * Otherwise, in a GUI/Qt context, the user is prompted with a modal
+      dialog asking whether to load as image or labels.
+"""
+
+from __future__ import annotations
+
+import os
+import warnings
+from collections.abc import Callable, Sequence
+from pathlib import Path
+
+from ._reader_infer import (  # noqa: F401
+    _infer_layer_mode_from_record,
+    _infer_layer_mode_from_source,
+    _looks_like_ome_source,
+    _normalize_image_type,
+)
+from ._reader_napari import (  # noqa: F401
+    _maybe_set_viewer_3d,
+    _strip_channel_axis,
+)
+from ._reader_omearrow import (  # noqa: F401
+    _read_one,
+    _read_parquet_rows,
+    _read_vortex_rows,
+)
+from ._reader_stack import (  # noqa: F401
+    _channel_names_from_pattern,
+    _collect_stack_files,
+    _infer_stack_scale_from_pattern,
+    _parse_stack_scale,
+    _prompt_stack_pattern,
+    _prompt_stack_scale,
+    _read_rgb_stack_pattern,
+    _replace_channel_placeholder,
+    _stack_default_dim_for_pattern,
+    _suggest_stack_pattern,
+)
+from ._reader_types import LayerData, PathLike
+
+__all__ = [
+    "napari_get_reader",
+    "reader_function",
+    "_infer_layer_mode_from_record",
+    "_infer_layer_mode_from_source",
+    "_looks_like_ome_source",
+    "_normalize_image_type",
+    "_maybe_set_viewer_3d",
+    "_strip_channel_axis",
+    "_read_one",
+    "_read_parquet_rows",
+    "_read_vortex_rows",
+    "_channel_names_from_pattern",
+    "_collect_stack_files",
+    "_infer_stack_scale_from_pattern",
+    "_parse_stack_scale",
+    "_prompt_stack_pattern",
+    "_prompt_stack_scale",
+    "_read_rgb_stack_pattern",
+    "_replace_channel_placeholder",
+    "_stack_default_dim_for_pattern",
+    "_suggest_stack_pattern",
+]
+
+# --------------------------------------------------------------------- #
+#  Mode selection (env var + GUI prompt)
+# --------------------------------------------------------------------- #
+
+
+def _get_layer_mode(
+    sample_path: str, *, image_type_hint: str | None = None
+) -> str:
+    """Decide whether to load as "image" or "labels".
+
+    Priority:
+    1. `NAPARI_OME_ARROW_LAYER_TYPE` env var (image/labels).
+    2. If in a Qt GUI context, show a modal dialog asking the user.
+    3. Otherwise, default to "image".
+
+    Args:
+        sample_path: Path used for prompt labeling.
+        image_type_hint: Optional inferred mode from metadata.
+
+    Returns:
+        The selected mode, "image" or "labels".
+
+    Raises:
+        RuntimeError: If the environment variable is invalid or the user
+            cancels the dialog.
+    """
+    # Env var override (used in headless/batch workflows).
+    mode = os.environ.get("NAPARI_OME_ARROW_LAYER_TYPE")
+    if mode is not None:
+        mode = mode.lower()
+        if mode in {"image", "labels"}:
+            return mode
+        raise RuntimeError(
+            f"Invalid NAPARI_OME_ARROW_LAYER_TYPE={mode!r}; expected 'image' or 'labels'."
+        )
+
+    # Metadata hint (best effort).
+    if image_type_hint in {"image", "labels"}:
+        return image_type_hint
+
+    # No env var → try to prompt in GUI context
+    try:
+        from qtpy import QtWidgets
+    except Exception:
+        # no Qt, probably headless: default to image
+        warnings.warn(
+            "NAPARI_OME_ARROW_LAYER_TYPE not set and Qt not available; "
+            "defaulting to 'image'.",
+            stacklevel=2,
+        )
+        return "image"
+
+    app = QtWidgets.QApplication.instance()
+    if app is None:
+        # Again, likely headless or non-Qt usage
+        warnings.warn(
+            "NAPARI_OME_ARROW_LAYER_TYPE not set and no QApplication instance; "
+            "defaulting to 'image'.",
+            stacklevel=2,
+        )
+        return "image"
+
+    # Build a simple modal choice dialog
+    msg = QtWidgets.QMessageBox()
+    msg.setWindowTitle("napari-ome-arrow: choose layer type")
+    msg.setText(
+        f"<p align='left'>How should '{Path(sample_path).name}' be loaded?<br><br>"
+        "You can also set NAPARI_OME_ARROW_LAYER_TYPE=image or labels to skip this prompt.</p>"
+    )
+
+    # Use ActionRole for ALL buttons so Qt does NOT reorder them
+    image_button = msg.addButton("Image", QtWidgets.QMessageBox.ActionRole)
+    labels_button = msg.addButton("Labels", QtWidgets.QMessageBox.ActionRole)
+    cancel_button = msg.addButton("Cancel", QtWidgets.QMessageBox.ActionRole)
+
+    # If you want Esc to behave as Cancel:
+    msg.setEscapeButton(cancel_button)
+
+    msg.exec_()
+    clicked = msg.clickedButton()
+
+    if clicked is labels_button:
+        return "labels"
+    if clicked is image_button:
+        return "image"
+
+    raise RuntimeError("User cancelled napari-ome-arrow load dialog.")
+
+
+# --------------------------------------------------------------------- #
+#  napari entry point: napari_get_reader
+# --------------------------------------------------------------------- #
+
+
+def napari_get_reader(
+    path: PathLike | Sequence[PathLike],
+) -> Callable[[PathLike | Sequence[PathLike]], list[LayerData]] | None:
+    """Return a reader callable for napari if the path is supported.
+
+    Args:
+        path: A single path or a sequence of paths provided by napari.
+
+    Returns:
+        Reader callable if the path is supported, otherwise None.
+    """
+    # napari may pass a list/tuple or a single path
+    first = str(path[0] if isinstance(path, (list, tuple)) else path).strip()
+
+    if _looks_like_ome_source(first):
+        return reader_function
+    return None
+
+
+# --------------------------------------------------------------------- #
+#  Reader implementation: reader_function
+# --------------------------------------------------------------------- #
+
+
+def reader_function(
+    path: PathLike | Sequence[PathLike],
+) -> list[LayerData]:
+    """Read one or more paths into napari layer data.
+
+    The user may be prompted (or an env var used) to decide "image" vs
+    "labels".
+
+    Args:
+        path: A single path or a sequence of paths provided by napari.
+
+    Returns:
+        List of layer tuples for napari.
+
+    Raises:
+        ValueError: If no readable inputs are found.
+    """
+    paths: list[str] = [
+        str(p) for p in (path if isinstance(path, (list, tuple)) else [path])
+    ]
+    layers: list[LayerData] = []
+
+    # Offer a stack pattern prompt when multiple compatible files are present.
+    stack_selection = _collect_stack_files(paths)
+    stack_pattern = None
+    if stack_selection is not None:
+        stack_pattern = _prompt_stack_pattern(*stack_selection)
+
+    # Use the original first path as context for the dialog label
+    mode_hint = None
+    if stack_pattern is not None:
+        stack_default_dim = _stack_default_dim_for_pattern(stack_pattern)
+        mode_hint = _infer_layer_mode_from_source(
+            stack_pattern, stack_default_dim=stack_default_dim
+        )
+    elif paths:
+        mode_hint = _infer_layer_mode_from_source(paths[0])
+    try:
+        mode = _get_layer_mode(
+            sample_path=paths[0], image_type_hint=mode_hint
+        )  # 'image' or 'labels'
+    except RuntimeError as e:
+        # If user canceled the dialog, propagate a clean error for napari
+        raise ValueError(str(e)) from e
+
+    if stack_pattern is not None:
+        try:
+            channel_names = _channel_names_from_pattern(
+                stack_pattern, stack_default_dim
+            )
+            resolved_stack_scale = None
+            if mode == "image" and channel_names and len(channel_names) > 1:
+                # Split each channel into separate layers for stack patterns.
+                inferred_stack_scale = _infer_stack_scale_from_pattern(
+                    stack_pattern, stack_default_dim
+                )
+                env_scale = os.environ.get("NAPARI_OME_ARROW_STACK_SCALE")
+                if env_scale:
+                    try:
+                        resolved_stack_scale = _parse_stack_scale(env_scale)
+                    except ValueError as exc:
+                        warnings.warn(
+                            f"Invalid NAPARI_OME_ARROW_STACK_SCALE '{env_scale}': {exc}.",
+                            stacklevel=2,
+                        )
+                        resolved_stack_scale = None
+                if (
+                    resolved_stack_scale is None
+                    and inferred_stack_scale is None
+                ):
+                    resolved_stack_scale = _prompt_stack_scale(
+                        sample_path=stack_pattern, default_scale=None
+                    )
+
+                for label in channel_names:
+                    channel_pattern = _replace_channel_placeholder(
+                        stack_pattern, label, stack_default_dim
+                    )
+                    channel_default_dim = _stack_default_dim_for_pattern(
+                        channel_pattern
+                    )
+                    try:
+                        arr, add_kwargs, layer_type = _read_one(
+                            channel_pattern,
+                            mode=mode,
+                            stack_default_dim=channel_default_dim,
+                            stack_scale_override=resolved_stack_scale,
+                        )
+                        arr, add_kwargs = _strip_channel_axis(arr, add_kwargs)
+                    except Exception as exc:
+                        try:
+                            arr, is_rgb = _read_rgb_stack_pattern(
+                                channel_pattern
+                            )
+                        except Exception:
+                            warnings.warn(
+                                f"Failed to read channel '{label}' from stack "
+                                f"pattern '{stack_pattern}': {exc}",
+                                stacklevel=2,
+                            )
+                            continue
+                        add_kwargs = {"name": Path(channel_pattern).name}
+                        if is_rgb:
+                            add_kwargs["rgb"] = True
+                        layer_type = "image"
+
+                    add_kwargs["name"] = (
+                        f"{add_kwargs.get('name', label)}[{label}]"
+                    )
+                    if not add_kwargs.get("rgb"):
+                        _maybe_set_viewer_3d(arr)
+                    layers.append((arr, add_kwargs, layer_type))
+            else:
+                # Single-layer stack read.
+                arr, add_kwargs, layer_type = _read_one(
+                    stack_pattern,
+                    mode=mode,
+                    stack_default_dim=stack_default_dim,
+                )
+                layers.append((arr, add_kwargs, layer_type))
+        except Exception as e:
+            warnings.warn(
+                f"Failed to read stack pattern '{stack_pattern}': {e}. "
+                "Loading files individually instead.",
+                stacklevel=2,
+            )
+        else:
+            return layers
+    elif stack_selection is not None and len(paths) == 1:
+        paths = [str(p) for p in stack_selection[0]]
+
+    for src in paths:
+        try:
+            parquet_layers = _read_parquet_rows(src, mode)
+            if parquet_layers is not None:
+                layers.extend(parquet_layers)
+                continue
+            vortex_layers = _read_vortex_rows(src, mode)
+            if vortex_layers is not None:
+                layers.extend(vortex_layers)
+                continue
+            layers.append(_read_one(src, mode=mode))
+        except Exception as e:
+            warnings.warn(
+                f"Failed to read '{src}' with napari-ome-arrow: {e}",
+                stacklevel=2,
+            )
+
+    if not layers:
+        raise ValueError("No readable inputs found for given path(s).")
+    return layers