ome-arrow 0.0.3__tar.gz → 0.0.4__tar.gz

{ome_arrow-0.0.3 → ome_arrow-0.0.4}/.github/workflows/publish-docs.yml

@@ -20,7 +20,7 @@ jobs:
     runs-on: ubuntu-24.04
     steps:
       - name: Checkout
-        uses: actions/checkout@v5
+        uses: actions/checkout@v6
         with:
           fetch-depth: 0
       - uses: actions/setup-python@v6

{ome_arrow-0.0.3 → ome_arrow-0.0.4}/.github/workflows/publish-pypi.yml

@@ -16,7 +16,7 @@ jobs:
       id-token: write
     steps:
       - name: Checkout
-        uses: actions/checkout@v5
+        uses: actions/checkout@v6
         with:
           fetch-depth: 0
       - name: Fetch tags

{ome_arrow-0.0.3 → ome_arrow-0.0.4}/.github/workflows/run-tests.yml

@@ -13,7 +13,7 @@ jobs:
     runs-on: ubuntu-24.04
     steps:
       # checks out the repo
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v6
       # run pre-commit
       - name: Python setup
         uses: actions/setup-python@v6
@@ -35,7 +35,7 @@ jobs:
       OS: ${{ matrix.os }}
     steps:
       - name: Checkout
-        uses: actions/checkout@v5
+        uses: actions/checkout@v6
       - name: Python setup
         uses: actions/setup-python@v6
         with:

{ome_arrow-0.0.3 → ome_arrow-0.0.4}/.pre-commit-config.yaml

@@ -39,12 +39,12 @@ repos:
     -   id: yamllint
         exclude: pre-commit-config.yaml
 -   repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: "v0.14.5"
+    rev: "v0.14.7"
     hooks:
     -   id: ruff-format
     -   id: ruff-check
 -   repo: https://github.com/rhysd/actionlint
-    rev: v1.7.8
+    rev: v1.7.9
     hooks:
     -   id: actionlint
 -   repo: https://gitlab.com/vojko.pribudic.foss/pre-commit-update

{ome_arrow-0.0.3 → ome_arrow-0.0.4}/CITATION.cff

@@ -29,6 +29,10 @@ abstract: >-
 keywords:
   - python
 license: BSD-3-Clause
+identifiers:
+  - description: Zenodo software DOI
+    type: doi
+    value: 10.5281/zenodo.17664969
 references:
   - authors:
       - name: "ExampleHuman CellProfiler Data Team"
@@ -60,3 +64,68 @@ references:
       - description: "OME Model Documentation — OME-TIFF Sample Data"
         type: url
         value: "https://ome-model.readthedocs.io/en/stable/ome-tiff/data.html"
+  - authors:
+      - family-names: Chandrasekaran
+        given-names: Srinivas Niranj
+      - family-names: Cimini
+        given-names: Beth A.
+      - family-names: Goodale
+        given-names: Amy
+      - family-names: Miller
+        given-names: Lisa
+      - family-names: Kost-Alimova
+        given-names: Maria
+      - family-names: Jamali
+        given-names: Nasim
+      - family-names: Doench
+        given-names: John G.
+      - family-names: Fritchman
+        given-names: Briana
+      - family-names: Skepner
+        given-names: Adam
+      - family-names: Melanson
+        given-names: Michelle
+      - family-names: Kalinin
+        given-names: Alexandr A.
+      - family-names: Arevalo
+        given-names: John
+      - family-names: Haghighi
+        given-names: Marzieh
+      - family-names: Caicedo
+        given-names: Juan C.
+      - family-names: Kuhn
+        given-names: Daniel
+      - family-names: Hernandez
+        given-names: Desiree
+      - family-names: Berstler
+        given-names: James
+      - family-names: Shafqat-Abbasi
+        given-names: Hamdah
+      - family-names: Root
+        given-names: David E.
+      - family-names: Swalley
+        given-names: Susanne E.
+      - family-names: Garg
+        given-names: Sakshi
+      - family-names: Singh
+        given-names: Shantanu
+      - family-names: Carpenter
+        given-names: Anne E.
+    date-accessed: "2024-08-21"
+    title: >-
+      Three million images and morphological profiles of cells treated with matched chemical and genetic perturbations
+    type: article
+    issn: 1548-7105
+    issue: 6
+    journal: Nature Methods
+    pages: 1114-1121
+    volume: 21
+    url: https://doi.org/10.1038/s41592-024-02241-6
+    date-published: "2024-06-01"
+    identifiers:
+      - type: doi
+        value: 10.1038/s41592-024-02241-6
+    notes: >-
+      JUMP (cpg0000-jump-pilot) was used to help demonstrate CytoDataFrame performance
+      with large data. See here for more information:
+      https://github.com/broadinstitute/cellpainting-gallery

{ome_arrow-0.0.3/src/ome_arrow.egg-info → ome_arrow-0.0.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ome-arrow
-Version: 0.0.3
+Version: 0.0.4
 Summary: Using OME specifications with Apache Arrow for fast, queryable, and language agnostic bioimage data.
 Author: Dave Bunten
 Classifier: Programming Language :: Python :: 3 :: Only
@@ -16,17 +16,18 @@ Requires-Dist: bioio-ome-tiff>=1.4
 Requires-Dist: bioio-ome-zarr>=3.0.3
 Requires-Dist: bioio-tifffile>=1.3
 Requires-Dist: fire>=0.7
-Requires-Dist: ipywidgets>=8.1.8
-Requires-Dist: jupyterlab-widgets>=3.0.16
 Requires-Dist: matplotlib>=3.10.7
 Requires-Dist: numpy>=2.2.6
 Requires-Dist: pandas>=2.2.3
 Requires-Dist: pillow>=12
 Requires-Dist: pyarrow>=22
-Requires-Dist: pyvista>=0.46.4
-Requires-Dist: trame>=3.12
-Requires-Dist: trame-vtk>=2.10
-Requires-Dist: trame-vuetify>=3.1
+Provides-Extra: viz
+Requires-Dist: ipywidgets>=8.1.8; extra == "viz"
+Requires-Dist: jupyterlab-widgets>=3.0.16; extra == "viz"
+Requires-Dist: pyvista>=0.46.4; extra == "viz"
+Requires-Dist: trame>=3.12; extra == "viz"
+Requires-Dist: trame-vtk>=2.10; extra == "viz"
+Requires-Dist: trame-vuetify>=3.1; extra == "viz"
 Dynamic: license-file
 
 <img height="200" src="https://raw.githubusercontent.com/wayscience/ome-arrow/main/docs/src/_static/logo.png?raw=true">
@@ -35,6 +36,7 @@ Dynamic: license-file
 [![Build Status](https://github.com/wayscience/ome-arrow/actions/workflows/run-tests.yml/badge.svg?branch=main)](https://github.com/wayscience/ome-arrow/actions/workflows/run-tests.yml?query=branch%3Amain)
 [![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff)
 [![uv](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/uv/main/assets/badge/v0.json)](https://github.com/astral-sh/uv)
+[![Software DOI badge](https://zenodo.org/badge/DOI/10.5281/zenodo.17664969.svg)](https://doi.org/10.5281/zenodo.17664969)
 
 # Open, interoperable, and queryable microscopy images with OME Arrow
 
@@ -52,6 +54,13 @@ OME Arrow enables image data to be stored alongside metadata or derived data suc
 Images in OME Arrow are composed of mutlilayer [structs](https://arrow.apache.org/docs/python/generated/pyarrow.struct.html) so they may be stored as values within tables.
 This means you can store, query, and build relationships on data from the same location using any system which is compatible with Apache Arrow (including Parquet) through common data interfaces (such as SQL and DuckDB).
 
+## Project focus
+
+This package is intentionally dedicated to work at a per-image level and not large batch handling (though it may be used for those purposes by users or in other projects).
+
+- For visualizing OME Arrow and OME Parquet data in Napari, please see the [`napari-ome-arrow`](https://github.com/WayScience/napari-ome-arrow) Napari plugin.
+- For more comprehensive handling of many images and features in the context of the OME Parquet format please see the [`CytoDataFrame`](https://github.com/cytomining/CytoDataFrame) project (and relevant [example notebook](https://github.com/cytomining/CytoDataFrame/blob/main/docs/src/examples/cytodataframe_at_a_glance.ipynb)).
+
 ## Installation
 
 Install OME Arrow from PyPI or from source:
@@ -89,7 +98,7 @@ oa_image.info()
 oa_image.view(how="matplotlib")
 
 # Display the image with pyvista
-# (great for ZYX 3D images).
+# (great for ZYX 3D images; install extras: `pip install 'ome-arrow[viz]'`).
 oa_image.view(how="pyvista")
 
 # Export to OME-Parquet.
@@ -107,5 +116,5 @@ OME Arrow is used or inspired by the following projects, check them out!
 
 - [`napari-ome-arrow`](https://github.com/WayScience/napari-ome-arrow): enables you to view OME Arrow and related images.
 - [`nViz`](https://github.com/WayScience/nViz): focuses on ingesting and visualizing various 3D image data.
-- [`CytoDataFrame`](https://github.com/cytomining/CytoDataFrame): provides a DataFrame-like experience for viewing feature and microscopy image data within Jupyter notebook interfaces.
+- [`CytoDataFrame`](https://github.com/cytomining/CytoDataFrame): provides a DataFrame-like experience for viewing feature and microscopy image data within Jupyter notebook interfaces and creating OME Parquet files.
 - [`coSMicQC`](https://github.com/cytomining/coSMicQC): performs quality control on microscopy feature datasets, visualized using CytoDataFrames.

{ome_arrow-0.0.3 → ome_arrow-0.0.4}/README.md

@@ -4,6 +4,7 @@
 [![Build Status](https://github.com/wayscience/ome-arrow/actions/workflows/run-tests.yml/badge.svg?branch=main)](https://github.com/wayscience/ome-arrow/actions/workflows/run-tests.yml?query=branch%3Amain)
 [![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff)
 [![uv](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/uv/main/assets/badge/v0.json)](https://github.com/astral-sh/uv)
+[![Software DOI badge](https://zenodo.org/badge/DOI/10.5281/zenodo.17664969.svg)](https://doi.org/10.5281/zenodo.17664969)
 
 # Open, interoperable, and queryable microscopy images with OME Arrow
 
@@ -21,6 +22,13 @@ OME Arrow enables image data to be stored alongside metadata or derived data suc
 Images in OME Arrow are composed of mutlilayer [structs](https://arrow.apache.org/docs/python/generated/pyarrow.struct.html) so they may be stored as values within tables.
 This means you can store, query, and build relationships on data from the same location using any system which is compatible with Apache Arrow (including Parquet) through common data interfaces (such as SQL and DuckDB).
 
+## Project focus
+
+This package is intentionally dedicated to work at a per-image level and not large batch handling (though it may be used for those purposes by users or in other projects).
+
+- For visualizing OME Arrow and OME Parquet data in Napari, please see the [`napari-ome-arrow`](https://github.com/WayScience/napari-ome-arrow) Napari plugin.
+- For more comprehensive handling of many images and features in the context of the OME Parquet format please see the [`CytoDataFrame`](https://github.com/cytomining/CytoDataFrame) project (and relevant [example notebook](https://github.com/cytomining/CytoDataFrame/blob/main/docs/src/examples/cytodataframe_at_a_glance.ipynb)).
+
 ## Installation
 
 Install OME Arrow from PyPI or from source:
@@ -58,7 +66,7 @@ oa_image.info()
 oa_image.view(how="matplotlib")
 
 # Display the image with pyvista
-# (great for ZYX 3D images).
+# (great for ZYX 3D images; install extras: `pip install 'ome-arrow[viz]'`).
 oa_image.view(how="pyvista")
 
 # Export to OME-Parquet.
@@ -76,5 +84,5 @@ OME Arrow is used or inspired by the following projects, check them out!
 
 - [`napari-ome-arrow`](https://github.com/WayScience/napari-ome-arrow): enables you to view OME Arrow and related images.
 - [`nViz`](https://github.com/WayScience/nViz): focuses on ingesting and visualizing various 3D image data.
-- [`CytoDataFrame`](https://github.com/cytomining/CytoDataFrame): provides a DataFrame-like experience for viewing feature and microscopy image data within Jupyter notebook interfaces.
+- [`CytoDataFrame`](https://github.com/cytomining/CytoDataFrame): provides a DataFrame-like experience for viewing feature and microscopy image data within Jupyter notebook interfaces and creating OME Parquet files.
 - [`coSMicQC`](https://github.com/cytomining/coSMicQC): performs quality control on microscopy feature datasets, visualized using CytoDataFrames.

{ome_arrow-0.0.3 → ome_arrow-0.0.4}/docs/src/examples/learning_to_fly_with_ome-arrow.ipynb

@@ -34,7 +34,7 @@
        "2D image, single-channel - shape (T=1, C=1, Z=1, Y=512, X=512)"
       ],
       "text/plain": [
-       "<ome_arrow.core.OMEArrow at 0x162d227d0>"
+       "<ome_arrow.core.OMEArrow at 0x176418210>"
       ]
      },
      "execution_count": 2,
@@ -129,7 +129,7 @@
        "3D image (z-stack), multi-channel (2 channels) - shape (T=1, C=2, Z=22, Y=128, X=128)"
       ],
       "text/plain": [
-       "<ome_arrow.core.OMEArrow at 0x1662b2810>"
+       "<ome_arrow.core.OMEArrow at 0x17be69110>"
       ]
      },
      "execution_count": 5,
@@ -167,12 +167,12 @@
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "e644f91c4e3843c39f130f05b628277e",
+       "model_id": "e438f2316a4b4348b00283242d346c63",
        "version_major": 2,
        "version_minor": 0
       },
       "text/plain": [
-       "Widget(value='<iframe src=\"http://localhost:55867/index.html?ui=P_0x1663cf990_0&reconnect=auto\" class=\"pyvista…"
+       "Widget(value='<iframe src=\"http://localhost:63799/index.html?ui=P_0x17bdef790_0&reconnect=auto\" class=\"pyvista…"
       ]
      },
      "metadata": {},
@@ -198,7 +198,7 @@
     {
      "data": {
       "text/plain": [
-       "<pyvista.plotting.plotter.Plotter at 0x1663cf990>"
+       "<pyvista.plotting.plotter.Plotter at 0x17bdef790>"
       ]
      },
      "execution_count": 6,
@@ -223,7 +223,7 @@
        "3D image (z-stack), multi-channel (2 channels) - shape (T=1, C=2, Z=22, Y=128, X=128)"
       ],
       "text/plain": [
-       "<ome_arrow.core.OMEArrow at 0x10aae1ad0>"
+       "<ome_arrow.core.OMEArrow at 0x1059985d0>"
       ]
      },
      "execution_count": 7,
@@ -261,7 +261,7 @@
        "3D image (z-stack), multi-channel (2 channels) - shape (T=1, C=2, Z=22, Y=128, X=128)"
       ],
       "text/plain": [
-       "<ome_arrow.core.OMEArrow at 0x1662019d0>"
+       "<ome_arrow.core.OMEArrow at 0x17f463c90>"
       ]
      },
      "execution_count": 8,
@@ -299,7 +299,7 @@
        "3D image (z-stack), multi-channel (2 channels) - shape (T=1, C=2, Z=22, Y=128, X=128)"
       ],
       "text/plain": [
-       "<ome_arrow.core.OMEArrow at 0x1663adad0>"
+       "<ome_arrow.core.OMEArrow at 0x17f434490>"
       ]
      },
      "execution_count": 9,
@@ -337,7 +337,7 @@
        "3D image (z-stack), multi-channel (2 channels) - shape (T=1, C=2, Z=22, Y=128, X=128)"
       ],
       "text/plain": [
-       "<ome_arrow.core.OMEArrow at 0x38064c810>"
+       "<ome_arrow.core.OMEArrow at 0x17bf44390>"
       ]
      },
      "execution_count": 10,
@@ -375,7 +375,7 @@
        "2D image, single-channel - shape (T=1, C=1, Z=1, Y=30, X=30)"
       ],
       "text/plain": [
-       "<ome_arrow.core.OMEArrow at 0x167243690>"
+       "<ome_arrow.core.OMEArrow at 0x35ff46510>"
       ]
      },
      "execution_count": 11,
@@ -405,6 +405,53 @@
     "    z_indices=[20],\n",
     ")"
    ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "eddf849a",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/html": [
+       "2D image, single-channel - shape (T=1, C=1, Z=1, Y=73, X=97)"
+      ],
+      "text/plain": [
+       "<ome_arrow.core.OMEArrow at 0x35ff67e10>"
+      ]
+     },
+     "execution_count": 12,
+     "metadata": {},
+     "output_type": "execute_result"
+    },
+    {
+     "data": {
+      "image/png": "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",
+      "text/plain": [
+       "<Figure size 640x480 with 1 Axes>"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    }
+   ],
+   "source": [
+    "# read from a multi-image OME Parquet file as OME-Arrow\n",
+    "# note: the Parquet file was created using the CytoDataFrame project\n",
+    "# which helps convert CellProfiler and Image data into OME-Parquet format.\n",
+    "# see here for more details:\n",
+    "# https://github.com/cytomining/CytoDataFrame/blob/main/docs/src/examples/cytodataframe_at_a_glance.ipynb\n",
+    "oa_image = OMEArrow(\n",
+    "    data=\"../../../tests/data/JUMP-BR00117006/BR00117006.ome.parquet\",\n",
+    "    # we can specify which column and row to read\n",
+    "    # (or rely on OMEArrow to find a suitable default)\n",
+    "    column_name=\"Image_FileName_OrigDNA_OMEArrow_LABL\",\n",
+    "    row_index=2,\n",
+    ")\n",
+    "# by default, the image and metadata are shown\n",
+    "oa_image"
+   ]
   }
  ],
  "metadata": {

{ome_arrow-0.0.3 → ome_arrow-0.0.4}/docs/src/examples/learning_to_fly_with_ome-arrow.py

@@ -80,3 +80,18 @@ stack.slice(
     c_indices=[0],
     z_indices=[20],
 )
+
+# read from a multi-image OME Parquet file as OME-Arrow
+# note: the Parquet file was created using the CytoDataFrame project
+# which helps convert CellProfiler and Image data into OME-Parquet format.
+# see here for more details:
+# https://github.com/cytomining/CytoDataFrame/blob/main/docs/src/examples/cytodataframe_at_a_glance.ipynb
+oa_image = OMEArrow(
+    data="../../../tests/data/JUMP-BR00117006/BR00117006.ome.parquet",
+    # we can specify which column and row to read
+    # (or rely on OMEArrow to find a suitable default)
+    column_name="Image_FileName_OrigDNA_OMEArrow_LABL",
+    row_index=2,
+)
+# by default, the image and metadata are shown
+oa_image

{ome_arrow-0.0.3 → ome_arrow-0.0.4}/pyproject.toml

@@ -24,13 +24,16 @@ dependencies = [
   "bioio-ome-zarr>=3.0.3",
   "bioio-tifffile>=1.3",
   "fire>=0.7",
-  "ipywidgets>=8.1.8",
-  "jupyterlab-widgets>=3.0.16",
   "matplotlib>=3.10.7",
   "numpy>=2.2.6",
   "pandas>=2.2.3",
   "pillow>=12",
   "pyarrow>=22",
+]
+
+optional-dependencies.viz = [
+  "ipywidgets>=8.1.8",
+  "jupyterlab-widgets>=3.0.16",
   "pyvista>=0.46.4",
   "trame>=3.12",
   "trame-vtk>=2.10",
@@ -49,6 +52,7 @@ docs = [
 ]
 notebooks = [
   "black>=25.1",
+  "ipykernel>=6.29.5",
   "isort>=6.0.1",
   "jupyterlab>=4.4.2",
   "jupyterlab-code-formatter>=3.0.2",

{ome_arrow-0.0.3 → ome_arrow-0.0.4}/src/ome_arrow/_version.py

@@ -28,7 +28,7 @@ version_tuple: VERSION_TUPLE
 commit_id: COMMIT_ID
 __commit_id__: COMMIT_ID
 
-__version__ = version = '0.0.3'
-__version_tuple__ = version_tuple = (0, 0, 3)
+__version__ = version = '0.0.4'
+__version_tuple__ = version_tuple = (0, 0, 4)
 
-__commit_id__ = commit_id = 'g401409c77'
+__commit_id__ = commit_id = 'g0496fa17a'

{ome_arrow-0.0.3 → ome_arrow-0.0.4}/src/ome_arrow/core.py

@@ -5,12 +5,11 @@ Core of the ome_arrow package, used for classes and such.
 from __future__ import annotations
 
 import pathlib
-from typing import Any, Dict, Iterable, Optional, Tuple
+from typing import TYPE_CHECKING, Any, Dict, Iterable, Optional, Tuple
 
 import matplotlib
 import numpy as np
 import pyarrow as pa
-import pyvista
 
 from ome_arrow.export import to_numpy, to_ome_parquet, to_ome_tiff, to_ome_zarr
 from ome_arrow.ingest import (
@@ -25,6 +24,10 @@ from ome_arrow.transform import slice_ome_arrow
 from ome_arrow.utils import describe_ome_arrow
 from ome_arrow.view import view_matplotlib, view_pyvista
 
+# if not in runtime, import pyvista for type hints
+if TYPE_CHECKING:
+    import pyvista
+
 
 class OMEArrow:
     """
@@ -47,6 +50,8 @@ class OMEArrow:
         self,
         data: str | dict | pa.StructScalar | "np.ndarray",
         tcz: Tuple[int, int, int] = (0, 0, 0),
+        column_name: str = "ome_arrow",
+        row_index: int = 0,
     ) -> None:
         """
         Construct an OMEArrow from:
@@ -91,7 +96,9 @@ class OMEArrow:
                 ".parquet",
                 ".pq",
             }:
-                self.data = from_ome_parquet(s)
+                self.data = from_ome_parquet(
+                    s, column_name=column_name, row_index=row_index
+                )
 
             # TIFF
             elif path.suffix.lower() in {".tif", ".tiff"} or s.lower().endswith(
@@ -293,7 +300,7 @@ class OMEArrow:
         clim: tuple[float, float] | None = None,
         show_axes: bool = True,
         scaling_values: tuple[float, float, float] | None = (1.0, 0.1, 0.1),
-    ) -> matplotlib.figure.Figure | pyvista.Plotter:
+    ) -> matplotlib.figure.Figure | "pyvista.Plotter":
         """
         Render an OME-Arrow record using Matplotlib or PyVista.
 

{ome_arrow-0.0.3 → ome_arrow-0.0.4}/src/ome_arrow/ingest.py

@@ -4,6 +4,7 @@ Converting to and from OME-Arrow formats.
 
 import itertools
 import re
+import warnings
 from datetime import datetime, timezone
 from pathlib import Path
 from typing import Any, Dict, List, Optional, Sequence, Tuple
@@ -820,42 +821,6 @@ def from_ome_parquet(
 ) -> pa.StructScalar:
     """
     Read an OME-Arrow record from a Parquet file and return a typed StructScalar.
-
-    Expected layout (as produced by `to_ome_parquet`):
-      - single Parquet file
-      - a single column (default name "ome_arrow") of `OME_ARROW_STRUCT` type
-      - one row (row_index=0)
-
-    This function is forgiving:
-      - If `column_name` is None or not found, it will auto-detect a struct column
-        that matches the OME-Arrow field names.
-      - If the table has multiple rows, you can choose which record to read
-        via `row_index`.
-
-    Parameters
-    ----------
-    parquet_path : str | Path
-        Path to the .parquet file.
-    column_name : Optional[str], default "ome_arrow"
-        Name of the column that stores the OME-Arrow struct. If None, auto-detect.
-    row_index : int, default 0
-        Which row to read if the table contains multiple rows.
-    strict_schema : bool, default False
-        If True, require the column's type to equal `OME_ARROW_STRUCT` exactly.
-        If False, we only require the column to be a Struct with the same field
-        names (order can vary).
-
-    Returns
-    -------
-    pa.StructScalar
-        A validated OME-Arrow struct scalar.
-
-    Raises
-    ------
-    FileNotFoundError
-        If the file does not exist.
-    ValueError
-        If a suitable column/row cannot be found or schema checks fail.
     """
     p = Path(parquet_path)
     if not p.exists():
@@ -874,7 +839,9 @@ def from_ome_parquet(
         col_fields = {f.name for f in t}
         return ome_fields == col_fields
 
+    requested_name = column_name
     candidate_col = None
+    autodetected_name = None
 
     if column_name is not None and column_name in table.column_names:
         arr = table[column_name]
@@ -898,10 +865,12 @@ def from_ome_parquet(
             if pa.types.is_struct(arr.type):
                 if strict_schema and arr.type == OME_ARROW_STRUCT:
                     candidate_col = arr
+                    autodetected_name = name
                     column_name = name
                     break
                 if not strict_schema and _struct_matches_ome_fields(arr.type):
                     candidate_col = arr
+                    autodetected_name = name
                     column_name = name
                     break
         if candidate_col is None:
@@ -911,21 +880,26 @@ def from_ome_parquet(
                 hint = f"column '{column_name}' not found and auto-detection failed."
             raise ValueError(f"Could not locate an OME-Arrow struct column: {hint}")
 
+    # Emit warning if auto-detection was used
+    if autodetected_name is not None and autodetected_name != requested_name:
+        warnings.warn(
+            f"Requested column '{requested_name}' was not usable or not found. "
+            f"Auto-detected OME-Arrow column '{autodetected_name}'.",
+            UserWarning,
+            stacklevel=2,
+        )
+
     # 2) Extract the row as a Python dict
-    #    (Using to_pylist() for the single element slice is simple & reliable.)
     record_dict: Dict[str, Any] = candidate_col.slice(row_index, 1).to_pylist()[0]
 
     # 3) Reconstruct a typed StructScalar using the canonical schema
-    #    (this validates field names/types and normalizes order)
     scalar = pa.scalar(record_dict, type=OME_ARROW_STRUCT)
 
     # Optional: soft validation via file-level metadata (if present)
     try:
         meta = table.schema.metadata or {}
-        meta.get(b"ome.arrow.type", b"").decode() == str(
-            OME_ARROW_TAG_TYPE
-        ) and meta.get(b"ome.arrow.version", b"").decode() == str(OME_ARROW_TAG_VERSION)
-        # You could log/print a warning if tag_ok is False, but don't fail.
+        meta.get(b"ome.arrow.type", b"").decode() == str(OME_ARROW_TAG_TYPE)
+        meta.get(b"ome.arrow.version", b"").decode() == str(OME_ARROW_TAG_VERSION)
     except Exception:
         pass