napari-ome-arrow 0.0.6

A Napari plugin for OME-Arrow and OME-Parquet bioimage data

napari-ome-arrow

napari-ome-arrow opens OME image data in napari using the OME-Arrow library.

Supported inputs

• Typed OME-Arrow dataset directories (*.ome-arrow)
• Nested OME-Arrow tables in Parquet (*.ome.parquet, *.parquet, *.pq)
• OME-Vortex files (*.ome.vortex, *.vortex)
• OME-TIFF and TIFF files (*.ome.tif, *.ome.tiff, *.tif, *.tiff)
• OME-Zarr stores (*.ome.zarr, *.zarr)
• Numbered image stacks and stack patterns containing <, >, or *
• NumPy arrays (*.npy)

Multi-image OME-Arrow datasets and multi-row nested tables are loaded as multiple napari layers.

Installation

Python 3.11 or newer is required.

Install the plugin into an existing napari environment:

pip install napari-ome-arrow

Or install napari with a Qt backend at the same time:

pip install "napari-ome-arrow[pyqt6]"

OME-Vortex support requires one additional extra:

pip install "napari-ome-arrow[vortex]"

Usage

Open napari, then drag a supported file or directory into the viewer. You can also start napari with a path:

napari sample.ome.parquet
napari images.ome-arrow

The plugin loads data as either image or labels layers. It chooses the layer type in this order:

1. NAPARI_OME_ARROW_LAYER_TYPE, when set to image or labels.
2. OME-Arrow image_type metadata, when available.
3. A napari prompt.
4. image when running without a Qt application.

Set the mode explicitly for scripts or repeatable commands:

NAPARI_OME_ARROW_LAYER_TYPE=labels napari segmentation.ome.parquet

For a numbered stack, select the files together or provide a pattern:

napari "stack/z<000-120>.tif"

Configuration

Environment variable	Purpose
NAPARI_OME_ARROW_LAYER_TYPE	Load as image or labels
NAPARI_OME_ARROW_PARQUET_COLUMN	Select an OME-Arrow struct column in Parquet
NAPARI_OME_ARROW_VORTEX_COLUMN	Select an OME-Arrow struct column in Vortex
NAPARI_OME_ARROW_STACK_SCALE	Set stack spacing as Z,Y,X or T,C,Z,Y,X

Multiple rows are displayed in napari's grid view. Image stacks with a real Z dimension open in 3D. If stack spacing is missing, the plugin can prompt for it when a Qt application is available.

Development

See CONTRIBUTING.md for setup and test instructions.

License

This project uses the BSD 3-Clause License. See LICENSE.

Report problems through the issue tracker.