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napari TileDB bioimaging

napari-tiledb-bioimg

Support reading and writing TileDB-Bioimaging image arrays within Napari

License MIT PyPI Python Version tests napari hub

This plugin supports reading and writing TileDB-BioImaging multi-resolution arrays within Napari.


Demo

https://github.com/TileDB-Inc/napari-tiledb-bioimg/assets/327706/b408d634-6ad0-4160-8571-18cf8e37b4cc

Installation

[pending PyPI release!] You can install napari-tiledb-bioimg via [pip]:

pip install napari-tiledb-bioimg

Quickstart

After ingesting data using tiledb-bioimg, then:

  • Local images can be loaded using Napari's File -> Open Folder, and selecting the TileDB array folder. Choose the napari-tiledb-bioimg plugin, if prompted.

  • Remote arrays (S3, TileDB Cloud) may be loaded using either the napari CLI command:

napari --plugin napari-tiledb-bioimg s3://<bucket>/<path/to/tiledb_array>
  • ... or the Napari viewer load command within the Python prompt:
# Within a Napari-enabled Python/IPython prompt, run:
import napari
viewer = napari.Viewer()

viewer.open("tiledb://<namespace>/<array name or UUID>", plugin="napari-tiledb-bioimg")

Contributing

Contributions are very welcome. Tests can be run with tox or pytest.

Installation from git:

pip install git+https://github.com/TileDB-Inc/napari-tiledb-bioimg.git

License

Distributed under the terms of the [MIT] license, "napari-tiledb-bioimg" is free and open source software.

Issues

If you encounter any problems, please file an issue along with a detailed description.

Version:

  • 0.0.1

Last updated:

  • 12 May 2023

First released:

  • 12 May 2023

License:

Supported data:

  • Information not submitted

Save extension:

  • Information not submitted

Save layers:

GitHub activity:

  • Stars: 7
  • Forks: 0
  • Issues + PRs: 2

Python versions supported:

Operating system:

Requirements:

  • dask
  • tiledb-bioimg (>=0.2.1)

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