Integrate TileDB-BioImaging with the napari Plugin

Learn How to render TileDB images in napari.

This tutorial explores the integration of TileDB-BioImaging with the napari viewer, achieved through the dedicated plugin, napari-tiledb-bioimg.

By combining TileDB’s efficient storage and access capabilities for large bioimaging datasets with napari’s intuitive visualization and analysis tools, researchers can unlock new levels of productivity and insight. This tutorial will guide you through the process of loading, visualizing, and interacting with your TileDB-stored bioimages within the napari environment, showing the power of this combined solution.

Setup

To use the napari viewer, you need to first install all the dependencies in an environment:

mamba create -n napari-env
mamba activate napari-env
mamba install -c conda-forge napari pyqt
pip install napari-tiledb-bioimg ‘tiledb-bioimg[full]’

View TileDB bioimages in napari

You can view TileDB bioimages in the napari viewer by using either the command-line interface (CLI) or the graphical user interface (GUI).

CLI

napari --plugin napari-tiledb-bioimg /path/to/your/tiledb/image

GUI

1. Launch napari.
2. From the Plugins menu, select TileDB (napari TileDB bioimaging).
3. In the plugin interface, navigate to and select your TileDB image.

Note

The napari-tiledb-bioimg plugin supports loading images from local files, S3 paths, and TileDB URIs.

napari example

Access images from cloud storage

You can directly view images stored on TileDB or Amazon S3.

Caution

To access images from S3, ensure you have configured your S3 credentials on your local system. For TileDB, ensure your TILEDB_API_TOKEN key is correctly set in the $HOME/.tiledb/cloud.json file.