Ingest Biomedical Images

Learn how to ingest a biomedical image with TileDB.

Ingesting your data into TileDB is the first step towards unlock the power TileDB offers you. For this reason, you have many options on how you can ingest your data into TileDB.

Programmatic API

To ingest biomedical images into TileDB with a programmatic API, you have two options. The most basic approach is to use the TileDB-BioImaging API showcased in the Quickstart guide.

With this approach, you can ingest biomedical images of any of the supported formats on your local machine or to a cloud provider URI (for example, Amazon S3), given you have set up your credentials.

Setup

Before you start ingesting your images, make sure you install TileDB-BioImaging on your machine.

pip install 'tiledb-bioimg[full]'

You can also install TileDB-BioImaging directly from source if you prefer.

git clone https://github.com/TileDB-Inc/TileDB-BioImaging.git
cd TileDB-BioImaging

Note

TileDB-BioImaging requires that you have the OpenSlide library installed in your system. You can find installation instructions tailored to your operating system under the official Openslide’s website.

Ome-Tiff

Python

OMETiffConverter.to_tiledb(src, dest, level_min=0)

OpenSlide

Python

OpenSlideConverter.to_tiledb(src, dest, level_min=0)

Ome-Zarr

Python

OMEZarrConverter.to_tiledb(src, dest, level_min=0)

PNG

Python

PNGConverter.to_tiledb(src, dest, level_min=0)

You can also use the wrappers’ API for a more concise view:

Ome-Tiff

Python

from_bioimg(src, dest, level_min=0, converter=Converters.OMETIFF)

OpenSlide

Python

from_tiledb(src, dest, level_min=0, converter=Converters.OSD)

Ome-Zarr

Python

OMEZarrConverter.to_tiledb(src, dest, level_min=0, converter=Converters.OMEZARR)

PNG

Python

PNGConverter.to_tiledb(src, dest, level_min=0, Converters.PNG)

Although the TileDB-BioImaging’s standalone API is powerful, you can also use an advanced ingestion API, that takes advantage of TileDB by scaling your ingestion, using distributed execution and parallelization.

Graphic User Interface

Apart from the programmatic API offered through TileDB, you can also use the TileDB UI Console to ingest your biomedical image data into TileDB, without the need of writing even a single line of code. With TileDB’s one-click ingestion, you can quickly kickstart your projects and focus more on discovery. You can learn more details in the Catalog: Biomedical Images section.