Python package for:

• converting images stored in popular Biomedical Imaging formats to groups of TileDB arrays (& vice versa)
• exposing an expressive and efficient API (powered by TileDB) for querying such data.

- OME-Zarr - OME-Tiff - Open-Slide 

- OME-Zarr - OME-Tiff 

• TileDB Cloud includes a built-in, pyramidal multi-resolution viewer: log in to TileDB Cloud to see an example image preview here
• Napari: https://github.com/TileDB-Inc/napari-tiledb-bioimg

• From PyPI:

  pip install 'tiledb-bioimg[full]' 

• From source:

  git clone https://github.com/TileDB-Inc/TileDB-BioImaging.git cd TileDB-BioImaging pip install -e '.[full]' 

How to convert imaging data from standard biomedical formats to group of TileDB arrays.

from tiledb.bioimg.converters.ome_zarr import OMEZarrConverter OMEZarrConverter.to_tiledb("path_to_ome_zarr_image", "tiledb_array_group_path")

from tiledb.bioimg.converters.ome_tiff import OMETiffConverter OMETiffConverter.to_tiledb("path_to_ome_tiff_image", "tiledb_array_group_path")

from tiledb.bioimg.converters.openslide import OpenSlideConverter OpenSlideConverter.to_tiledb("path_to_open_slide_image", "tiledb_array_group_path")

API Documentation is auto-generated. Following the instructions below:

quartodoc build && quarto preview