TileDB-BioImaging

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.

Features

Ingestion to TileDB Groups of Arrays

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

Export from TileDB-Bioimaging Arrays to:

- OME-Zarr
- OME-Tiff

Visualization Options

• 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

Installation Prerequisites

OpenSlide Python requires that OpenSlide be installed separately prior to its installation.

Prior to proceeding with the below installation instructions, please install OpenSlide as recommended by the OpenSlide Python library.

Quick Installation

• 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]'
  

Windows Installation

After installing Openslide you should make sure that you create a link between your installation path and the following default path C:\openslide-win64\ .

mklink /D C:\openslide-win64\ [your-installation-path]\openslide-win64-20221217\

You can install the latest versions of Openslide for windows using the pre-built packages found in the project's github page: https://github.com/openslide/openslide-bin/releases

or in their website: https://openslide.org/download/

Examples

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

OME-Zarr to TileDB Group of Arrays

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

OME-Tiff to TileDB Group of Arrays

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

Open Slide to TileDB Group of Arrays

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

Documentation

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

quartodoc build && quarto preview