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
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.
-
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]'
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/
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