Awesome
<a href="https://tiledb.com"><img src="https://github.com/TileDB-Inc/TileDB/raw/dev/doc/source/_static/tiledb-logo_color_no_margin_@4x.png" alt="TileDB logo" width="400"></a>
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
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