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.
Note: this project is in an early stage and under heavy development. Breaking changes to the underlying data format and the API are to be expected.
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]'
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
"path_to_ome_zarr_image", "tiledb_array_group_path") OMEZarrConverter.to_tiledb(
OME-Tiff to TileDB Group of Arrays
from tiledb.bioimg.converters.ome_tiff import OMETiffConverter
"path_to_ome_tiff_image", "tiledb_array_group_path") OMETiffConverter.to_tiledb(
Open Slide to TileDB Group of Arrays
from tiledb.bioimg.converters.openslide import OpenSlideConverter
"path_to_open_slide_image", "tiledb_array_group_path") OpenSlideConverter.to_tiledb(
Documentation
API Documentation
is auto-generated. Following the instructions below:
quartodoc build && quarto preview