BioImaging
TileDB provides a set of tools for working with multi-resolution whole-slide microscopy images.
- TileDB Cloud BioImaging: integrated viewer, data management, access control, and computation for bioimaging datasets.
- Includes support for fast batch ingestion of large image sets from AWS S3 or any supported storage system using TileDB Task Graphs.
- Includes support for chunked ingestion of larger-than-memory images.
- OpenSlide Python API: this package additionally provides an OpenSlide Python-compatible API which may be used with image-groups stored using any TileDB backend.
- napari-tiledb-bioimg: Napari Plugin for loading TileDB BioImage arrays, supporting visualization of pyramidal images and analysis using Napari tools and plugins.
To get started with TileDB bioimaging, install the
tiledb-bioimg package from the Python Package Index:pip install tiledb-bioimg[full]
To use
tiledb-bioimg in a Python program, import the converters from the tiledb.bioimg namespace:# Python
from tiledb.bioimg.converters.ome_tiff import OMETiffConverter
from tiledb.bioimg.converters.openslide import OpenSlideConverter
Each converter provides a
to_tiledb function taking a source path and storage destination for the converted TileDB multi-resolution image group. For example:OMETiffConverter.to_tiledb(src, dest, level_min=0)
OpenSlideConverter(src, dest, level_min=0)
TileDB Cloud includes utilities for large-scale ingestion from images stored in an AWS S3 bucket or other supported object store.
pip install tiledb-cloud
Next, use the
tiledb.cloud.bioimg.ingest function:# `images` will be converted in bulk using
# `dest` as the base output path.
tiledb.cloud.bioimg.ingest(
source=images,
output=base_dest)
Image data may be read with either the OpenSlide Python-compatible API, or using the TileDB-Py API directly.
from tiledb.bioimg.openslide import TileDBOpenSlide
# Construct OpenSlide API wrapper
img = TileDBOpenSlide(tiledb_image_path)
# Read image data at `level`
# from starting `(x0,y0)` location to
# `(x + size_x, y + size_y)`
# Returns NumPy array
data = img.read_level((x0, y0), level, (size_x, size_y))
The napari-tiledb-bioimg plugin provides support for opening TileDB bioimage-arrays in the Napari visualization and analysis platform. (see the [demo video] on the repository README).
Install via the Napari plugin manager by searching for "TileDB", or install with pip inside of a Napari Python environment:
pip install napari-tiledb-bioimg
Please get in touch if you are interested working with TileDB BioImages in other visualization software, or specific analysis tools.
TileDB-BioImg stores multi-resolution images as a group of arrays, with one dense array per resolution level. For example, given an input TIFF file with three resolution layer pages:
2132x2488
4266x4978
17068x19918
The following directory structure will be created:
Image.tdb # TileDB Group
|- l_0.tdb # TileDB Array, 17068x19918
|- l_1.tdb # TileDB Array, 4266x4978
|- l_2.tdb # TileDB Array, 2132x2488
Image-level metadata is stored as TileDB Group metadata, and individual level metadata is stored with resolution-level array.
The TileDB BioImg library provides a utility function to export a TileDB BioImage to several OME formats.
# Export TileDB BioImg to an OME-TIFF file
OMETiffConverter.from_tiledb(tiledb_img_path, output_path)
# Export TileDB BioImg to an OME-Zarr directory
OMEZarrConverter.from_tiledb(tiledb_img_path, output_path)
Last modified 23d ago