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]'
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
4 maintainers
Metadata
4 maintainers
Release files for tiledb-bioimg 0.3.10
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| File | Size | Uploaded | Provenance | |
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| tiledb_bioimg-0.3.10.tar.gz | 38.4 MB | Without provenance | Details |
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| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| tiledb_bioimg-0.3.10-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 38.4 MB
Release files / tiledb_bioimg-0.3.10.tar.gz
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