Package supports all bio-imaging functionality provided by TileDB
Project description
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 pretty 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
Ingestion from TileDB Groups of Arrays to:
- OME-Zarr
- OME-Tiff
Visualization Options
Quick Installation
-
From PyPI:
pip install tiledb-bioimg[full]
-
From source:
git clone https://github.com/TileDB-Inc/TileDB-BioImaging.git cd TileDB-BioImaging # If you use zsh replace .[full] with .\[full\] pip install -e .[full]
Note: For tiff
support ([tiff]
or [full]
extra dependencies) on Python 3.7, you
should first install our tifffile fork rather
than the older PyPI upstream package:
pip install tifffile@git+https://github.com/TileDB-Inc/tifffile.git@gsa/python-3.7
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:
cd docs && make html
will generate a docs/_build
directory, where you can now open the index.html
Project details
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