tiledb-bioimg 0.2.13

Package supports all bio-imaging functionality provided by TileDB

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