<a href="https://tiledb.com"><img src="https://github.com/TileDB-Inc/TileDB/raw/dev/doc/source/_static/tiledb-logo_color_no_margin_@4x.png" alt="TileDB logo" width="400"></a>
[](https://github.com/TileDB-Inc/TileDB-BioImaging/actions/workflows/ci.yml)
# 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](https://cloud.tiledb.com) includes a built-in, pyramidal multi-resolution viewer: log in to TileDB Cloud to see an example image preview [here](https://cloud.tiledb.com/biomedical-imaging/TileDB-Inc/dbb7dfcc-28b3-40e5-916f-6509a666d950/preview)
- Napari: https://github.com/TileDB-Inc/napari-tiledb-bioimg
## Installation Prerequisites
OpenSlide Python requires that OpenSlide be installed separately prior to its installation.
Prior to proceeding with the below installation instructions, please [install OpenSlide as recommended by the OpenSlide Python library](https://openslide.org/api/python/#:~:text=OpenSlide%20Python%20requires%20OpenSlide%2C%20which%20must%20be%20installed%20separately).
## 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\ `.
```cmd
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
```python
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
```python
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
```python
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:
```shell
quartodoc build && quarto preview
```
Raw data
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