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[](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.
**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
### 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
## Quick Installation
- From PyPI:
# If you use zsh replace [full] with \[full\]
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](https://github.com/TileDB-Inc/tifffile) 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
```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
cd docs && make html
```
will generate a `docs/_build` directory, where you can now open the `index.html`
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