Metadata-Version: 2.1
Name: tiledb-bioimg
Version: 0.2.3
Summary: Package supports all bio-imaging functionality provided by TileDB
Home-page: https://github.com/TileDB-Inc/TileDB-Bioimaging
Author: TileDB, Inc.
Author-email: help@tiledb.io
License: MIT
Project-URL: Bug Tracker, https://github.com/TileDB-Inc/TileDB-Bioimaging/issues
Project-URL: Documentation, https://docs.tiledb.com
Keywords: tiledb,bioimaging
Platform: any
Classifier: Development Status :: 2 - Pre-Alpha
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Information Technology
Classifier: Intended Audience :: Science/Research
Classifier: Programming Language :: Python
Classifier: Topic :: Software Development :: Libraries :: Python Modules
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Image Processing
Classifier: Operating System :: Unix
Classifier: Operating System :: POSIX :: Linux
Classifier: Operating System :: MacOS :: MacOS X
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: License :: OSI Approved :: MIT License
Requires-Python: >=3.7
Description-Content-Type: text/markdown
Provides-Extra: zarr
Provides-Extra: openslide
Provides-Extra: tiff
Provides-Extra: cloud
Provides-Extra: full
License-File: LICENSE

<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>

[![TileDB-BioImaging CI](https://github.com/TileDB-Inc/TileDB-BioImaging/actions/workflows/ci.yml/badge.svg)](https://github.com/TileDB-Inc/TileDB-BioImaging/actions/workflows/ci.yml)
![Coverage Badge](https://img.shields.io/endpoint?url=https://gist.githubusercontent.com/ktsitsi/32d48185733a4e7375e80e3e35fab452/raw/gist_bioimg.json)

# 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

- [TileDB Cloud](https://cloud.tiledb.com)
- 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

      # 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`
