{"id":18610606,"url":"https://github.com/tiledb-inc/tiledb-bioimaging","last_synced_at":"2025-06-18T14:38:43.645Z","repository":{"id":60812291,"uuid":"516424536","full_name":"TileDB-Inc/TileDB-BioImaging","owner":"TileDB-Inc","description":"Package providing bioimaging functionality using TileDB. 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OME-Zarr\n    - OME-Tiff\n    - Open-Slide\n\n### Export from TileDB-Bioimaging Arrays to:\n    - OME-Zarr\n    - OME-Tiff\n\n### Visualization Options\n\n- [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)\n- Napari: https://github.com/TileDB-Inc/napari-tiledb-bioimg\n\n## Installation Prerequisites\n\nOpenSlide Python requires that OpenSlide be installed separately prior to its installation.\n\nPrior 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).\n\n## Quick Installation\n\n- From PyPI:\n\n      pip install 'tiledb-bioimg[full]'\n\n- From source:\n\n      git clone https://github.com/TileDB-Inc/TileDB-BioImaging.git\n      cd TileDB-BioImaging\n\n      pip install -e '.[full]'\n\n## Windows Installation\n\nAfter installing `Openslide` you should make sure that you create a link between your installation path and\nthe following default path `C:\\openslide-win64\\ `.\n\n```cmd\nmklink /D C:\\openslide-win64\\ [your-installation-path]\\openslide-win64-20221217\\\n```\n\nYou can install the latest versions of `Openslide` for windows using the pre-built packages\nfound in the project's github page:\n`https://github.com/openslide/openslide-bin/releases`\n\nor in their website:\n`https://openslide.org/download/`\n\n\n## Examples\nHow to convert imaging data from standard biomedical formats to group of TileDB arrays.\n\n### OME-Zarr to TileDB Group of Arrays\n```python\nfrom tiledb.bioimg.converters.ome_zarr import OMEZarrConverter\nOMEZarrConverter.to_tiledb(\"path_to_ome_zarr_image\", \"tiledb_array_group_path\")\n```\n\n### OME-Tiff to TileDB Group of Arrays\n```python\nfrom tiledb.bioimg.converters.ome_tiff import OMETiffConverter\nOMETiffConverter.to_tiledb(\"path_to_ome_tiff_image\", \"tiledb_array_group_path\")\n```\n\n### Open Slide to TileDB Group of Arrays\n```python\nfrom tiledb.bioimg.converters.openslide import OpenSlideConverter\nOpenSlideConverter.to_tiledb(\"path_to_open_slide_image\", \"tiledb_array_group_path\")\n```\n\n## Documentation\n`API Documentation` is auto-generated. Following the instructions below:\n\n```shell\nquartodoc build \u0026\u0026 quarto preview\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ftiledb-inc%2Ftiledb-bioimaging","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Ftiledb-inc%2Ftiledb-bioimaging","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ftiledb-inc%2Ftiledb-bioimaging/lists"}