Python tool that uses Philips' SDK to write slides in an intermediary raw format.

• Philips iSyntax SDK (https://openpathology.philips.com)

The iSyntax SDK must be downloaded separately from Philips and the relevant license agreement agreed to before any conversion can take place.

Basic usage is:

isyntax2raw write_tiles /path/to/input.isyntax /path/to/tile/directory

Please see isyntax2raw write_tiles --help for detailed information.

Output tile width and height can optionally be specified; default values are detailed in --help.

A directory structure containing the pyramid tiles at all resolutions and macro/label images will be created. The default format is N5. Additional metadata is written to a JSON file. Be mindful of available disk space, as larger .isyntax files can result in >20 GB of tiles.

Use of a n5 or zarr --file_type will result in losslessly compressed output. These are the only formats that are currently supported by the downstream raw2ometiff.

The iSyntax converter is distributed under the terms of the BSD license. Please see LICENSE.txt for further details.

• Currently assumes brightfield (RGB, 8 bits per channel) without really checking the metadata. Probably should check bit depths etc.