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iSyntax to raw format converter
Python
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chris-allan Merge pull request #8 from melissalinkert/xml-template
Write METADATA.ome.xml by filling in template
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MANIFEST.in Refer to license and include in distribution Nov 13, 2019
README.md iSyntax SDK verbiage Dec 5, 2019
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README.md

AppVeyor status

iSyntax Converter

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

Requirements

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

Usage

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.

License

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

Areas to improve

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