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iSyntax to raw format converter
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chris-allan Merge pull request #8 from melissalinkert/xml-template
Write METADATA.ome.xml by filling in template
Latest commit f1b067a Jan 6, 2020
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isyntax2raw Reorder imports to be more in line with Pythonic convention Jan 6, 2020
.gitignore Add release version file to .gitignore Oct 23, 2019
LICENSE.txt Initial commit Oct 1, 2019 Refer to license and include in distribution Nov 13, 2019 iSyntax SDK verbiage Dec 5, 2019
setup.cfg Package up isyntax2raw Oct 22, 2019 Fix flake8 errors Jan 6, 2020 Correct location of release version file Oct 23, 2019

AppVeyor status

iSyntax Converter

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


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.

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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