Metadata-Version: 2.1
Name: isyntax2raw
Version: 0.4.0
Summary: iSyntax to raw format converter
Home-page: https://github.com/glencoesoftware/isyntax2raw
Author: Glencoe Software, Inc.
Author-email: info@glencoesoftware.com
License: License :: OSI Approved :: BSD License
Description: [![AppVeyor status](https://ci.appveyor.com/api/projects/status/github/isyntax2raw)](https://ci.appveyor.com/project/gs-jenkins/isyntax2raw)
        
        # iSyntax Converter
        
        Python tool that uses Philips' SDK to write slides in an intermediary raw format.
        
        ## Requirements
        
        * Python 3.6+
        * 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.
        
        As of version 0.4.0, which has a Python 3.6+ requirement, the supported
        iSyntax SDK versions and environments are as follows:
        
        * iSyntax SDK 1.2.1 (CentOS 7, Ubuntu 18.04, Windows 10 64-bit)
        * iSyntax SDK 2.0 (CentOS 8, Ubuntu 18.04, Windows 10 64-bit)
        
        ## Usage
        
        Basic usage is:
        
            isyntax2raw write_tiles /path/to/input.isyntax /path/to/directory.zarr
        
        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 Zarr.  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 the Zarr file type will result in losslessly compressed output.  This
        is the only format currently supported by the downstream `raw2ometiff` (as of
        version 0.3.0).
        
        ## Background color
        
        Any missing tiles are filled with 0 by default, which displays as black.
        The fill value can be changed using the `--fill_color` option, which accepts
        a single integer between 0 and 255 inclusive.  Setting `--fill_color=255`
        will cause any missing tiles to display as white.
        
        ## Performance
        
        This package is __highly__ sensitive to underlying hardware as well as
        the following configuration options:
        
         * `--max_workers`
         * `--tile_width`
         * `--tile_height`
         * `--batch_size`
        
        On systems with significant I/O bandwidth, particularly SATA or
        NVMe based storage, we have found sharply diminishing returns with worker
        counts > 4.  There are significant performance gains to be had utilizing
        larger tile sizes but be mindful of the consequences on the downstream
        workflow.  You may find increasing the batch size on systems with very
        high single core performance to give modest performance gains.
        
        In general, expect to need to tune the above settings and measure
        relative performance.
        
        ## 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.
        
Platform: any
Requires-Python: >=3.6
Description-Content-Type: text/markdown
