Working with iSyntax files¶
I you are like me and are stuck with iSyntax files, then they first need to be converted to TIFF. The following script will parse the isyntax file to make a config file and a BigTiff file.
First, change directories so you are in the isyntax directory of this repo , and download an example iSyntax file from the Phillips Website.
$ cd isyntax
$ curl -o ex1.isyntax https://zenodo.org/record/5037046/files/testslide.isyntax?download=1
Next, get the Phillips SDK. You need to create a log in first.
You will need to follow the installation instructions for your specific operating system. Once you have it installed, open a python terminal and run:
If you get ModuleNotFoundError: No module named ‘pixelengine’ then you do not have this installed properly. Ask Phillips tech support for help.
> Note you need to ensure that you have the Phillips SDK installed and available. It is not possible for this toolkit
Once you have the Phillips SDK installed, you can run the conversion script.
$ python isyntax_to_tiff.py --input 1.isyntax --tif BIGTIFF --sparse 0 --startlevel 0
This will create a file called ex1_BIG_sparse.tiff.
Now you can create the configuration file and proceed as normal.
> Note: Since the isyntax_to_tiff.py is maintained by Phillips, its name or usage might change. Please consult the Phillips documentation.