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://www.openpathology.philips.com/wp-content/uploads/AnimalSlides/1.isyntax
Next, get the Phillips SDK. You need to create a log in first.
You will need to follow ithe 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.
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.