ModuleNotFoundError: No module named 'pixelengine' in python

Question

ModuleNotFoundError: No module named 'pixelengine' in python while converting the phiips isyntax format file into OME-TIFF.

By following this documentation https://www.glencoesoftware.com/blog/2019/12/09/converting-whole-slide-images-to-OME-TIFF.html#footnotes

I used python 3.6 in ubuntu 18.04.

First I download and install the philips sdk as per given instruction in documentation.

Then I downloaded isyntax2raw and install it.

After executing this command in terminal
isyntax2raw write_tiles 20200207_140740.isyntax /home/user/

The error comes

Traceback (most recent call last): File "/home/dilip/anaconda3/envs/myenv/bin/isyntax2raw", line 11, in load_entry_point('isyntax2raw==0.0.0', 'console_scripts', 'isyntax2raw')() File "/home/dilip/anaconda3/envs/myenv/lib/python3.6/site-packages/pkg_resources/init.py", line 490, in load_entry_point return get_distribution(dist).load_entry_point(group, name) File "/home/dilip/anaconda3/envs/myenv/lib/python3.6/site-packages/pkg_resources/init.py", line 2859, in load_entry_point return ep.load() File "/home/dilip/anaconda3/envs/myenv/lib/python3.6/site-packages/pkg_resources/init.py", line 2450, in load return self.resolve() File "/home/dilip/anaconda3/envs/myenv/lib/python3.6/site-packages/pkg_resources/init.py", line 2456, in resolve module = import(self.module_name, fromlist=['name'], level=0) File "/home/dilip/anaconda3/envs/myenv/lib/python3.6/site-packages/isyntax2raw-0.0.0-py3.6.egg/isyntax2raw/init.py", line 15, in ModuleNotFoundError: No module named 'pixelengine'

Answer 1

Since a few months Philips has added some sample scripts to transform isyntax to TIFF, extract patches, or visualize. To access these scripts you have to create an account on openpathology and then go to the SDK section.