Preparation Steps for Whole Slide Images (WSIs) Processing

1. Environment Setup:

   • First and foremost, ensure that openslide is properly installed and configured on your system. This library is essential for handling WSIs.
   • Additionally, install pma_python to interact with Pathomation software for digital microscopy.

2. Converting WSIs:

   • For WSIs saved in the .mds format, utilize the convert2tiff.py script to convert them to TIFF format. This conversion is crucial for compatibility with most image processing tools.

3. Analyzing WSIs:

   • To examine the layers within WSIs, run the openslidetest1.py script. This script allows you to print out and inspect the different layers of the images.

Ensure all dependencies and libraries are correctly installed before proceeding with the scripts above for a smooth and efficient workflow.

Reference

[1] https://www.pathomation.com/

[2] https://github.com/Pathomation/pma_python

[3] https://openslide.org/api/python/

[4] https://openslide.org/

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