3. Example Notebooks

Here you will find a collection of jupyter notebooks using py-lmd to highlight the different applications of py-lmd.

Contents:

• 3.1. Generate a Cutting XML from segmentation mask using the Segmentation Loader.
  • 3.1.1. Load Segmentation Mask
  • 3.1.2. Define cell sets
  • 3.1.3. Calibration points
  • 3.1.4. XML generation
  • 3.1.5. write to XML
• 3.2. Generate cutting XML from exported results from QUPath
  • 3.2.1. Import libraries and define helper functions
  • 3.2.2. Import GEOjson regions
  • 3.2.3. Calibration points
  • 3.2.4. Clean up Dataframe
  • 3.2.5. Generate shape collection
  • 3.2.6. write to XML
• 3.3. Convert SVG graphic into LMD excision instructions
  • 3.3.1. Visualize Results
  • 3.3.2. Export to XML