Deep learning

• Deep Java Library
  • DJL engines
  • Getting started with QuPath + DJL
  • Using a DJL Model Zoo
  • Future plans
  • Appendix: CUDA via Conda
• Bioimage Model Zoo
  • QuPath Bioimage Model Zoo extension
• InstanSeg
  • Requirements
  • Set-up
  • Using InstanSeg
  • Scripting
  • Citing
• StarDist
  • Getting the StarDist extension
  • Getting pretrained models
  • Detecting nuclei
  • Customizing detection
  • Advanced options
  • Differences from StarDist Fiji
• WSInfer
  • Requirements
  • Set-up
  • Whole Slide Inference
  • Additional Options
  • Using your own models
  • Scripting
  • Identifying TILs (overlaying predictions of two models)
• GPU support
  • Explaining the problem
  • DJL & auto-detecting the GPU
  • Which versions do I need?
  • Conda environments