Basic Functionalities

• Read and Visualize a WSI
  • About this demo
  • Set Up Plotting
  • Reading in a WSI
  • Reading WSI regions
  • Tissue Masking
• Stain Normalization
  • Why normalize colour?
  • About this demo
  • Reading in a WSI
  • Extract a tile from the WSI
  • Stain normalizing a tile
  • Custom staining
• Masking tissue region in whole slide images
  • About this demo
  • Importing related libraries
  • Downloading the required files
  • Reading a WSI and its Thumbnail
  • Generating tissue mask in 1 line of code
  • Generating tissue masks for batch
• Patch extraction from Histology Images
  • About this demo
  • Importing related libraries
  • Downloading the required files
  • Reading image and annotation file
  • Patches based on point annotations
  • Generate fixed-size patches
• Patch Prediction Models
  • About this demo
  • Importing related libraries
  • Downloading the required files
  • Get predictions for a set of patches
  • Predict patch labels in 2 lines of code
  • Get predictions for patches within an image tile
  • Patch-level prediction in 2 lines of code for big histology tiles
  • Get predictions for patches within a WSI
• Semantic Segmentation Models
  • About this demo
  • Semantic segmentation using TIAToolbox pretrained models
  • Semantic segmentation using user-trained (external) models
• Advanced Model Handling in TIAToolbox
  • About this demo
  • 1. Injecting your model into the TIAToolbox prediction framework
  • Injecting pretrained patch classification models
  • 2. Dealing with exotic data formats
• Nucleus Instance Segmentation
  • About this demo
  • Nucleus instance segmentation and classification using TIAToolbox’s pretrained HoVer-Net model
• Multi-Task Segmentation Models
  • About this demo
  • Multi-Task Segmentation using TIAToolbox pretrained models
• Whole Slide Image Registration
  • About this notebook
  • Setting up the environment