Jupyter Notebooks

• About the Example Notebooks
  • Local Machine
  • Google Colab
  • Structure of the examples directory
  • A) Examples of TIAToolbox functionalities
  • B) Examples of high-level analysis (pipelines) using TIAToolbox

• 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

• Pipelines
  • Prediction of Molecular Pathways and Key Mutations
    • About this demo
    • Available models
    • Tumour segmentation using TIAToolbox pretrained models
    • WSI prediction using TIAToolbox pretrained models
  • Slide Graph Pipeline
    • Introduction
    • Preparation: Imports, Helpers, & Data Split
    • Fixing Randomness
    • Loading Data
    • Generating a Graph from a WSI
    • Graph Neural Network
    • Visualize Node Activation of Graph Neural Network
  • Slide Graph Full-pipeline Notebook
    • About this notebook
    • Introduction
    • Preparation: Imports, Helpers, & Data Split
    • Generating Graphs from WSIs
    • The Graph Neural Network