Usage

To use TIA Toolbox in a project:

import tiatoolbox

Reading WSI Image Data

• wsireader

• OpenSlideWSIReader

• OmnyxJP2WSIReader

• VirtualWSIReader

• TIFFWSIReader

Accessing Metadata

• WSIMeta

Functional

The wsicore module also includes some functional syntax for quickly obtaining information about a slide or generating tiles.

• slide_info

• save_tiles

Stain Extraction

• Stain Extraction

Stain Normalization

• get_normalizer

• StainNormalizer

• CustomNormalizer

• RuifrokNormalizer

• MacenkoNormalizer

• VahadaneNormalizer

• ReinhardNormalizer

Tissue Masking

• Tissue Mask

Stain Augmentation

• Augmentation

Patch Extraction

• get_patch_extractor

• PointsPatchExtractor

• SlidingWindowPatchExtractor

Graph Construction

• Slide Graph Constructor

Tile Pyramid Generation

• Tile Pyramid Generator

• Zoomify

Dataset

• Kather Dataset

Deep Learning Models

Engine

• Patch Prediction

• Semantic Segmentation

• Feature Extraction

• Nucleus Instance Segmnetation

Neural Network Architectures

• Torch Vision CNNs

• Simplified U-Nets

• HoVerNet

• HoVerNet+

• MicroNet

Pipelines:

• IDARS

Utilities

• Image

• Transforms

• Miscellaneous

• Exceptions

• Visualization