usage.rst

Usage

To use TIA Toolbox in a project:

import tiatoolbox

Reading WSI Image Data

• :obj:`wsireader <tiatoolbox.wsicore.wsireader>`

• :obj:`WSIReader <tiatoolbox.wsicore.wsireader.WSIReader>`

  • :obj:`DICOMWSIReader <tiatoolbox.wsicore.wsireader.DICOMWSIReader>`
  • :obj:`NGFFWSIReader <tiatoolbox.wsicore.wsireader.NGFFWSIReader>`
  • :obj:`OmnyxJP2WSIReader <tiatoolbox.wsicore.wsireader.OmnyxJP2WSIReader>`
  • :obj:`OpenSlideWSIReader <tiatoolbox.wsicore.wsireader.OpenSlideWSIReader>`
  • :obj:`TIFFWSIReader <tiatoolbox.wsicore.wsireader.TIFFWSIReader>`
  • :obj:`VirtualWSIReader <tiatoolbox.wsicore.wsireader.VirtualWSIReader>`

Accessing Metadata

• :obj:`WSIMeta <tiatoolbox.wsicore.wsimeta.WSIMeta>`

Functional

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

• :obj:`slide_info <tiatoolbox.wsicore.slide_info>`
• :obj:`save_tiles <tiatoolbox.wsicore.save_tiles>`

Stain Extraction

• :obj:`Stain Extraction <tiatoolbox.tools.stainextract>`

Stain Normalization

• :obj:`get_normalizer <tiatoolbox.tools.stainnorm.get_normalizer>`
• :obj:`StainNormalizer <tiatoolbox.tools.stainnorm.StainNormalizer>`
• :obj:`CustomNormalizer <tiatoolbox.tools.stainnorm.CustomNormalizer>`
• :obj:`RuifrokNormalizer <tiatoolbox.tools.stainnorm.RuifrokNormalizer>`
• :obj:`MacenkoNormalizer <tiatoolbox.tools.stainnorm.MacenkoNormalizer>`
• :obj:`VahadaneNormalizer <tiatoolbox.tools.stainnorm.VahadaneNormalizer>`
• :obj:`ReinhardNormalizer <tiatoolbox.tools.stainnorm.ReinhardNormalizer>`

Tissue Masking

• :obj:`Tissue Mask <tiatoolbox.tools.tissuemask>`

Stain Augmentation

• :obj:`Stain Augmentation <tiatoolbox.tools.stainaugment>`

Patch Extraction

• :obj:`get_patch_extractor <tiatoolbox.tools.patchextraction.get_patch_extractor>`
• :obj:`PointsPatchExtractor <tiatoolbox.tools.patchextraction.PointsPatchExtractor>`
• :obj:`SlidingWindowPatchExtractor <tiatoolbox.tools.patchextraction.SlidingWindowPatchExtractor>`

Graph Construction

• :obj:`Slide Graph Constructor <tiatoolbox.tools.graph.SlideGraphConstructor>`

Tile Pyramid Generation

• :obj:`Tile Pyramid Generator <tiatoolbox.tools.pyramid.TilePyramidGenerator>`
• :obj:`Zoomify <tiatoolbox.tools.pyramid.ZoomifyGenerator>`

Dataset

• :obj:`Kather Dataset <tiatoolbox.models.dataset.info.KatherPatchDataset>`

Deep Learning Models

Engine

• :obj:`Patch Prediction <tiatoolbox.models.engine.patch_predictor.PatchPredictor>`
• :obj:`Semantic Segmentation <tiatoolbox.models.engine.semantic_segmentor.SemanticSegmentor>`
• :obj:`Feature Extraction <tiatoolbox.models.engine.semantic_segmentor.DeepFeatureExtractor>`
• :obj:`Nucleus Instance Segmnetation <tiatoolbox.models.engine.nucleus_instance_segmentor.NucleusInstanceSegmentor>`

Neural Network Architectures

• :obj:`Torch Vision CNNs <tiatoolbox.models.architecture.vanilla>`
• :obj:`Simplified U-Nets <tiatoolbox.models.architecture.unet>`
• :obj:`HoVerNet <tiatoolbox.models.architecture.hovernet.HoVerNet>`
• :obj:`HoVerNet+ <tiatoolbox.models.architecture.hovernetplus.HoVerNetPlus>`
• :obj:`MicroNet <tiatoolbox.models.architecture.micronet.MicroNet>`
• :obj:`MapDe <tiatoolbox.models.architecture.mapde.MapDe>`
• :obj:`SCCNN <tiatoolbox.models.architecture.sccnn.SCCNN>`

Pipelines:

• :obj:`IDARS <tiatoolbox.models.architecture.idars>`

Utilities

• :obj:`Environment Detection <tiatoolbox.utils.env_detection>`
• :obj:`Exceptions <tiatoolbox.utils.exceptions>`
• :obj:`Image <tiatoolbox.utils.image>`
• :obj:`Metrics <tiatoolbox.utils.metrics>`
• :obj:`Miscellaneous <tiatoolbox.utils.misc>`
• :obj:`Transforms <tiatoolbox.utils.transforms>`
• :obj:`Visualization <tiatoolbox.utils.visualization>`