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Introduction

  • Installation
  • Overview
  • Extensions
  • Quickstart
  • Setting up a Project
  • Datasets
  • Slide Processing
  • Training
  • Evaluation
  • Layer Activations
  • Uncertainty Quantification
  • Generating Features
  • Multiple-Instance Learning (MIL)
  • Self-Supervised Learning (SSL)
  • Generative Networks (GANs)
  • Saliency Maps
  • Tissue Segmentation
  • Cell Segmentation
  • Custom Training Loops
  • Slideflow Studio: Live Visualization
  • Troubleshooting

Developer Notes

  • TFRecords: Reading and Writing
  • Dataloaders: Sampling and Augmentation
  • Custom Feature Extractors
  • Strong Supervision with Tile Labels
  • Creating a Slideflow Plugin

API

  • histox
  • histox.Project
  • histox.Dataset
  • histox.DatasetFeatures
  • histox.Heatmap
  • histox.ModelParams
  • histox.Mosaic
  • histox.SlideMap
  • histox.biscuit
  • histox.cellseg
  • histox.io
  • histox.io.tensorflow
  • histox.io.torch
  • histox.gan
  • histox.grad
  • histox.mil
  • histox.model
  • histox.model.tensorflow
  • histox.model.torch
  • histox.norm
  • histox.simclr
  • histox.slide
  • histox.slide.qc
  • histox.stats
  • histox.util
  • histox.studio

Tutorials

  • Tutorial 1: Model training (simple)
  • Tutorial 2: Model training (advanced)
  • Tutorial 3: Using a custom architecture
  • Tutorial 4: Model evaluation & heatmaps
  • Tutorial 5: Creating a mosaic map
  • Tutorial 6: Custom slide filtering
  • Tutorial 7: Training with custom augmentations
  • Tutorial 8: Multiple-Instance Learning
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