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Table of Contents

3.0

Introduction

Installation
Overview
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

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