User Guide¶
Welcome to the Histolytics User Guide. The user guide introduces the essential features of Histolytics. Each section focuses on a specific topic, explaining its implementation in Histolytics with clear, reproducible examples. The user guide is divided in to three main topics:
- Segmentation
- Basics of Spatial Analysis (after you have segmented your data)
- WSI-level analysis workflow examples
Segmentation¶
In the Segmentation section, you will find how to:
- Get Started with Panoptic Segmentation in Histolytics
- Selecting Backbone Architectures for Panoptic Segmentation Models
- Finetuning Panoptic Segmentation Models
- Selecting Sub Regions of Your WSI for Segmentation
- WSI-level Panoptic Segmentation: Putting It All Together
Spatial Analysis (Basics)¶
In the Spatial Analysis (Basics) section, you will find how to:
- Apply Spatial Querying to WSI-scale Panoptic Segmentation Maps
- Apply Spatial Partitioning to Selected Regions of Panoptic Segmentation Maps
- Apply Legendgrams in your Spatial Plots
- Fit Graphs to Nuclei Segmentation Data & Extract Graph Features
- Extract Neighborhood Features from Nuclei Segmentation Data
- Apply Clustering & Extract Cluster Features from Nuclei Segmentation Data
- Rasterizing Vector Data
- Extract Nuclear Features from Nuclei Segmentation Data and H&E Images
- Extract Stromal Features from H&E Images
- Apply Medial Lines to Tissue Segmentation Data
WSI Analysis Workflows¶
In the WSI Analysis Workflows, you will find real world examples on feature extraction at WSI-scale: