SegTraQ documentation

SegTraQ (Segmentation and Transcript Assignment Quality Control) is a Python toolkit for quantitative and visual quality control of segmentation and transcript assignment in spatial omics data.

⚠️ Note: SegTraQ is under active development. Features, interfaces, and functionality may change in upcoming releases.

Contents:

• The baseline (bl) accessor
• The clustering stability (cs) accessor
• The region similarity (rs) accessor
• The supervised (sp) accessor
• The point statistics (ps) accessor
• The volume (vl) accessor
• The plotting (pl) accessor
• The SegTraQ (SegTraQ) class
• Utility functions

Tutorials:

• Data Preparation
• Module: Baseline Metrics
• Module: Clustering Stability
• Module: Region Similarity
• Module: Volume (3D)
• Module: Supervised Metrics
• Module: Point Statistics
• Module: Plotting
• Plotting
• Technology Focus: 10x Genomics Xenium (Simplified)
• Technology Focus: 10x Genomics Xenium