traceratops documentation

Date: May 28, 2026 Version: 0.5.0

A toolbox for trace analysis, visualization and quality assessment. Corresponding to the post-processing of pyHiM data, compatible with the 4DN FISH Omics Format.

Getting Started

• Installation
• Changelog

Tutorials

• Getting started with notebooks
• Using the --pipe argument
• 01 - Merge Multi-ROI
• 02 - Quality Control
• 03 - Filter Thresholds
• 04 - Filter Duplicates
• 05 - Split Traces
• 06 - Assign Masks & Split Labels
• 07 - Matrix Visualization
• 08 - Multiway Co-localization
• 09 - Compare Datasets

Scripts

• Localization
• Trace
• Matrix
• Plot

Contribute

• Contributing guide
• Installation [DEV]
• Documentation
• PR checklists
• Release guide