User Guide
This page is an orientation map for the rest of the documentation. Each topic now has its own dedicated page under Concepts, Workflows, and Pipeline Steps — use the task-oriented links below to jump straight to what you need.
New to the package? Start with the Tutorial, which runs a complete pipeline on simulated data and shows the output of every step.
Find what you need
| I want to… | Go to |
|---|---|
Understand how analyze() routes steps by dispatch | The Pipeline Model |
| See where SMLMAnalysis sits in the JuliaSMLM ecosystem | The JuliaSMLM Ecosystem |
| Know what an SMLD stores and how provenance is tracked | Data Model & Provenance |
| Install the package and its unregistered dependencies | Installation & Setup |
Run a full pipeline from an AnalysisConfig | Running a Pipeline |
| Set the output detail level (verbosity) | Running a Pipeline |
| Process multiple files, or chunk one long movie | Multi-Dataset Acquisitions |
| Analyze multiple color channels and overlay them | Multi-Channel Analysis |
| Save intermediate state and resume a session later | I/O & Resume |
Import SMART / MIC microscope .h5 data | I/O & Resume |
| Add a custom step to the pipeline | Extending the Pipeline |
| Diagnose a failure or an unexpected result | Troubleshooting |
Configure a step
Every pipeline step has a reference page documenting its config fields, the algorithm it dispatches to, and the diagnostic outputs it writes:
Detection & Fitting · Quality Filter · Intensity Filter · Frame Connection · Drift Correction · Density Filter · Rendering · Bayesian Grouping (BaGoL) · Clustering
Multi-channel steps: Composite Render · Cross-Alignment · Cross-Correlation
CRLB-vs-observed uncertainty calibration is configured inside frame connection via FrameConnectConfig(calibration = CalibrationConfig(...)), so it is documented on the Frame Connection page rather than as its own step.
See Pipeline Steps: Overview for the full list and the ordering rules (DetectFitConfig must come first; most other steps are freely orderable, repeatable, or optional), and the API Reference for every exported config, info, and function.