JuliaSMLM

Julia tools for single-molecule localization microscopy (SMLM).

$Diffraction-limited vs single-molecule localization rendering of "JuliaSMLM"$

JuliaSMLM is a collection of composable, high-performance Julia packages covering the full SMLM workflow — from simulating raw camera data, through localization and post-processing, to rendering and quantitative analysis. Packages share a common data model (SMLMData.jl) so they snap together into pipelines, and performance-critical steps offer automatic GPU acceleration with CPU fallback.

Under active development. The JuliaSMLM ecosystem grows continuously — new packages are added and existing ones refined over time, so expect this list to keep expanding.

All packages below are registered in the Julia General registry — install any of them with the standard package manager, for example:

using Pkg
Pkg.add("SMLMAnalysis")                          # the full detection → rendering pipeline
Pkg.add(["SMLMData", "SMLMSim", "SMLMRender"])   # or individual building blocks

Packages

Pipeline

Package	Description
SMLMAnalysis.jl · docs	End-to-end analysis pipeline from a single config: detection, fitting, filtering, frame connection, drift correction, and rendering, with provenance tracking. Start here if you want the whole workflow.

Core

Package	Description
SMLMData.jl · docs	Foundational data types (emitters, cameras, SMLD containers) shared across the ecosystem. Most packages re-export what you need.
MicroscopePSFs.jl · docs	2D/3D point-spread-function models and pixel-integration tools for optical simulation and fitting.

Simulation

Package	Description
SMLMSim.jl · docs	Simulate realistic SMLM data: static super-resolution patterns with blinking photophysics, and diffusion/interaction dynamics for single-particle tracking.

Localization

Package	Description
SMLMBoxer.jl · docs	Particle detection and ROI extraction via difference-of-Gaussians filtering, with GPU acceleration and sCMOS variance weighting.
GaussMLE.jl · docs	Fast maximum-likelihood fitting of Gaussian-PSF parameters, with automatic GPU acceleration.

Post-processing

Package	Description
SMLMFrameConnection.jl · docs	Link localizations from the same blinking event across frames into single, higher-precision localizations.
SMLMBaGoL.jl · docs	Bayesian Grouping of Localizations (BaGoL): merge an emitter's repeated blinks into single emitters, reaching precision beyond raw localizations.
SMLMDriftCorrection.jl · docs	Fiducial-free intra- and inter-dataset drift correction (2D/3D) via entropy minimization.

Rendering & visualization

Package	Description
SMLMRender.jl	Render point-cloud localizations into images (histogram, Gaussian-blob, or outline) with flexible color mapping.
SMLMView.jl · docs	WGLMakie-based interactive viewer for N-dimensional microscopy data.

Analysis

Package	Description
SMLMClustering.jl · docs	Clustering and spatial statistics (DBSCAN, HDBSCAN, Voronoi/SR-Tesseler) for localization data.

Conventions

Packages across the ecosystem follow shared conventions so data moves between them without surprises. See the Pixel Indexing Convention for how images and coordinates are indexed.

Also from this org

ModelContextProtocol.jl — a Julia implementation of the Model Context Protocol (MCP) for integrating tools and resources with LLMs.

Contributing

Issues and pull requests are welcome on any JuliaSMLM repository. Each package is developed and versioned independently and registered through the Julia General registry.