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Installation & Setup

Requirements

  • Julia 1.12 or newer.

  • A CUDA-capable GPU is recommended. The fitting step uses GaussMLE, which is GPU-accelerated via CUDA; see the GaussMLE documentation for GPU/CPU options.

  • Start Julia with multiple threads — several steps (drift correction, frame connection) are threaded:

    julia -t auto --project=.

Installing

Once SMLMAnalysis is registered in the Julia General registry, installation will be the usual one-liner:

using Pkg
Pkg.add("SMLMAnalysis")
Registration status

SMLMAnalysis is being prepared for registration. Until it and its JuliaSMLM dependencies are registered, install from source as below. (This page will switch to Pkg.add once the registration is live.)

From source (current)

Clone the repository and instantiate its environment:

git clone https://github.com/JuliaSMLM/SMLMAnalysis.jl
cd SMLMAnalysis.jl
julia -t auto --project=. -e 'using Pkg; Pkg.instantiate()'

Then:

using SMLMAnalysis

using SMLMAnalysis re-exports the key ecosystem types and verbs (cameras, emitter types, the step configs, cluster, render, run_bagol, frameconnect, …), so for most work no further imports are needed.

Verifying the install

A quick end-to-end check on simulated data:

using SMLMAnalysis

# Simulate a small dataset and its image stack (SMLMSim, re-exported)
# then run a minimal pipeline:
config = AnalysisConfig(
    camera = cam,
    steps = [
        DetectFitConfig(boxer = BoxerConfig(boxsize = 9, psf_sigma = 0.130)),
        RenderConfig(zoom = 10),
    ],
)
(result, info) = analyze(images, config)
@show length(result.smld.emitters)

See Getting Started for a full simulated walkthrough, and Running a Pipeline for the config-driven and step-by-step styles.

Building the documentation

The documentation is built from the main checkout of the repository (its docs/ environment anchors its path-sourced JuliaSMLM dependencies relative to that checkout):

julia --project=docs -e 'using Pkg; Pkg.develop(path="."); Pkg.instantiate()'
julia --project=docs docs/make.jl