Optical and analysis methods for measuring the organization, dynamics, and interactions of proteins in living cells.
We develop open-source software both for single-molecule localization microscopy and for controlling the custom microscopes it runs on. Each capability is offered in two ecosystems: a modern, actively developed Julia stack and an established, peer-reviewed MATLAB toolbox.
A modular, high-performance Julia ecosystem for single-molecule localization microscopy (SMLM) that spans the full workflow, from simulating raw camera data through emitter detection, fitting, drift correction, and frame connection, to super-resolution rendering and quantitative analysis. Its packages share a common data model, so they compose into end-to-end pipelines, and performance-critical steps run on the GPU with a transparent CPU fallback, letting the same code scale from a laptop to a workstation. Built as small, composable packages and openly, actively developed, it is designed to be extended as readily as it is used.
github.com/JuliaSMLM
The Single Molecule Imaging Toolbox Extraordinaire, a comprehensive, mature MATLAB toolbox for SMLM: localization, drift correction, single-particle tracking, clustering, and downstream analysis.
JOSS 8(90):5563 (2023) · github.com/LidkeLab/smite
A native-Julia package for microscope and instrument control: hardware abstraction for the cameras, stages, lasers, and other devices of custom-built microscopes, and the acquisition-side companion to the Julia analysis stack. In development.
github.com/LidkeLab/MicroscopeControl.jl
MATLAB Instrument Control, an object-oriented package for controlling the cameras, stages, lasers, and other hardware of custom-built fluorescence microscopes.
JOSS 10(105):7275 (2025) · github.com/LidkeLab/matlab-instrument-control
All of our software is on GitHub across the two organizations: