ThunderSTORM Origami Analyzer

June 22, 2026 · View on GitHub

Automated DNA origami analysis of ThunderSTORM localization data and reconstruction of super-resolution images.

ThunderSTORM Origami Analyzer reads exported ThunderSTORM single-molecule localization microscopy (SMLM) tables, applies quality-control filters, reconstructs super-resolution images, runs nearest-neighbour and blinking-trace analysis, and automatically detects DNA origami structures — producing summary plots, statistics, and result files.

It is available both as a standalone desktop application (Windows, macOS, Linux) and as an ImageJ / Fiji plugin.

Download

.. raw:: html

Windows

Download for Windows

Windows 10 / 11 · MSI Installer
Run the installer

macOS

Download for macOS ARM64
Download for macOS Intel

macOS 12+ · DMG · Open the DMG and drag the app to Applications.

Linux (AppImage)

Download AppImage for Linux

All distributions · No install needed:
chmod +x ThunderSTORMAnalyzer.AppImage && ./ThunderSTORMAnalyzer.AppImage

Linux (Flatpak)

Download for Linux

All distributions · Install via:
flatpak install ThunderSTORMAnalyzer.flatpak

Download Fiji plugin

Links above always point to the latest release. All releases and release notes are on the Releases page.

Features

  • Import of ThunderSTORM localization tables (auto-detects ThunderSTORM column names).
  • Automated quality filtering on intensity, localization uncertainty, PSF sigma, and a 3σ cut.
  • Super-resolution image reconstruction from localization coordinates.
  • Localization statistics and quality-control summaries.
  • Histograms for intensity, uncertainty, and PSF sigma.
  • Nearest-neighbour distance (NND) analysis with KDE peak fitting.
  • Blinking-trace analysis over acquisition frames.
  • Automatic detection of collinear DNA origami structures (triplets / N-spot).
  • Batch processing of multiple datasets with cross-dataset comparison plots.
  • Automatic generation of result folders, plots, and summary tables.

Intended for educational and research use in SMLM workflows — DNA-PAINT, PAINT, STORM, and related nanobiotechnology experiments.

Software built with:

This cross-platform app was generated by Briefcase (https://briefcase.readthedocs.io/) — part of The BeeWare Project (https://beeware.org/).