Skip to content

Image analysis at AMF spans single-molecule localisation, deconvolution, segmentation, and 3D rendering. This page maps the analysis tooling per instrument and points you at the open-source and commercial software the facility supports.

Where to start

Pick the path that matches you:

  • “I just collected data, what now?” Jump to By instrument for the recommended pipeline on your microscope.
  • “I want to learn the methods first” See the Open-source toolkit and the Learn more reading list.
  • “I have a tricky pipeline question” Talk to your super-user, or contact an imaging scientist.

By instrument

Quick reference per instrument: vendor software for acquisition and on-instrument analysis, plus the freeware your super-user is most likely to recommend for further processing.

Instrument Vendor software Recommended freeware
Abbelight SAFe-360 Nikon NIS-Elements + Abbelight NEO and SAFe Insight Picasso, ThunderSTORM, SMAP
Nikon AX with NSPARC NIS-Elements C-ER with NSPARC plugin (Clarify.ai, AI denoising) Fiji, DeconvolutionLab2
Abberior STED ExpertLine Imspector Fiji, Huygens (deconvolution)
ONI NanoImager ONI CODI (cloud platform) Picasso, ThunderSTORM
Nikon N-STORM NIS-Elements with N-STORM module Picasso, ThunderSTORM
AFM Cypher ES Asylum Research AR (Igor Pro) Gwyddion (general AFM analysis)

The vendor software handles acquisition, drift correction, and basic visualisation. For anything beyond that (custom batch processing, advanced 3D fitting, deep-learning denoising, multi-modal correlation), the freeware below is where most users go.

Open-source toolkit

SMLM analysis (Abbelight, ONI, N-STORM)

  • Picasso (Jungmann lab). Fast localisation and DNA-PAINT analysis. The default for most newcomers; well-documented.
  • ThunderSTORM. Fiji plugin. Handles 2D and 3D fitting, drift correction, and rendering.
  • SMAP (Ries lab). Matlab-based with advanced features: 3D PSF fitting, multi-channel registration, qPAINT counting.
  • DECODE. Deep-learning localisation; useful when emitter density is high.

Deconvolution (Abberior STED, Nikon AX, NSPARC)

  • DeconvolutionLab2. Free Fiji plugin; supports Richardson-Lucy and Tikhonov.
  • Huygens. Commercial, but with a free trial; widely considered the gold standard.

General image processing and visualisation

  • Fiji / ImageJ. The universal microscopy toolkit. If you only learn one tool, learn this one.
  • napari. Modern 3D and multi-channel viewer, with a fast-growing Python plugin ecosystem.

Machine-learning workflows

  • CARE. Content-aware image restoration: denoising, projection, and super-resolution from low-SNR data.
  • StarDist. Star-convex object detection: nuclei and cell segmentation, robust on diverse samples.

Commercial software available at the facility

Beyond the vendor-bundled software, the facility licences these packages on the analysis workstations:

  • Imaris. 3D rendering, particle tracking, and statistics. Excellent for live-cell and volumetric data.
  • Huygens. Deconvolution across all our fluorescence instruments.
  • NIS-Elements (Nikon). Acquisition and offline analysis on Abbelight, AX-NSPARC, and N-STORM.
  • Imspector (Abberior). STED acquisition; basic analysis built in.
  • Abbelight NEO and SAFe Insight. SMLM acquisition with on-the-fly drift correction and rendering.
  • ONI CODI. Cloud-based pipelines bundled with the NanoImager.
  • Asylum Research AR (in Igor Pro). Bundled with the AFM; topology and nanomechanics.

If you need access to additional commercial software, contact the facility manager.

Help and learning

For pipeline questions

  • Your super-user is the first stop for routine questions on the instrument you trained on.
  • An imaging scientist for methodology design, multi-modal pipelines, and tricky cases.
  • The image.sc forum. Globally active; fast responses; the developers of the major tools answer here.

For learning the methods

Stuck? Email superresolution@tue.nl or talk to your super-user.