Huygens Object Analyzer

Obtain reliable object statistics from 3D-5D images.

Objects in 3D-5D (multichannel, time series) images can be quickly and easily analyzed with Huygens Object Analyzer for Huygens Essential and Professional and Object Analyzer Basic for Huygens Localizer. Statistics of objects are produced with just a few button clicks. Object segmentation - which is often considered being a challenging and subjective task - is made easy with algorithms that set the seed and threshold levels optimally, offering instant feedback like number of objects per channel. Additional tools like watershed segmentation, object filtering, and advanced region of interest (ROI) settings are at hand to fine-tune 3D object segmentation. The segmented objects are directly visualized by the high-end continuous Iso Surface Ray Tracing renderer and ready for immediate analysis. Various analysis modes and presets are available to quickly answer your specific research question.

Image description
3D volume analysis of kinetochore complex structures involved in cell division. Image kindly provided by Livio Kleij (facility) and Martijn Vroomans, Medical Oncology, UMC Utrecht, The Netherlands.


Interactive Scene

Interactive 1
Rotate, analyze, discard and anchor objects using only your mouse cursor.

Easy Segmentation

Obtain reliable results using ROI, watershed and cluster analysis options.

Many Object Statistics

Window OA Distance
Object statistics in a clear table and graph, and can be exported for further analysis.


Both my facility users and I are very impressed with the new (and not so new) features, and some of my new users are really enjoying the object analyzer and the ROI options!

Dr. Zoltan Cseresnyes, research associate and co-manager Confocal and 2-Photon Microscopy Core Facility, MDC Berlin, Germany.

Main features

  • Obtain both visual and quantitative information for all kinds of object-related research questions.
  • Automatically segment your data, or use custom settings for the segmentation.
  • Use sophisticated algorithms for watershed and cluster-based analysis
  • Run a full analysis of your 3D/Multi-channel/Time series with a single mouse-click.
  • Measure/count cells, (intra-)nuclei, (intra)-cellular organelles or other types of objects instantly.
  • Perform Object Colocalization (intersecting volume and intensity).
  • Measure intensities, distances, volume, width and length, and more.
  • Intuitively select Anchors (reference objects) and Regions Of Interest (ROI).
  • Measure nearness between objects in the same or other channel.
  • Refine your analysis with versatile object filter options.
  • Create and edit templates with the Object Analysis Workflow Designer.
  • Export your object statistics for use in spreadsheets (.txt or .csv) or Matlab (.m).

Use in research

Aoyama-Ishiwatari, S, Okazaki, T, Iemura, S et al. NUDT21 links mitochondrial IPS-1 to RLR-containing stress granules and 3 activates host antiviral defense.
Huygens was used for deconvolution and 3D object volume counting with the Object Analyzer
J. Immunol. 206, 154-163 (2021)

Berndt-Paetz, M, Herbst, L, Weimann, A et al. IC/BPS-associated alterations of M2 and M3 muscarinic acetylcholine receptor trafficking in human detrusor.
Analysis of 3D Object volume and receptor membrane localization was performed with Huygens deconvolution and the Object Analyzer.
Neurourol. Urodyn. 38, 1818- 1827 (2019)

For more, see Scientific Publications

Images may contain misalignments between 3D slices or between time frames, which hinder object analysis. Such misalignments can be corrected with the Huygens Object Stabilizer.

Object Stabilizer

More information

Expert tutorial
Support page
Webinar Object Analyzer