Huygens Object Analyzer

(available as Compact or Advanced)

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 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 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 Vromans, 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

As per Huygens release 24.04 there are two options for object analysis: the Object Analyzer Compact and Advanced.
The Object analyzer Compact gives you the basic toolset for analyzing your images. The Object Analyzer Advanced gives you all the additional functionalities Huygens has to offer. Below you can find the main features of both options.

Features included in both Object Analyzer Compact and Advanced:

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.
Color objects based on some of their properties. Example: objects with the same parent can be given the same color, or objects obtain different colors depending on their distance to a reference object.
Export your object statistics for use in spreadsheets (.txt or .csv) or Matlab (.m).
Learn to use the possibilities of the Object Analyzer with interactive tutorials.

Features exclusive to the Object Analyzer Advanced:

Save your actions in a template to easily reproduce your experiment.
Create and edit templates with the Object Analysis Workflow Designer.
Set up batch analysis workflows in the Workflow Processor.
Use advanced analysis tools (Cluster analysis, shrink wrap, surface-to-surface distances).
Use a custom selection to combine analysis parameters freely.
Segment, track¹ and analyze time series.

1 Also requires an Object Tracking license.

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