Huygens Products

Huygens Software refers to different image processing packages, available for multiple platforms. Packages are intended for deconvolution, restoration, interactive analysis and volume visualization of 2D, 3D, multi-channel and time series images from brightfield and fluorescence microscopes. Huygens Software is named after Christiaan Huygens who discovered the diffraction of light waves.

Huygens offers several different deconvolution algorithms to recover objects from images that are degraded by blurring and noise. In microscopy, blurring is largely due to diffraction-limited imaging by the instrument; the noise is usually photon noise. Huygens calculates a depth-dependent point spread function (PSF) automatically from the microscopy meta data, so that objects subjected to spherical abberation at deeper levels are restored with a PSF adapted to local conditions, yielding better resolution. For even better accuracy, Huygens can also generate (distill) an experimental PSF from fluorescent bead images to achieve the most accurate mathematical description of the microscope. Additional Restoration tools are available to correct for imaging artefacts such as unwanted movement between 3D and /or Time slices, crosstalk, chromatic aberration, and hot pixels.

Our Huygens software will significantly improve your microscopy images!

The Huygens software comes in different flavors: (Essential, Professional, Core), offering solutions for both single users and multi-user facilities. There is even an a web-based interface, Huygens Remote Manager, available for submitting deconvolution tasks via your internet browser to the compute engine Huygens Core. Huygens Essential and Professional make high quality deconvolution available for everyone, by combining the most advanced deconvolution algorithms with an easy-to-use wizard. Huygens improves the resolution and contrast in your microscopy images significantly, while effectively removing haze and noise. In this way, structures and details which would otherwise remain hidden become clearly visible. Besides deconvolution, Huygens offers a wide range of other Restoration Options to correct for other most common artifacts present in raw microscopy data. Additional Server and GPU-based Options ensure maximization of hardware performance, and optional 3D-5D Visualization and Analysis tools complement your Huygens image processing workflow.

A wizard-based user interface in Essential guides you step by step through the deconvolution process.

In the preprocessing stage the intelligent wizard will check the microscopy parameters for possible problematic optical conditions of your image. During the deconvolution process, Huygens will also correct your data for spherical aberration, as well as bleaching. You are in charge!!! Whenever you are not fully satisfied with the results, you can always stop the deconvolution process in every stage and re-run it with different settings.


Some advantages of the Huygens deconvolution:
  • Multi channel images are processed sequentially, allowing you to select the best result of each channel.
  • Time series deconvolution of 3D and 2D images (multi)-channel images is extremely easy by selecting time series as one file.
  • The intelligent 4D-channel cropping tool allows you to trim images along four dimensions and delete uninteresting channels to reduce the load on your computer's processing power.
  • The Batch Processor allows the scheduling of massive amounts of data with pre-made parameter templates. You can continue with your other research work when Huygens delivers the data you need, quickly and reliably.


The various Visualization Tools in Huygens Essential and Professional help you to analyze your image in detail. With the Twin Slicer and the Gallery Tool you can easily view your multi-dimensional data, and compare your results with the original image side-by-side. A MIP Renderer enables you to obtain a spatial projection of your data from any given point of view. The Ortho-slicer gives you information of a specific point or area in all three dimensions. The SFP Renderer is also available for visualizing your object from different angles and gives you physically realistic detailed views of your 3D data over time, while the Surface Renderer and the Movie Maker make the visualization of dynamic objects in your data very easy. All visualization tools can be used without needing an expensive graphics card, because our tools do not use conventional techniques of polygonal rendering.

The Twin Slicer

The Twin Slicer allows you to synchronize views of two images, measure distances, plot line profiles, etc. In Basic Mode, image comparison is intuitive and easy, while the Advanced Mode gives the user the freedom to rotate the cutting plane to any arbitrary orientation, link (synchronize) or unlink viewing parameters between the two images, and more.

The Twin Slicer (click to open larger view).

The MIP Renderer

The maximum intensity projection (MIP) renderer projects the voxels with maximum intensity that fall in the way of parallel rays traced from the viewpoint to the plane of projection. This allows you to obtain a direct spatial projection of your 3D microscopy data from the viewpoint you wish.

The MIP Renderer (click to open larger view).

The SFP Renderer

The Volume Renderer or SFP Renderer is based on taking the 3D microscopy image as a distribution of fluorescent material, simulating what happens if the material is excited and how the subsequently emitted light travels to the observer. The computational work is done by the Simulated Fluorescence Process algorithm. The unique properties of this algorithm enable it to create depth cue rich images from unprocessed data.

Because the SFP algorithm does not rely on boundaries or sharp gradients, it is eminently suited to render 3D microscopic data sets. The SFP algorithm is based on ray tracing it does not require a special graphic card.

The Huygens SFP Renderer (click to open larger view).

The Ortho-Slicer

The Ortho-Slicer is designed to show the same point in 3D space from 3 orthogonal directions. If you move one of the slices, the others will follow to make sure that the center of each of the slices intersects in the same point in space. This behaviour makes the Ortho Slicer a useful tool to study small objects in 3D.

The Surface Renderer

The Surface Renderer enables you to represent your microscopy data in a convenient way to clearly see separated volumes. Not only is it capable of iso-surface rendering; but also of showing MIP projections together with the surfaces to be used as a reference to the original microscopic voxel data. Because the Surface Renderer is based on rendering continuous surfaces with fast ray tracing algorithms, there is no need for a special graphic card. The fast ray tracers can utilize 64 bit multiprocessor systems, and are therefore able to render very large microscopic volume data to high resolution output images.

The Surface Renderer (click to open larger view).


The Colocalization Analyzer

With the Colocalization Analyzer you can obtain information about the amount of spatial overlap between different data channels, in 3D stacks or 3D time series. As this overlapping can be defined in many ways, Huygens gives you the colocalization coefficients most commonly used in the scientific literature: Pearson, Overlap, and Manders M and K.

The Colocalization Analyzer (click to open larger view).

The Object Analyzer

The Object Analyzer is a great tool to label and analyze 3D and 4D single and multi-channel single objects and their statistics. With the 3D region of interest (ROI) selector tool you can limit the analysis to a certain volume only, but also crop your original data precisely like you want it for further analysis. Next to analyzing single objects or groups you can also analyze the whole dataset in all its aspects by clicking on one single button. This tool provides information about objects in different channels and time points: it reports physical properties, how objects relate spatially to each other or to reference objects, and how they overlap.

The Object Analyzer (click to open larger view).

The Object Stabilizer

The Object Stabilizer can measure and correct for cell motion, thermal drift, shaking, and other types of movement (x-y-z translation and axial rotation). Both the measurement and subsequent stabilization are done in 3D and at sub-pixel level. The Stabilizer not only stabilizes 2D or 3D time series, but it also allows the alignment of slices within a 3D stack.

Images show the sum of four time frames (300 s. lapse) of an apoptotic cell stained with fluorescent H2B nuclear protein. Courtesy of M. Varecha and M. Kozubek, Masaryk University, Czech Republic.

The Object Tracker

The Object Tracker is equipped with a wizard for optimized object detection and fast track filtering. The integrated Track Analyzer analyzes object position, speed and flow, and enables the user to visualize and export results in histograms and plots, and as CSV files.

The Track Analyzer (click to open larger view).

Advanced users and Facilities

Huygens Essential combines the power of deconvolution with a simplified, wizard-guided interface. For the more advanced users, Scientific Volume Imaging also offers Huygens Professional and Huygens Scripting which are the most powerful deconvolution packages available today, especially to process very large data.

For imaging facilities, Huygens Core is available to provide a centralized image restoration center that can be controlled remotely, for example with a web interface such as HRM.


The quality of the deconvolution algorithms in our software is backed by a long list of scientific publications. To mention some of them:

  • Verschure P.J., van der Kraan I., Manders E.M.M. and van Driel R. Spatial relationship between transcription sites and chromosome territories. J. Cell Biology (1999) 147, 1, pp 13-24 (get pdf).
  • Visser A.E. and Aten J.A. Chromosomes as well as chromosomal subdomains constitute distinct units in interphase nuclei. J. Cell Science (1999) 112, pp 3353-3360 (get pdf).*Hell S.W., Schrader M. and Van Der Voort H.T.M. Far-Field fluorescence microscopy with three-dimensional resolution in the 100-nm Range. J. of Microscopy (1997) 187 Pt1, pp 1-7 (get pdf).


If you still encounter some problems with our user-friendly Huygens Software, we provide first-line and online support to help you with your image deconvolution and analysis. This has made Huygens Sofware distinct compared to other Deconvolution packages in the market.

More information can be obtained via your local resellers or directly from our company.

More information

For detailed information on the way Huygens works, please read the following Huygens Deconvolution.

For more information about features and modules, see: