Huygens Products

The Huygens Software includes different image processing options, available for multiple platforms. Packages are intended for deconvolution for brightfield and all types of fluorescence microscopy images, restoration, interactive analysis and volume visualization in 2D, 3D, multi-channel and time. Additional Server and GPU-based Options ensure maximization of hardware performance. The Huygens Software is named after Christiaan Huygens who discovered the diffraction of light waves.

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. We also offer an Huygens web-based interface, Huygens Remote Manager, available for submitting deconvolution tasks via your internet browser to the compute engine Huygens Core.

You are welcome to explore all these options by downloading the Huygens software and request a trail license, or to receive pricing information!

A wizard-based user interface in Essential guides you step by step through the deconvolution process.
(click to open larger view).


Huygens offers several different deconvolution algorithms to restore images degraded by blurring and 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. 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.

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 a complete time sequence, 2D or 3D with multi-channel, is optimized.
  • 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 deconvolved data you need, quickly and reliably.
  • With the very user-friendly deconvolution option Deconvolution Express you can perform automated deconvolution with parameters estimated by the software, for a quick and easy result.

Server/CPU and GPU Options

To speed up Huygens deconvolution, the Huygens software can be combined with GPU acceleration reporting an acceleration factor up to 30 times! More information about fast high-quality results of Huygens GPU deconvolution can be found on our GPU page!

Huygens uses by default up to 6 CPU cores and one socket (Desktop version). One of the following server options can be added to your license to increase the preformance:
  • Small Server Up to 12 CPU cores and two sockets.
  • Medium server Up to 24 CPU cores and four sockets.
  • Large server Up to 48 CPU cores and eight sockets.
  • Extra Large server More than 48 CPU cores and more than eight sockets.
If the hardware is equipped with an Nvidia CUDA GPU card, Huygens can use by default up to 1024 cores and 2 GB VIDEORAM (Small GPU version). The following GPU options can be added to your license:
  • Medium GPU option between 1024 and 3072 GPU cores and between 2 to 4 GB VIDEORAM (no hardware included).
  • Large GPU option between 3072 and 8,192 cores and maximum 24 GB VIDEORAM (no hardware included).

Visualization Options

The various Visualization Tools in Huygens Essential and Professional help you to visualize and 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. With the SFP Renderer you can visualize your object from different angles and gives you 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.

Visualization Tools (included in Huygens basics free of charge)

The Twin Slicer

The Twin Slicer allows you to synchronize views of two images, measure distances, plot line profiles, etc. The twin slicer 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 from 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 prefer.

The MIP Renderer (click to open larger view).

The SFP Renderer

The Volume Renderer or SFP Renderer is based on considering 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. The SFP algorithm is based on ray tracing, and 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 with adjustable sliders to study small objects in 3D.

The Ortho-Slicer (click to open larger view).

The Gallery tool shows all individual Z slices or time serie frames in one overview, and allows for detailed inspection of the slices with the Detailed Tile viewer.The overview can be customized and saved for e.g. presentation purposes.

The Gallery Tool (click to open larger view).

Visualization Options

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 Movie Maker

The Movie Maker is a tool that allows you to easily create sophisticated animations of your multi-channel 3D images combining the powerful Huygens Visualization renderers. Movies can be exported as AVI or TIFF images.

The Movie Maker (click to open larger view).

Analysis Options

Several interactive analysis tools are available for Huygens to accurately perform 3D-4D measurements, and to obtain and export statistics about object(s), colocalization, and cell/object trajectories.

The Colocalization Analyzer

With the Colocalization Analyzer you can obtain information about the amount of spatial overlap between different data channels, in 2D images, 3D stacks or time series. As this overlapping can be defined in many ways, Huygens gives you the colocalization coefficients most commonly used in the scientific literature, as Pearson, Spearman, Manders M and K, Overlap.

The Colocalization Analyzer (click to open larger view).

The Object Analyzer

The Object Analyzer is a great tool to segment and analyze 3D and 4D single and multi-channel images analyzing single objects and their statistics (number, volume, surface, overlap etc.). 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 for further analysis. 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 Tracker

The Object Tracker is a wizard-based module 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).

Restoration Options

For other major factors distorting image quality like Hot pixels, Instability, Chromatic Aberration and Cross Talk we have developed the following Restoration Tools and Options:

Restoration Tools (included in Huygens basics free of charge)

The Hot Pixel Remover

The Hot Pixel Remover estimates and removes local hot pixels in any image. Using specific filters, it detects the hot pixels and replaces them with the median of the neighbors. The result is a hot-pixel-free-image that is ready for deconvolution.

The Hot Pixel Remover (click to open larger view).

Restoration Options

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 z-slices within a 3D stack.

The Stabilizer wizard (click to open larger view).

The Stitcher wizard

The wizard-driven Stitcher automatically aligns and stitches tiles of 2D, 3D, and 3D-time multichannel images, also for LIF and CZI files. Vignetting and shading can be automatically estimated and corrected with an advanced Huygens automatic algorithm, or a darkfield/flatfield image can be manually loaded for correction. Deconvolution is integrated and can be combined with stitching into one simple, efficient workflow.

The Stitcher wizard (click to open larger view).

The Chromatic Abberation Corrector

The Chromatic Aberration Corrector estimates and corrects for chromatic shifts between different channels of multi-channel images. Besides removing misalignments, it can also automatically estimate and correct for differences in scaling and rotation between channels.

The Chromatic Aberration Corrector (click to open larger view).

The Crostalk Corrector

The Crosstalk Corrector estimates and corrects for crosstalk, also known as bleedthrough. Crosstalk can occur if there is spectral overlap between different channels, and signal is recorded from a specific dye whereas the detector is already reserved for another dye. Crosstalk in multi channel images up to 32 channels can be easily estimated, visualized, and corrected with this tool.

The Crostalk Corrector (click to open larger view).

Advanced users and Facilities

Huygens Essential combines the power of deconvolution with a simplified, wizard-guided interface and the immediate deconvolution button. 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).
  • 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).

More information

For detailed information on the way Huygens works, you can find more information on Image Restoration and Huygens Deconvolution.