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Huygens software refers to different Fluorescence Microscope image processing packages fromScientific Volume Imaging, avaliable for multiple platforms, made for


of 2D and 3D Multi Channel microscopy images or Time Series.

The restoration is based on different deconvolution algorithms, that permit the recovery of objects from images that are degraded by blurring and noise. In microscopy the blurring is largely due to diffraction limited imaging by the instrument; the noise is usually Photon Noise.

Huygens software is named after the Dutch physicist Christiaan Huygens, famous among other things for his Huygens Principle.

Part of the Huygens Software are, among others:


Follow their links to see how they work!!! Some of the software functionalities require a License String to work, but there are also many FreeWare tools that can run without any license. In any case you can always get a free test license to try all the functionalities. For that, just Contact Svi.

What is deconvolution, and how does the Huygens Software do it? Read more details in → Doing Deconvolution.

All products


See the full list of avaliable products and supported platforms.

Download


You can download the software and the user manuals from our Download Section.

Documentation


A good starting point in this wiki to learn how to use the Huygens Software is the Tutorials page.

For more details you can take a look at the available online Huygens Documentation.


References


Scientific references to SVI software.

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Huygens 4.3 Release 

When not specified, changes apply to all Huygens Software products. Labels indicate particular products only: E = Huygens Essential, P = Huygens Professional, S = Huygens Scripting, C = Huygens Core.


(E/P) New Crosstalk Corrector option

  • This new optional tool estimates and corrects channel bleed-through (crosstalk/crossover) for up to 32 different channels automatically.
  • Correction is linear and can be applied interactively using the 2D histogram.
  • Correction values are plotted in a crosstalk coefficient matrix, which can also be manually adjusted.

New batch Colocalization analysis and histograms creation in Huygens Core

  • Added colocalization to the Huygens template readers and task processors. Huygens Core can now compute colocalizaton coefficients and create colocalization maps for pairs of channels in batch mode. A new version of the Huygens Remote Manager will soon be released offering the option to perform colocalization analysis after deconvolution.
  • Added 'histogram' task to the Huygens template readers and task processors. Huygens Core can now create 1D/2D histograms in batch mode.

(E/P) STED

  • Improved LIF support: parse the LIF type for Pulsed, CW non-gated or CW gated STED.
  • Added 'stabilization' stage for STED data to the PSF distiller.
  • Improved SNR control in STED deconvolution.
  • PSF Distiller supports STED data.
  • PSF Distiller estimates STED parameters.

(E/P) Object Tracker

  • New analysis type in the Object Tracker for tracking rotation angle and speed.
  • Implemented saving and loading track data.
  • Possibility to save track detection settings in a template file.
  • Added the Track Analyzer to the main menus and pop-up menus.
  • Tracker works now more robust with small number of samples or time frames.

(E/P) Twin Slicer

  • The line profile within the Twin slicer now updates when slicing through time.
  • Added a channel selector to the basic mode of the Twin slicer and in the view mode in Huygens Essential.
  • Plot more than one intensity line profile at once in the Twin slicer.
  • Remove all arrows and markers from the graph in the Twin Slicer at once, instead of removing them one by one.
  • When creating a new intensity profile it is now possible to plot easily along lines parallel to the axes. This can be achieved by pressing 'Shift' while drawing an arbitrary line with the mouse.
  • Events previously managed with the 'Ctrl' key are now managed with the 'Shift' key. The Ctrl-LeftMouse is now being used to simulate the Middle Mouse button (see also minor changes).
  • The Twin Slicer now shows a "Shortcut Info"-tab explaining all the available shortcuts (key- and mouse-events).

(E/P/S) Usage Report

  • New feature: Usage report tool under the Help menu to visualize and list the use of the different Huygens tools.

Minor changes

  • (All) One-button mice no longer supported.
  • (All) Added possibility to simulate a middle mouse button: 'Ctrl' + 'Left' click.
  • (P) Added convert-tools that already existed in Essential to Huygens Professional. Convert, mirror, flip image, which you can find under Tool > Convert...
  • (P) New button for quick access to the Batch Processor in Huygens Professional.
  • (E/S/C) Report restoration scaling factors. This was only possible in Huygens Professional so far.
  • (E/P) The result file of the Chromatic Shift Corrector is now named "....._aligned" instead of "..... _corrected".
  • Added 'manual' background mode to the Deconvolution Wizard.
  • Backgrounds in byte and integer images are computed with floating point precision. The resulting value is very close to the value obtained by converting the image to floating point prior to background computation.
  • (All) New channel selector widget for easy access and control for viewing different channels.
  • Much reduced memory usage when generating very large PSFs at negligible accuracy loss.

Bug fixes

  • (E/P) The lower threshold slider in the Object Tracker was reset when the upper got enabled and vice versa.
  • (E/P) In the Deconvolution Wizard, the template background values were not displayed or taken into account if the user decided to go through the Wizard stages after loading a template.
  • (E/P) The MIP renderer threw an error when setting 'Custom colors' if the image had more than 4 channels.
  • (All) Applying a negative baseline on byte images, resulted in a wrap around of the negative baseline (e.g. -2 -> 254), which would result in all values to be below zero, which are mapped to 0.
  • Add a fallback value for the socket count: 1. This fixes crash issues with virtual machines.
  • Reading LSM files often led to an unnecessary scaling (division by 2).
  • Files of type ome-xml created with the Bio-formats library could not be opened.