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Huygens Essential

Deconvolution a few mouse clicks away


Huygens Essential is an image processing software package, part of the Huygens Software , tailored for deconvolution of microscopic images. Its wizard driven user interface guides you through the process of deconvolving microscopic images. Huygens Essential is able to deconvolve a wide variety of images ranging from 2D widefield (WF) images to 4D Multi Channel multi-photon confocal images. To facilitate comparison of raw and deconvolved data, or results from different deconvolution runs the Essential is equipped with a dual 4D slicer tool. Powerful and fast renderers produce different representations of your data, not needing any special graphic card.



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Huygens Essential's wizard driven user interface.



Based on the same image processing engine as Huygens Professional , Huygens Essential combines the quality and speed of the algorithms available in Huygens Professional with the ease of use of a wizard driven intelligent user interface. Also, Huygens Essential is based on cross-platform technology which makes it available on a large range of platforms.

Features


Processing stages


Huygens Essential is build with a processing stages. In the first pre-processing stage, the intelligent parameter checker scrutinizes the Microscopic Parameters . It marks suspicious optical conditions and warns you of UnderSampling conditions. You can save the confirmed parameters in a Parameter Template for future re-use in other images.



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Huygens Essential wizard.
The wizard marks suspicious optical conditions and warns you of under sampling conditions.



In the next stages you can use the automatic cropping tool, inspect the Image Histogram to spot clipping or saturation and inspect the image BackGround .



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Huygens Essential wizard.
The wizard asks to open the cropping tool or crop the image automatically.




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Huygens Essential wizard.
The image histogram is an essential tool for detecting clipping and inspecting the image background level.



Intelligent 4D cropping tool


The 4D cropping tool allows you to trim images along four dimensions and to delete uninteresting channels. In that way you deploy your computers processing power to only the interesting parts of the image. Still, situations occur where your system's memory is not sufficiently large to allow it to be deconvolved as a whole. In these cases the image is split into bricks (see Brick Splitting ). The bricks are deconvolved one by one; the results seamlessly fitted together again.



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The cropper.
The 4D cropping tool allows you to trim images along four dimensions and to delete uninteresting channels.



PSF generation


With Huygens Essential it is possible to load a measured Point Spread Function (PSF) to deconvolve your images. When a measured PSF is not available, Huygens Essential automatically uses a theoretical PSF. This theoretical PSF is computed from the Microscopic Parameters that come with your image and which you have double-checked in the preprocessing 'P' stage or in stage one. Because a theoretical PSF can be generated without any user intervention, Huygens Essential does the calculation in the background without any notice.

Step by step deconvolution


The wizard will guide you in deconvolving the different data channels in a interactive way. You can vary the Restoration Parameters if you want, comparing the Image Restoration results with the original data using the Twin Slicer . When all the channels are restored, you can merge them easily to save the final image.



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The Huygens Twin Slicer.
The Twin Slicer allows you to synchronize views of two images, measure distances, plot line profiles, and more.




Visualization and analysis


Apart from the Image Restoration tools described in this article, Huygens Essential also has optional tools for Volume Visualization and Interactive Analysis , described in those other linked articles.



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Surface renderer. The Surface Renderer enables you to represent your microscopy data in a convenient way to clearly see separated volumes. It is not only capable of iso-surface rendering; it is also able to show MIP projections together with the surfaces to be used as a reference to the original microscopic voxel data.




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SFP Renderer.
This 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 (SFP) algorithm.




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The Huygens Movie Maker.
The Movie Maker is a tool that allows you to easily create sophisticated animations of your multi-channel 3D images using the powerful SFP, MIP, and surface renderers. The AVI movies can be played by Windows Media Player, Apple Quicktime, and other players that support the MJPEG standard.



Documentation


Huygens Essential comes with two manuals.

The first one is the user manual which offers clear documentation on Huygens Essential. It explains the different processing stages of the wizard interface, the separate cropper and viewer windows, how to use Essential with multi-channel images and time-serie images and it explains terms as Blacklevel, Sampling densities, data aquisition pitfalls and how to compute microscopic parameters.


( Huygens Manual )
( Alternative Cover )

The second one is the SVI Deconvolution Recipes for image restoration. It contains specialized knowledge and tips on topics like recording microscopic images, how to get a Point Spread Function and information on Doing Deconvolution .

See the Tutorials section for more documentation.

Download


Download Huygens Essential and its user manual.