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Other Options



Besides blurring, noise, and spherical aberration - which can be effectively corrected by deconvolution - there are other major factors distorting image quality. Below you will see the available Options and Tools for both:

Microscopy Optical Options

Each optical option is specifically designed to take into account the optical properties of that type of microscope for Deconvolution:




Restoration Options

Available starting from 590€ / 780$ ex VAT

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

Screen shot Description
ObjectStabilizer2.png 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 stabilizes 2D or 3D time series, and slices within a 3D stack.

Huygens Stitching Wizard  - HPRT P30 327 ReTbr1 20x cortex3_005.png The Stitcher wizard.

The wizard-driven Stitcher automatically aligns and stitches tiles of 2D, 3D, and 3D-time multichannel images of LIF and CZI files. Vignetting and shading can be automatically estimated and corrected with an advanced Huygens 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.

ChromaticShiftCorr.png The Chromatic Aberration 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.

CrosstalkCorrector_estimate.png The Crosstalk Corrector.

The Crosstalk Corrector estimates and corrects for crosstalk, also known as bleedthrough. This 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.



Restoration Tools

(included in Huygens basics free of charge)

Screen shot Description
Huygens_HotPixelRemover.png 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.





Functional Options

Available from 590€ / 780$ ex VAT

Huygens Time Series option - Allows automated deconvolution of time series. and correction of time-dependent background, bleaching and z-drift.

Huygens Full File Readers option - Support for extended input file formats.

Huygens <-> LAS AF/X option - Allows full exchange of LIF images and metadata between the Leica LAS AF/X (3.3 or higher) and Huygens.

Huygens PSF Distiller option is a wizard guided option that can be used to obtain an experimental or distilled Point Spread Function (PSF) from acquired single and multi-channel bead images. A screen shot of the wizard is shown below. Chromatic shifts will be automatically reported and can be corrected by the Chromatic Shift Corrector.

The PSF Distiller wizard

PsfDistiller2.PNG



Server (CPU) and GPU Options

Huygens uses by default up to 6 CPU cores and one socket (Desktop version). To speed up the Huygens software, one of the following server options can be added to your license. CPUs can be either single or hyper-threaded. The performance of Huygens can increase significantly with the use of GPU acceleration. See also system benchmark results and GPU benchmarks.

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 512 cores and 2 GB VIDEORAM (Small GPU version). The following GPU options can be added to your license:

Medium GPU option between 512 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).

More information about Huygens and GPU use can be found on the HuygensGPU wiki page.
You are welcome to explore these options using a free trial, or to receive pricing information.



Supported Operating Systems and Hardware

Our software can make optimal use of the number of CPU and GPU cores in your hardware (see under 'CPU/GPU Options'), and is based on cross platform technology which makes SVI one of the few software companies in the microscopy field that have their software available on Microsoft Windows, Apple Mac OS X and Linux. All our applications have the same look and feel on all platforms, except where the differences are created by the window manager of the operating system that is being used. For a comparison of speed of deconvolution with Huygens on various hardware configurations and platforms (Linux, Mac and Windows) you may want to have a look at the benchmark results.
The hardware that is recommended below represents the minimum requirements. Please contact us for more detailed advise at info at svi.nl.


 Windows

Windows Vista, Windows 7, Windows 8, Windows 10
Processor: AMD Athlon or Intel Pentium 4 and higher. Recommended RAM: 4 GB or more

 GNU/Linux

Debian, Ubuntu, CentOS, openSUSE and Red Hat (recent versions) are supported, but Huygens works on many other Linux distributions.
Processor: Intel. Recommended RAM: 4 GB or more.

Apple OS X

OS X 10.8 (Mountain Lion), OS X 10.9 (Mavericks), OS X 10.10 (Yosemite), OS X 10.11 (El Capitan) is required for full 64 bit capabilities, and for full multiprocessor support.
Processor: AMD Athlon or Intel Pentium 4 and higher. Recommended RAM: 4 GB or more.