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Microscope types supported by Huygens




The Huygens Software offers a wide variation of deconvolution options for Deconvolution, which are specifically designed to take the deconvolution properties of each microscope type into account. It is however also possible to use Huygens for other microscope types that do not have a specific deconvolution option. Below an overview is given of all supported microscope types in Huygens and corresponding microscope option and settings.

Confocal Microscopy

For confocal microscopes, there is a dedicated Huygens deconvolution option: The confocal deconvolution option.

Widefield Microscopy

For widefield microscopes, there is a dedicated Huygens deconvolution option. The widefield deconvolution option.

2-Photon or Multi-Photon Microscopy

For 2-photon of multi-photon microscopes, there is a dedicated Huygens deconvolution option. The multi-photon deconvolution option in the Huygens Software can work for either Widefield Multi-Photon as well as Confocal Multi-Photon. See the Microscope Types: the number of photons involved in the fluorescence process is a Microscopic Parameter that you have to enter when describing the image. As there are 'widefield' and 'confocal' multi photon microscopes, the multi photon option gives access to both. Two (or multi) photon data has more in common with confocal data than with wide field data, but is handled differently by the Huygens software.
For instance:

different PSF generator, though it shares parts with the confocal generator.
the reconstruct-PSF tool uses different a-priori knowledge about what the PSF should look like
a number of basic values is computed differently, for instance the Nyquist rate, the expected two-point resolution, and so on.

For 2-photon microscopes, the Multi photon excitation parameter must be set to two in your microscopic parameters (show via right-click on your image while in Huygens)

Structured Illumination Microscopy (SIM) from Apotome systems


The Point Spread Function (PSF) can be attempted to be determined experimentally and theoretically. For the experimental PSF, we think that treating the bead images as recorded with a Spinning-disc microscope could be sufficient.

You can also try to deconvolve your data using a theoretical PSF. We think that ApoTome also has a strong widefield component (almost constant light flux along the volume), so you could introduce this component in Huygens in a theoretical spinning disc PSF by increasing the pinhole spacing (to 4 micron for instance) or opening up and setting the pinhole size to 500nm.

Learn more: Apotome Structured Illumination

Total Internal Reflection Microscopy (TIRF)

TIRF (Total Internal Reflection Fluorescence) deals mostly with 2D images. Huygens can handle 2D images by internally treating them as part of a 3D stack from which most planes happen to be missing.

Strictly speaking Huygens does not generate TIRF Theoretical PSFs, but customers report good results with high NA confocal PSFs. Proceed by setting the Microscope type of your image to confocal and NA ~ 1.4.

Learn more: https://svi.nl/TotalInternalReflection

Spinning Disk (Nipkow Disk) Microscopy

For Spinning Disk or Nipkow Disk microscopes, there is a dedicated Huygens deconvolution option: The Spinning Disk deconvolution option.

Brightfield Microscopy

For brightfield microscopes, the Widefield deconvolution option is used.

For versions 21.10 and higher, this can best be done in the Deconvolution Wizard in either Huygens Essential or Huygens Professional. If the microscopic parameters specify the image as "brightfield" the image will first be inverted automatically by the Deconvolution Wizard. This is done because dense objects should have high intensity vallues in our deconvolution algorithms. Automatically the Tikhonov Miller algorithm will be selected. This algorithm is strongly advised for all brightfield or equivalent images as this algorithm does not amplify the background noise.

For the other deconvolution tools, the PSF distiller and the renderers the image should first be inverted manually. In Huygens Essential this can be done by choosing the option 'invert image' from the 'Tools' menu. In Huygens Professional select the image and go to 'Deconvolution', 'Operations window', 'Arithmetic', 'One image', and then 'Invert'.

Learn more: Brightfield Microscope

Yokogawa disk Microscopy


STED Microscopy

For 2D-3D STED microscopes, there is a dedicated Huygens deconvolution option: The STED deconvolution option.
STED microscopy allows super-resolution imaging in the 50nm range. Unfortunately, this increased deconvolution resolution also leads to a drawback: because many fluorophores are depleted by the depletion laser, this also results in a lower signal (fewer photons) being captured by the detector. Because of the Poisson nature of photon statistics, the signal-to-noise ratio of the resulting image will decrease compared to normal confocal imaging. Therefore the SNR value in STED images will be much lower compared to their confocal counterpart. Luckily, Huygens deconvolution of STED images offers a great solution. Since 2012, the Huygens software is able to generate a theoretical PSF based on STED microscope parameters. This theoretical PSF can be used in the deconvolution process, which will significantly reduce the noise in the image, and will increase the contrast of up to 10 times. Additionally, the Huygens deconvolution algorithms are able to increase the resolution in the image with a factor of 2 in both lateral and axial direction. See also STED-Deconvolution.

Ligth sheet Microscopy (LSFM)

Almost all, if not any, Light Sheet setup is supported by this dedicated Huygens deconvolution option: The Light Sheet deconvolution option.

Re-scan Confocal Microscopy

For Re-scan microscopes, there is a dedicated Huygens deconvolution option: The Re-Scan deconvolution option.

Airyscan and nanoSPAD Microscopy

For Zeiss Airyscan microscopes, there is a dedicated Huygens deconvolution option: The Array Detector deconvolution option.

Single Molecule Localization Microscopy (SMLM)

The Huygens Localizer is a stand-alone software package for fast & high performance processing of Single Molecule Localization Microscopy data (SMLM), such as Photoactivated Localization Microscopy (PALM), Stochastic Optical Reconstruction Microscopy (STORM), Ground State Depletion (GSD), and DNA PAINT images.