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News

Huygens software version 17.10 released!

Thursday 02 of November, 2017
Scientific Volume Imaging proudly announces that the Huygens Software version 17.10 is available for download!

The new version includes, for example, improvements in the Colocalization analyzer, in the Hot pixel remover, in the Deconvolution Express and image feeder. Furthermore, the 17.10 includes a feature that a lot of our users requested: real time deconvolution on ROI's, with direct feedback for the SNR.

More detailed information about what is new can be found here.

The new 17.10 version was showcased during the What's New webinar organized the 21st of November. Watch the recordings here if you want to know more about the new version of Huygens!




GPU deconvolution: impressive Huygens GPU performance with NVIDIA's brand-new Volta-based Tesla V100 card

Thursday 12 of October, 2017
SVI has recently performed GPU deconvolution benchmarks for several 3D image dimensions with three state-of-the-art GPU cards.
The brand-new NVidia Volta-based Tesla V100 shows an impressive acceleration compared to the the (Pascal) P100 and GTX Titan Xp cards, which had already demonstrated extremely fast deconvolution performance in previous Huygens benchmark tests.

The acceleration factor shown in the chart below is relative to a 6 core (12 threads) Intel(R) Xeon(R) CPU E5-1650 v4 @ 3.60GHz.
The acceleration factor was determined by comparing the average time per iteration over a total of 100 iterations using the Huygens CMLE algorithm.



500x500x40 1000x1000x50 1000x1000x100 1600x1600x100 1600x1600x200 0 5 10 15 20 25 Huygens deconvolution GPU acceleration *Acceleration relative to Intel(R) Xeon(R) CPU E5-1650 v4 @ 3.60GHz. Higher is better V100 P100 GTX Titan Xp Image pixel dimension (X * Y * Z) Acceleration factor * NVIDIA GPU cards: www.svi.nl

The Huygens Image Contest 2017 is open!

Friday 29 of September, 2017
Send the best images or videos deconvolved and rendered with the Huygens software to have the chance to win a Chromebook! Images can be sent to contest at svi.nl before 1st of December 2017. If the file is too large to be sent by email you can use this upload site. Winners will be informed before 15th of December 2017. More information can be found via this link. Good luck!

O Paloheimo Pieris Brassicae

Image from Mrs. Outi Paloheimo, BioMediTech and Tampere Imaging Facility of BioMediTech, University of Tampere, Finland

SVI-Huygens at NIH

Wednesday 20 of September, 2017
SVI is happy to announce that at the end of the year we will be at NIH for the workshop “Huygens Deconvolution, Visualization and Analysis”. The workshop is on Thursday 30th of November, for facility managers and experienced users​, and Friday 1st of December 2017, for all users. The location is room 3LRC1 and 3LRC2, 5601 FISHERS LN, ROCKVILLE, MD 20852.

You can join both in person and via GoToMeeting. For more information and registration, please consult this online form.

We thank the local organizers Dr. J. Kabat and Dr. O. Schwartz, Biological Imaging Facility, RTB/NIAID, for the organization.

WorkshopNIH


The program of the two days is:

November 30, 2017 “Deconvolution and Image Restoration with Huygens”
Experienced users and facility managers
Location: Room 3LRC1 & 3LRC2

  • 9.00 - 9.15 : Welcome– Coffee/Tea

  • 9.15 – 10.00 : Presentation. How to get the best out of your microscopic (super-resolution) images - Huygens image restoration
General introduction to microscopic image formation and restoration. Light/Wave properties, Deconvolution, Point spread function (theoretical vs experimental), imaging issues and pitfalls

  • 10.00 - 10.10 : Short break

  • 10:10 - 11.00 : Huygens Deconvolution (Express and Wizard) and Batch processing
Deconvolve your images with the Deconvolution Express or Wizard, and schedule multiple jobs with the Batch Processor. (With Hands on)

  • 11:00 – 11:20 : Quiz (hands-on)
Find and fix imaging issues

  • 11:20 - 11:35 : Huygens solutions to address many users (simultaneously)
Huygens FLOATING option, Online web interface Huygens Remote Manager with Huygens Core.

  • 11:35 - 12:05 : File formats, data size and handling.

  • 12:05 – 12:25 : Huygens Light Sheet and Fusion wizard
SPIM/Light sheet images can be deconvolved with our new Huygens Light Sheet optical option that takes the specific optical properties of these microscopes into account, as for example SPIM excitation mode, thickness of the sheet, light sheet NA and fill factor and direction. Deconvolution, scattering correction, and restoration (fusion) of multiview SPIM/Light sheet data is combined to facilitate the efficient use of computational resources. (With Hands on)

  • 12:25 - 13:30 : Lunch Break

  • 13:30 – 14:00 : Twin Slicer (hands-on)
Attendees will get some hands-on experience with using the Twin Slicer

  • 14:00 - 14.30 : PSF Distiller
Attendees will get experience with distilling PSFs from bead images, also focusing on STED applications. (With Hands on)

  • 14:30 – 15:00 : Object Stabilizer
Correcting unwanted movement and vibration with the Object Stabilizer. (With Hands on)

  • 15.00 - 15.15 : Short break

  • 15:15 – 16:00 : Chromatic Shift and Cross Talk Correction
How do imaging artifacts affect my analysis? - and how to treat such data.

  • 16:00 - 16:30 : 3D Stitching with deconvolution and automated vignetting correction
The Huygens Stitcher will be demonstrated. Combined automated stitching, deconvolution, and vignetting correction minimizes computer workload and saves time.

  • 16:30 – 17:30 : How to best deconvolve my images: essence of the day
What algorithm should I choose, differences between microscope types, optimal parameter settings, deconvolution artifacts and how to prevent them. With Hands on. The session will be concluded by a discussion on your specific datasets, applications and imaging issues.
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December 1, 2017 “Deconvolution and Image Analysis with Huygens”
All users
Location: Room 3LRC1 & 3LRC2

  • 9.00 - 9.15 : Welcome– Coffee/Tea

  • 9.15 – 10.00 : Presentation. How to get the best out of your microscopic (super-resolution) images - Huygens image restoration
General introduction to microscopic image formation and restoration. Light/Wave properties, Deconvolution, Point spread function (theoretical vs experimental), imaging issues and pitfalls

  • 10.00 - 10.10 : Short break

  • 10:10 - 11.00 : Huygens Deconvolution (Express and Wizard) and Batch processing
Deconvolve your images with the Deconvolution Express or Wizard, and schedule multiple jobs with the Batch Processor. (With Hands on)

  • 11:00 – 11:20 : Quiz (hands-on)
Find and fix imaging issues

  • 11:20 - 11:40 : Short introduction - Chromatic Shift and CrossTalk Correction, and Image Stabilization
How do imaging artifacts affect my analysis? - and how to treat such data.

  • 11:40 - 12:05 : File formats, data size and handling.

  • 12:05 – 12:25 : Huygens Light Sheet and Fusion wizard
SPIM/Light sheet images can be deconvolved with our new Huygens Light Sheet optical option that takes the specific optical properties of these microscopes into account, as for example SPIM excitation mode, thickness of the sheet, light sheet NA and fill factor and direction. Deconvolution, scattering correction, and restoration (fusion) of multiview SPIM/Light sheet data is combined to facilitate the efficient use of computational resources. (With Hands on)

  • 12:25 - 13:30 : Lunch Break

  • 13:30 - 14.00 : Twin and Orthogonal Slicers (with hands-on)

  • 14:00 - 14.45 : MIP, SFP and Surface Rendering (with hands-on)

  • 14:45 – 15.00 : Movie Maker (with hands-on)

  • 15:00 – 15.15 : Huygens solutions to address many users (simultaneously)
Huygens FLOATING option, Online web interface Huygens Remote Manager with Huygens Core.

  • 15.15 - 15.30 : Short break

  • 15:30 – 16:00 – Colocalization Analyzer
How to measure colocalization, which coefficients should I use, and how to do this with Huygens

  • 16:00 – 16:30 : Object Analyzer
Analyzing your microscopy images with the Object Analyzer

  • 16:30 – 17:00 : Object Tracker
How to detect and analyze tracks of moving objects with the Object Tracker

  • 17:00 – 18:00 : How to best deconvolve my images: essence of the day
What algorithm should I choose, differences between microscope types, optimal parameter settings, deconvolution artifacts and how to prevent them. With Hands on. The session will be concluded by a discussion on your specific datasets, applications and imaging issues.

Are you already following @svi_huygens on Twitter?

Wednesday 16 of August, 2017
If you are a Twitter user, follow us at @svi_huygens! You will be updated about the latest news in Huygens and you will find beautiful pictures and videos. A lot of them have been sent by our users, so we take the chance to thank them once again.

Voulez-vous améliorer vos résultats de déconvolution avec Huygens?

Tuesday 15 of August, 2017
SVI organisera un webinaire pour Optimiser les résultats de déconvolution avec Huygens le 10 Octobre à 15:30 CET. Ce webinaire vous offre un aperçu général du workflow d'imagerie pour la déconvolution, depuis l'acquisition d'image jusqu'à la procédure de déconvolution, afin d'optimiser vos résultats. Nous vous expliquerons la procédure de déconvolution Huygens en mettant l'accent sur le Parameter Editor et le Deconvolution Wizard. L'inscription à le webinaire est fermé. Vous pouvez trouver la vidéo sur ce lien jusqu'au 17 Octobre.

Huygens helps you obtaining more accurate colocalization results: Huygens webinar

Monday 17 of July, 2017
SVI will organize the 26th of September 2017 a webinar about Optimizing colocalization studies with Huygens. Colocalization studies provide an important insight on several biological processes, and Huygens can help you in getting the most accurate colocalization results. Huygens deconvolution improves resolution, contrast and signal to noise ratio, reducing the effect of Blur And Noise in Colocalization studies. Our Restoration Options also correct the images for the other aberrations, getting them ready for an accurate analysis. For what concerns the analysis, the Colocalization Analyzer works more at the level of the whole image, and the Object Analyzer also provides colocalization measurements at the object level. The webinar registration is closed. You can find more information about the webinar schedule via this link.

Webinar about Optimization of deconvolution for extremely low-signal and noisy data

Friday 30 of June, 2017
Noise in microscopy images is surely one of the strongest limiting factors in the study of morphology and dynamics of the cells, and in proceeding in a reliable visualization and analysis of the structures of interest. Deconvolution offers a great help in reducing noise and still preserving the small details of the object. Very noisy images, with extremely low signal, can be optimally addresses by Huygens deconvolution. The webinar about Optimizing deconvolution: focus on extremely low signal data was organized the 18th July 2017 to guide you through the optimal methodologies to deconvolve extremely low signal data with Huygens. The webinar about Optimization of Huygens deconvolution for Low signal data is no longer available on our website. In case you are interested in its registration, you are welcome to contact us at sales at svi.nl.

Webinars are regularly organized by Scientific Volume Imaging. You can find more information about the webinar schedule via this link.

New Huygens tutorial movies: Object Tracker, Crosstalk Corrector and Object Stabilizer

Thursday 22 of June, 2017
We have recently added three new video to our Tutorial Movies: Object Tracker, Crosstalk Corrector and Object Stabilizer. The tutorial movies are very useful to get a quick overview of the option and an introduction on how to use it.

  • The Object Tracker. A tutorial about the Huygens Object Tracker, giving a short demonstration about the Huygens Object Tracker and Track Analyzer. (4.02 min). Link to Tutorial Object Tracker.

  • The Crosstalk Corrector. The Huygens 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. (3.24 min). Link to Tutorial Crosstalk Corrector.

  • The Object Stabilizer. The Huygens 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. (4.39 min). Link to Tutorial Object Stabilizer.

Contact Information

Scientific Volume Imaging B.V.

Laapersveld 63
1213 VB Hilversum
The Netherlands


Phone: +31 (0)35 64216 26
Fax: +31 (0)35 683 7971
E-mail: info at svi.nl

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