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SVI course on Huygens Software




Program


Date : October 12th + 13th, 2017
Location: Scientific Volume Imaging headquarters, Hilversum (NL)


Important instructions to participants


Images can be uploaded via our Upload page

Please bring with you:
  • Images to restore / analyze. You can also upload them, see link above.
  • Please include the Microscopy Parameters of those images
  • If possible, your laptop - with Huygens and test licenses pre-installed (these will be send to you)


Demo images

  • Demo images - will be made available soon and will also be available at the course site.




Day 1: Deconvolution, Data handling, and Visualization


8.30 - 8:50 : Welcome - Coffee/Tea

8:50 - 9.50 : Introduction

General introduction to microscopy Image Formation and Image Restoration (Hans)
  • Light/Wave properties
  • Deconvolution algorithms
  • Point spread function - Optical Transfer Function

9:50 - 10:05 : Get started with Huygens

  • Installation (Linda + Paul)
  • 4K monitor support and changing the GUI appearance (Paul)
  • Opening images in Huygens directly, via Drag and Drop, or via LASX (Linda).

10:05 - 10:25 : Converting and rescaling of image data

How to prepare images in Huygens, treat large image data, converting image dimensions, scaling, and File formats (Frans)
HANDS-ON
10.25 - 10:40 : Short break

10:40 - 11.50 : Huygens and Batch processing

How to start a deconvolution job in Huygens Essential and Huygens (Professional), and how to schedule multiple deconvolution tasks with the Batch Processor (Wouter)

11:50- 12.15 : Research talks participants

Attendants are encouraged to present with one slice the specific research question they want to address with Huygens. The lunch is after the Research talks, so you are encouraged to keep your Research talk as a "small appetizer" for the lunch discussion!

12.15 - 13:40 : Lunch break


13.40 - 14:20 : Visualization I

Twin Slicer and OrthoSlicer fine tricks (Gitta)
HANDS-ON

14:20 - 15:00 : Visualization II

14:20 - 14:35 : Huygens MIP and SFP renderers (Frans)
HANDS-ON
14:35 - 15:00: Huygens Surface renderer and Movie Maker (Paul)
HANDS-ON
15:00 - 15:15 : Short break

15:15 - 16:10 : How to best deconvolve my images

What algorithm should I choose, differences between microscope types, optimal parameter settings, deconvolution artefacts and how to prevent them (Peter)
HANDS-ON

16:10 - 16:40 : PSF distiller

Distilling an experimental PSF from bead images, PSF quality (Giulia)
HANDS-ON
16:40 - 17:00: Short break

17:00 - 17:40 : Huygens solutions for support and to address many users (simultaneously)

- Promote Huygens use at the facility (Daniel)
- Batch processing
- Remote Display use
- Huygens latest FLOATING option
- Online web interface Huygens Remote Manager with the Huygens Core (Daniel)
HANDS-ON

17:40 - 18:00 : What's New and What's Coming - A Developer's View.

What has recently been introduced in Huygens and what is yet to come (Daniel)

18:00 End of day one




Day 2: Huygens Restoration and Analysis



8:45 - 9:45: Acquisition Pitfalls

How to deal with image distortions and acquisition pitfalls
Issues that will be addressed are for example noise, blurring, bleaching, hotpixels, spherical aberration, bleedthrough, drift. (Vincent)

9:45 - 10:00: CrossTalk Corrector

Correcting bleedthrough with the CrossTalk Corrector (Vincent)

10:00 - 10:20 : Chromatic Aberration Corrector

Correcting chromatic aberration with the Chromatic Aberration Corrector (Paul)
HANDS-ON
10:20 - 10:35 Short break

10:35 - 11:00 : Object Stabilizer + Object Tracker

Correcting unwanted movement and drift with the Object Stabilizer. How to detect and analyze tracks of moving objects with the Object Tracker (Giulia)
HANDS-ON

11:00 - 11:20 : Quiz

Find and fix imaging issues
HANDS-ON

11:20 - 12:00 : Colocalization Analyzer

Colocalization Analyzer (Pascal+Remko)

12:00 - 12.30 : Object Analyzer

Analyzing you microscopy images with the Object Analyzer (Remko)

12.30 - 13.30 : Lunch break



13:30 - 14:40 : Parallel sessions (in consultation with participants)


13:30 - 14:40 Working with your own data or demo images (with the SVI staff)

13:30 - 14:00 : Stitcher
Automatic vignetting, deconvolution and stitching in one workflow (Vincent)

14:00 - 14:40 : SPIM Deconvolution - Fusion Wizard (Optional)
Deconvolution and fusion of SPIM data in one Wizard (Peter)


14:40 - 16:30 : Working with your own data or demo images (with the SVI staff)


16:30 : Evaluation, Graduation, and Drinks

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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