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SVI course on Huygens Software



You can subscribe now for this course

Preliminary Program


Date : May 8 (afternoon ) + 9 + 10, 2019
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 (Wednesday): Deconvolution and Data handling


13.30 - 14:00 : Welcome - Coffee/Tea

14:00 - 15:00 : Introduction

General introduction to microscopy Image Formation and Image Restoration
  • Light/Wave properties, Spatial frequencies
  • Deconvolution algorithms
  • Point spread function - Optical Transfer Function
  • Super-resolution

15:00 - 15:15 : Get started with Huygens

  • Installation, Opening images in Huygens directly, via Drag and Drop.

15:15 - 15:35 : Converting and rescaling of image data

How to prepare images in Huygens, treat large image data, converting image dimensions, scaling, and File formats
HANDS-ON

15.35 - 15:50 : Short break


15:50 - 17:15 : Huygens Deconvolution Wizard and Batch Processor

Deconvolution in Huygens Essential and Huygens (Professional), how to schedule multiple deconvolution tasks with the Batch Processor

17:15 - 17.45 : 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!

17:45 - 18:00 : Discussion - questions


18:00 End of day one






Day 2: Deconvolution and Quantification of image data


8.30 - 9:00 : Welcome - Coffee/Tea

9:00 - 9:45 : Deconvolution of different microscopy datasets

Using Huygens for images from a variety of different microscope types: widefield, confocal, spinning disk, Multi-photon, STED 3D, Light Sheet, Array (Airyscan) Detector systems.
HANDS-ON

9:45 - 10:20 : Deconvolution Express, and Batch Express vs Batch Processor

Using Huygens for automated and batch deconvolution. How to best prepare data for quantification studies.
HANDS-ON
10.20 - 10:40 : Short break

10:40 - 11:10 : PSF distiller

Distilling an experimental PSF from bead images, PSF quality (Giulia)
HANDS-ON

11:10 - 12:15 : 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

12.15 - 13:40 : Lunch break


13.40 - 14:20 : Visualization I

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

14:20 - 15:00 : Visualization II

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

15:00 - 15:15 : Short break


15:15 - 15:45 : Tile Stitching

Automatic vignetting, deconvolution and stitching in one workflow (Daniel)

15:45 - 16:15 : Light Sheet Deconvolution - Fusion Wizard (Optional)

Deconvolution and fusion of Light Sheet data in one Wizard (Peter)

16:15 - 17:00 : Colocalization Analyzer

Colocalization Analyzer (Michel)

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 3: Huygens Restoration and Analysis



8:45 - 9:40: 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.

9:40 - 10:00: CrossTalk Corrector

Correcting bleedthrough with the CrossTalk Corrector

10:00 - 10:45 Chromatic Aberration Corrector

Correcting chromatic aberration with the Chromatic Aberration Corrector
HANDS-ON

10:45 - 11:00 Short break


11:00 - 11:15 : Hot & Cold Pixel remover

HANDS-ON

11:15 - 11:35 : Bleaching Corrector

HANDS-ON

11:35- 12:10 : 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
HANDS-ON

12:10 - 12:30 : Quiz

Find and fix imaging issues with Huygens
HANDS-ON

12.30 - 13.30 : Lunch break


12:30 - 13:30 : Object Analyzer

Analyzing you microscopy images with the Object Analyzer


13:30 - 16:15 : Working with your own data or demo images (with the SVI staff)

Images from you or your colleagues that you brought with you will be discussed. Imaging problems will be identified and the appropriate Huygens tools will be selected and applied to fix these. Subsequent analysis strategies will be discussed and performed with Huygens to get the most optimal results out of the data. SVI demo images are made available if needed. During this session, we can make use of powerful servers with multiple GPU cards to ensure that even large datasets can be processed.

16:15 : 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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