SVI course on Huygens Software
You can subscribe now for this course
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 - 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 : IntroductionGeneral introduction to microscopy Image Formation and Image Restoration
- Light/Wave properties, Spatial frequencies
- Deconvolution algorithms
- Point spread function - Optical Transfer Function
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 dataHow to prepare images in Huygens, treat large image data, converting image dimensions, scaling, and File formats
15.35 - 15:50 : Short break
15:50 - 17:15 : Huygens Deconvolution Wizard and Batch ProcessorDeconvolution in Huygens Essential and Huygens (Professional), how to schedule multiple deconvolution tasks with the Batch Processor
17:15 - 17.45 : Research talks participantsAttendants 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 datasetsUsing Huygens for images from a variety of different microscope types: widefield, confocal, spinning disk, Multi-photon, STED 3D, Light Sheet, Array (Airyscan) Detector systems.
9:45 - 10:20 : Deconvolution Express, and Batch Express vs Batch ProcessorUsing Huygens for automated and batch deconvolution. How to best prepare data for quantification studies.
10.20 - 10:40 : Short break
10:40 - 11:10 : PSF distillerDistilling an experimental PSF from bead images, PSF quality (Giulia)
11:10 - 12:15 : How to best deconvolve my imagesWhat algorithm should I choose, differences between microscope types, optimal parameter settings, deconvolution artefacts and how to prevent them (Peter)
12.15 - 13:40 : Lunch break
13.40 - 14:20 : Visualization ITwin Slicer and OrthoSlicer fine tricks (Paul)
14:20 - 15:00 : Visualization II14:20 - 14:35 : Huygens MIP and SFP renderers (Michel)
14:35 - 15:00: Huygens Surface renderer and Movie Maker (Paul)
15:00 - 15:15 : Short break
15:15 - 15:45 : Tile StitchingAutomatic 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 AnalyzerColocalization 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)
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 PitfallsHow 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 CorrectorCorrecting bleedthrough with the CrossTalk Corrector
10:00 - 10:45 Chromatic Aberration CorrectorCorrecting chromatic aberration with the Chromatic Aberration Corrector
10:45 - 11:00 Short break
11:00 - 11:15 : Hot & Cold Pixel removerHANDS-ON
11:15 - 11:35 : Bleaching CorrectorHANDS-ON
11:35- 12:10 : Object Stabilizer + Object TrackerCorrecting unwanted movement and drift with the Object Stabilizer. How to detect and analyze tracks of moving objects with the Object Tracker
12:10 - 12:30 : QuizFind and fix imaging issues with Huygens