Hands-on Light Sheet Microscopy Workshop


A workshop for you?

This Light Sheet Microscopy Workshop brings together young scientists and experts in the field of light sheet microscopy.

We aim to give you an overview on current best practice in light sheet microscopy along with tips & tricks for every step from methodological aspects all the way to data analysis and to facilitate increased awareness of both the prospects and the limitations of light sheet microscopy.

Who can attend?

The workshop is intended for PhD students and postdocs engaged or interested in light sheet microscopy.

Please note that you are not guaranteed a seat at the workshop, if you do not meet the target group requirements. Registrations will be considered in the order in which they are received.

Time & Place

  • 19th - 22nd of August, 2024
  • Aarhus University
  • The Skou Building, Høegh-Guldbergs Gade 10, C.F. Møllers Allé 6, 8000 Aarhus C, Denmark

Registration will open soon

Would you like to reserve a spot?

Or do you have questions or problems? Reach out to us in our contact form.

Workshop fee: 3,000 DKK

About the Workshop

Light sheet microscopy offers intermediate-to-high optical resolution, good optical sectionning capabilities and high speed - perhaps the right choice for your research? Designing a proper experimental setup that fits your experiment may be challenging and may require a lot of time. This workshop will take you through each step from methodological aspects to data analyses:

    

  • CLEARING Is the clearing technique expanding or shrinking the sample? Is it conserving endogenously expressed fluorophores? You will learn about the different clearing methods.
  • IMMUNOSTAINING & IMAGING How should refractive index and toxicity be considered during imaging? Get hands-on time at both the Zeiss Lightsheet 7 microscope and the Miltenyi Blaze light sheet microscope.
  • BIG DATA STORAGE, 3D DATA DISPLAY & ANALYSIS How can quantitative data be extracted from 3D data sets? Get familiar with free-ware options in Fiji/Image J as well as with commercial solutions like Arivis (Zeiss).

        

Altogether, our aim is to give you an overview on current best practice in light sheet microscopy, to provide tips and tricks on each step and to ensure that you obtain basic light sheet microscopy experience by performing each step yourself. Finally, there will be the possibility to present a poster.

Experts will be happy to answer your questions along the way!   

Participants should bring their own laptop (with mouse for convenience) for the Arivis data anlysis part. It is necessary to remote connect to the Acquifer Hive system where Arivis runs. If you would like to take your data home with you, bring a large hard drive (min 1TB).


To make optimal use of the workshop, bring your own sample. For support, contact us before you start clearing (at least 3 weeks before the beginning of the workshop). Contact us at imaging@biomed.au.dk 


Preliminary Programme

Workshop Overview

Day 1 10:30 - 17:00 + Welcome Reception 18:00 - 20:00
Day 2 09:00 - 17:30
Day 3 09:00 - 17:30
Day 4 09:00 - 13:00

Programme Monday 19th of August, 2024

10:30 - 11:00 Welcome & Introduction                                                                    
11:00 - 11:30 Theoretical session
11:30 - 12:30 Theoretical session
12:30 - 13:30 Lunch break                                                                                          
13:30 - 14:30                           Theoretical session                                                                                                                                                                                                    
14:30 - 17:00 Sessions
18:00 - 20:00                   Poster Presentations & Welcome get-together                                                                                                          

Programme Tuesday 20th of August, 2024

09:00 - 09:30 Hands-on tissue clearing   
09:30 - 10:30 Parallel sessions on Zeiss Lighsheet7, Flamingo (RG Huisken) and Arivis       
10:30 - 11:00 Coffee break                                                                                  
11:00 - 12:00 Parallel sessions on Zeiss Lighsheet7, Flamingo (RG Huisken) and Arivis
12:00 - 13:00 Lunch break                                                                                   
13:00 - 14:30 Parallel sessions on Zeiss Lighsheet7, Flamingo (RG Huisken) and Arivis
14:30 - 15:00 Coffee break                                                                                 
15:00 - 16:00 Parallel sessions on Zeiss Lighsheet7, Flamingo (RG Huisken) and Arivis
16:00 - 16:30 Afternoon snack                                                                         
16:30 - 17:30 Theoretical sessions                                                                

Programme Wednesday 21th of August, 2024

09:00 - 09:30 Theoretical session
09:30 - 10:30 Parallel sessions on Zeiss Lighsheet7, Flamingo (RG Huisken) and Arivis       
10:30 - 11:00 Coffee break                                                                                  
11:00 - 12:00 Parallel sessions on Zeiss Lighsheet7, Flamingo (RG Huisken) and Arivis
12:00 - 13:00 Lunch break                                                                                   
13:00 - 13:30 Theoretical sessions 
13:30 - 14:30 Parallel sessions on Zeiss Lighsheet7, Flamingo (RG Huisken) and Arivis
14:30 - 15:00    Coffee break                                                                                            
15:00 - 16:00 Parallel sessions on Zeiss Lighsheet7, Flamingo (RG Huisken) and Arivis
16:00 - 16:30   Afternoon snack                                                                                
16:30 - 17:30.   Theoretical session                                                                             

Programme Thursday 22nd of August, 2024

09:00 - 11:00

Talks:

- TBA

- TBA

Optional: run last analysis scripts (start in the morning)

11:00 - 12:00  Group presentations
12:00 - 13:00 Lunch break & Farewell                                                        

Consulting Industry Experts & Invited Speakers

Clearing & Imaging

Jacques Paysan                               Application specialist, Zeiss
Maria Trullson Application specialist, Zeiss
Mostafa Aakhte PostDoc, Huisken Lab
Steven Edwards Light sheet microscopy expert, SciLifeLab, Royal Institute of Technology (KTH)

Big Data Storage & Analysis

Olaf Selchow Consultant, Acquifer (Bruker)
David Wiles Application engineer, Arivis (Zeiss)
Molly McQuilken Business Development Manager, Arivis (Zeiss)

 Invited Speakers    

TBA                            

Practical Information

Signing up

When signing up, you will be asked for EAN or CVR numbers. For the correct numbers, please consult the person in your lab in charge of invoicing and finances. These are unique numbers for your university/institution: EAN (European Article Number) used for digital invoicing, CVR (Central Business Register) used to identify businesses. In stead of a CVR number, a VAT number may be used, if your institution is VAT registered.

   

Poster presentation & Welcome Reception

Please bring a poster on the 19th of August 2024 where the The Bioimaging Core Facility organises poster presentations along with informal catering. Participation is free of charge.

Poster dimensions: A0 upright are preferred

   

Practicalities

Please bring your own laptop every day.

   

Accomodation & Venue

> Accommodation will need to be organised by each participant. We are unfortunately unable to provide accomodation.

> Aarhus is a fairly small city with most accomodations within walking distance.

Public transportation in Aarhus

Tourist information Aarhus

Aarhus University Campus Map (in DK only; type in the building number/name in the search field)

> For Aarhus University app, download AU Find for iOS or Android

   

Certification

A workshop certificate will be sent by e-mail to participants, upon request, after the workshop.

Collaborators & Sponsors

Zeiss, Acquifer (Bruker)