Program

8:30-9:00 Registration and coffee

9:00-9:10 Welcome note

Fritjof Helmchen University of Zurich, Switzerland

9:10 - 10:40 Session 1 - Developers

Fabian Voigt  Harvard University, MA, USA
Expanding the bag of optical tricks for neuroscience

Nikita Vladimirov University of Zurich, Switzerland
The 10 years of mesoSPIM: lessons, updates and outlook

Simon Watkins University of Pittsburgh, PA, USA Keynote
Pushing the mesoSPIM to submicron resolution with chemistry and computing (online)

10:40-11:00 Coffee break

11:00 - 12:20 Session 2 - Tissue Clearing 

Anna Maria Reuss University Hospital Zurich, Switzerland
aDISCO - A Broadly Applicable Method for 3D Microscopy of Archival Paraffin-Embedded Human Tissues

Hei Ming Lai  The Chinese University of Hong Kong, HK
Customizing mesoSPIM-based workflows for clinical 3D tissue diagnostics (online)

Christophe Lamy University of Geneva, Switzerland
Human anatomy at the age of optical dissection

12:20 - 13:00  Lunch

13:00 – 13:50 Poster session, industry demos

13:50 - 15:30 Session 3 - Industrial solutions to imaging

Ando Zehrer  Teledyne Photometrics, Germany
The Iris15: Teledyne Photometrics contribution to the MesoSPIM initiative 

Jon Daniels Applied Scientific Instrumentation (ASI), USA
Modular Microscope and Automation Solutions

Ralf Kruse  Mitutoyo Europe
TAGLENS – Ultrafast Focus Shift by Sound

Otmane Bouchareb  INSCOPER, France
Imaging software solution for automated and smart microscopy

Nicolaas van der Voort   SVI Huygens, Netherlands
Powerful mesoSPIM image processing in the Huygens Software: a journey from Deconvolution, Fusion & Stitching to image visualization.

15:30-16:00 Coffee break

16:00-18:00 Session 4 - Microscopy methods
 
Kevin Dean University of Texas Southwestern, TX, USA
Navigate, MCT-ASLM, and Altair-ASLM: Intelligent, Multiscale, Easy-to-Assemble Light-Sheet Platforms

Prayag Murawala MDIBL, Bar Harbour ME, USA
Enhanced mesoSPIM for high-resolution mapping of brainstem locomotor circuits

Jenna Hanmer University of Nottingham, UK
Whole-brain imaging in rodents using MRI and light-sheet microscopy: A cross-scale, multi-modal approach

Adam Glaser Allen Institute, WA, USA   Keynote
New technologies for mapping centimeter scale tissues with nanoscale resolution (online)

18:00-19:30 Apero and get-together

8:30 - 9:00 Welcome coffee

9:00 - 10:20 Session 5 - Big data analysis and AI

Stephan Preibisch  HHMI Janelia, Ashburn, VA, USA
BigStitcher-Spark: Software for peta-scale alignment of light sheet microscopy acquisitions.

Alan Watson University of Pittsburgh, PA, USA
Automating mesoSPIM Data Postprocessing.

Dimokratis Karamanlis University of Geneva, Switzerland
LightSuite: A high-throughput pipeline for localizing experience in the cleared mouse brain

10:20 - 11:00 Coffee break

11:00 - 12:30 Session 6 - Data analysis solutions

Michael Mahlert Oxford Instruments / Bitplane 
Interactive 3D and 4D image visualization and high throughput analysis with Imaris

Michael Morehead  SyGlass
syGlass: Visualization, Annotation, and Communication of Very Large Image Volumes in Virtual Reality

Tamara Manuelian  ZEISS Research Microscopy Solutions
ZEISS Beyond Imaging: How to manage, explore & analyze your imagery with ZEISS Software Solutions

Joel Lüthi University of Zurich, Switzerland
Fractal: An open-source framework for reproducible bioimage analysis at scale using OME-Zarrs

12:20-13:00 Lunch

13:00 – 13:50 Poster session, industry demos

13:50 - 15:20 Session 7 - Applications

Esther Stoeckli University of Zurich, Switzerland
mesoSPIM facilitates the analysis of neural circuit formation

Laura Baudis University of Zurich, Switzerland
Looking for dark matter with colour centres

Christelle Langevin INRAE, University of Parìs-Saclay,  France
Advancing animal health with tissue clearing and deep tissue imaging

15:20-15:50 Coffee break

15:50 - 17:30 Session 8 - Applications 

Laura Batti  Wyss Geneva, Switzerland
Light-Sheet Microscopy: empowering advancement in neuroscience and medicine

Akanksha Jain  University of Zürich, Switzerland
Unveiling the choreography of human brain development: Longterm lightsheet imaging unveils morphodynamics in human brain organoids

Melvin Alappat  University of Zürich, Switzerland
Clearly sweet and painful: Investigating the effect of western diet on myelin homeostasis

Thomas Naert  University of Ghent, Belgium
Pythia: AI-predictable CRISPR-Cas9 editing meets mesoSPIM for visualizing precise genomic integrations and edits

17:30 - 17:40 Concluding remarks

Nikita Vladimirov

17:40-19:00 Apero and farewell.

Maker Day

Learn how to build, modify and troubleshoot your mesoSPIM
 

Stations

Station 1 (Y55-H12): Beam walking 

Station 2 (Y55-H12): Laser coupling into Kineflex fiber. Power measurement

Station 3 (Y55-H12): Disassembly and reassembly of BT-mesoSPIM excitation arms. Laser alignment into the arms. Introduction to the NI hardware

Station 4 (ZMB, Y44-J-33): Imaging with BT-mesoSPIM. Light-sheet alignment with a sample. Using the script editor eg for timelapse imaging

Station 5 (ZMB, Y44-J-33): Sample mounting 

Schedule

9:00-10:30 Session 1

Five groups on 5 stations

10:30-11:00 Coffee break  

11:00-12:30 Session 2

Five groups on 5 stations

12:30-13:30 Lunch  

13:30-15:00 Open source microscopy flash talks

15 min per talk. Room Y55-H12
Fabian Voigt (Harvard) 
Kevin Dean (UT Southwestern)
Sharon King (St Jude)
Nikita Vladimirov (UZH) 
Tchern Lenn (UCL) 

15:00-18:00 Wrap up

Drinks at Irchel bar