Swiss Light-sheet Microscopy Workshop 24-25 Apr 2019
Irchel Campus, UZH Zürich

UPDATE 29.04.2019

Thanks to all participants, speakers, companies and involved people, we had a great meeting last week!

Please write to if you need a Certificate of Attendance.

Keep you eyes open for the meeting last year, we might have heared something through the grape wine;)





UPDATE 18.04.2019


The Meeting is coming closer! Click following link to download the Meetings Booklet:


Happy Easter and see you soon!



UPDATE 3rd April 2019


  • The Demo session on thursday evening will allow registered participants to see the various microscopes in action.
  • We have recieved many requests for imaging own samples on the mesoSPIM and due to time restrictions, please note that we can not accept more samples to be imaged on Friday 26th.
  • So far we still have room for the Zeiss Z1 Microscope, please write to if you plan to bring samples suitable for this microscope.
  • In general, all participants that have registered for friday can join the imaging sessions that will happen throughout the day on samples brought here by workshop participants


UPDATE 12th March 2019:



To all participants who have submitted an abstract:

We will select 5 speakers among all submitted abstracts and inform those that are selected via email in the coming days.

If you are not selected but have submitted an abstract we look forward to your poster presentation. Our poster boards are 180 x 135 cm (landscape-format) with no further poster guidelines.



The aim of the event is to strengthen the local and international network and facilitate the exchange of ideas between the lightsheet users and developers.


Kishan Dholakia University of St. Andrews
Jan Huisken MIR, Madison
Lars Hufnagel EMBL, Heidelberg
Florian Jug MPI-MCBG, Dresden
Daniel Kirschenbaum USZ, Zurich
Prisca Liberali FMI, Basel
Christian Mosimann UZH, Zurich
Stéphane Pagès Wyss Center, Geneva
Francesca Peri UZH, Zurich
Paola Perin University of Pavia
Stefan Preibisch MDC, Berlin
Nicolas Renier ICM, Paris
Raju Tomer Columbia University, New York
Fabian Voigt UZH, Zurich

Day 1 - 24 April 2019

New technology developments in lightsheet microscopy • The latest applications in lightsheet microscopy • Sample preparation including clearing techniques and immunolabelling • Data visualization and analysis • New approaches in post-processing


Registration – coffee and croissants



Fritjof Helmchen, Brain Research Institute, UZH

Urs Ziegler, Center for Microscopy and Image Analysis, UZH

Morning Session

Chair: TBA


Kishan Dholakia: "Enhancing Light Sheet Microscopy using shaped light and sound"

University of St. Andrews


Nikita Vladimirov: Multiview light-sheet microscopy in microfluidic device using a deformable mirror

Max-Delbrueck Centre, Berlin


Prisca Liberali: Self-organization in intestinal organoid development

Friedrich Miescher Institute, Basel


Jonathan T.C. Liu: High-throughput nondestructive anatomic 3D pathology with open-top light-sheet microscopy

University of Washington, Seattle, USA


Keynote lecture

Raju Tomer: Towards quantitative imaging of large cleared samples with Light Sheet Microscopy

Columbia University


Lunch - Poster session – Company Exhibitions - Y-Lichthof

Afternoon session

Chair: TBA


Francesca Peri: Brain imaging across scales: studying neuronal-immune interactions during the development of the CNS

University of Zurich


Daniel Kirschenbaum: "3D histology of Alzheimer disease"

University Hospital Zurich


Ruman Gerst: MISA++: A modular and high-performance framework for analysis of light sheet microscopy images

Leibniz Institute for Natural Product Research and Infection Biology - HKI Center Jena


Keynote lecture

Nicolas Renier: Scaling analysis tools to map intact adult mouse brains using light sheet microscopy

ICM - Brain and Spine Institute, Paris


Coffee break and networking - Y-Lichthof

Afternoon session: Post-processing and data analysis

Chair: TBA


Stephan Preibisch: BigStitcher: Reconstructing high-resolution image datasets of cleared and expanded samples

Max-Delbrück-Centrum, Berlin


Carlo Beretta: "One software to bring them all...": Bridging Open Source and Commercial Software with Arivis Vision4D and InViewR.

CellNetworks, Math-Clinic, University Heidelberg. Application talk (Arivis)


Florian Jug: Content-Aware Image Restoration for Light and Electron Microscopy

Max Planck Institute, Dresden


Wine & Cheesse - Poster session - Company Exhibition


Day 2 - 25 April 2019

New technology developments and the latest applications in lightsheet microscopy • Company presentations • Hands-on sessions and practical demonstrations with the custom lightsheet microscope developed by Fabian Voigt • Demonstrations of virtual reality visualization of lightsheet data

Morning Session

Chair: TBA


Lars Hufnagel: TBA

EMBL, Heidelberg


Fabian Voigt: The mesoSPIM Initative



Maëva Luxey: Seeing is believing: a light sheet microscopy atlas of the developing vertebrate limb

DUW Zoology, University of Basel


Paola Perin: Three-dimensional imaging and segmentation of the rat choroid plexus

University of Pavia


Stéphane Pagès: Development of a full service imaging platform – from sample clarification to 3D VR visualization

Wyss Center, Geneva


Coffee break and networking – Y-Lichthof


Alvaro Gomariz: A Convolutional Neural Network-Based Pipeline for the Characterization of Large Bone Marrow Images in 3D Microscopy

University Hospital and University Zurich and ETH Zurich


Marleen Gloger: Defining cell proliferation triggers and dynamics during lymphangiogenesis

Uppsala University, Sweden


Keynote lecture

Jan Huisken: Flamingo: a customizable and shareable light sheet microscope


Morgridge Institute for Research, Madison


Lunch - Poster Session - Company Exhibitions

Afternoon session



Mathias Pasche-Drews: Advances in back-illuminated Scientific CMOS technology.



Peter Zehetmayer: Big Image Data - Storage, Processing and Analysis with Local Private Cloud Computing.



Oliver Bauhofer: X-CLARITY Tissue Clearing System: Accelerate your tissue clearing without loosing structure or function.



Sebastian Konrad: "And in the arivis Platform find them all": Image Analysis with Machine Learning, interfaces to Open Source and Virtual Reality for fast and efficient quantification of 4D image data.



Monika Löschinger: Luxendo Light Sheet Microscopes - born from research, made for all.

Luxendo (bruker)


Michael Desert & André Jelicic: Solution for high compression rate, efficient transfer and archiving of light sheet microscopy imaging.

Dotphoton, Geneva University


Dieter Goehlmann: Imaris Solutions for Big Data



Wolf Heusermann: The A-Z of Cubic clearing protocols for various tissue

Biozentrum Basel Application talk (Zeiss)
15h45 Closing remarks F. Helmchen


Coffee break and networking



Time reserved for demos by companies



Day 3 - 26 April 2019

Hands-On Session

For registered participants for day 3 we offer the opportunity for users to bring their own samples and image/ analyse them with the support of the experts on the system. Schedule of individual time-slots for day 3 will be announced during the meeting.

We have following microscopes for testing:

- the mesoSPIM exclusively for cleared samples (CLARITY, CUBIC, iDISCO, BABB) with labels excitable by laserlines: 405, 488, 515, 561, 594 and 647 nm

- Zeiss Z.1 for samples in regular water based buffers (e.g. zebrafish) for fluorophores excitable by laserlines: 405, 445, 488, 561 and 638 nm.

ZEISS Lightsheet Z.1

- Luxendo InVi SPIM. The InVi SPIM offers precisely controlled environmental conditions, maximized photo-efficiency and short illumination times for long-term 3D imaging of cell culture applications and small embryos at the subcellular level.
- Luxendo MuVi SPIM. The MuVi SPIM features a unique 4-axis concept that enables four orthogonal views of the specimen without the rotation of the sample. The simultaneous acquisition from two sides brings unparalleled acquisition speed, correction of shadowing effects and high precision of data fusion. It is optimal for imaging large gel-embedded samples or cleared samples.

For data visualization and analysis:

- Arivis Analysis Software software for visualization, sharing, analysis and presentation of multi -channel 2D, 3D and 4D image data of almost unlimited size.

Please check again here for updates on how we will deal with data handling (i.e. prior upload, SSD, Cloudservice)