Get Started with Tissue Clearing

July 11 - 13 | Basel & Online

Optical clearing is needed in the microscopy toolbox to tackle the problem that biological tissue isn’t transparent. Together with the  IMCF Basel we are hosting for the first time a Workshop dedicated to  the topic of Tissue Clearing.
Join us in Basel or online and explore this rapidly expanding technology!

From July 11 – 13 you will get the chance to dive deep into one clearing technique, get a theoretical introduction and learn more about various applications. We are very happy to have specialists for ECI Clearing, Cubic Clearing & Smart Clearing that will share their experience with us.

The workshop consists of lectures (online/offline) as well as a hands-on workshop where you will be able to execute the process of tissue clearing and sample imaging yourself over the course of three days. Depending on your interest and on your location, you can decide to attend the lectures and / or can practice tissue clearing yourself in our hands-on workshop.
You will find the program and further info below.

We are looking forward to an interesting workshop with you!

Lecture Sessions (Onsite & Online) July 11 - 12
Program | July 11


The Art of Clearing:

  • What is Light?
  • Light and Matter – How do they interact?
  • Some Methods of Tissue Clearing

Jacques Paysan


2ECi tissue clearing to recapitulate the human dopaminergic system in brain organoids

  • 2ECi (dehydration + Ethyl cinnamate RI matching) tissue clearing 
  • Brain organoids
  • Reconstruction of neuronal morphologies 
  • Human dopaminergic system


Daniel Reumann


The LifeCanvas 3D Histology Pipeline

  • SHIELD Tissue preservation
  • Clear+ Tissue delipidation/clearing
  • Active immunolabeling with SmartBatch+
  • Lightsheet imaging
  • Data Analysis and management

Brian Nyguen


End of Day 1 | Coffee Break


Program | July 12


Seeing is Believing!

  • Whole-mount Immunostaining on “big” samples
  • Lightsheet imaging
  • Data Analysis: 3D reconstruction and Surface rendering
  • Development of Neuromuscular system

Maëva Luxey 


Invisible samples: A challenge for microscopy

  • Lightsheet imaging
  • Confocal imaging
  • ScaleS clearing
  • Spinal cord regeneration in zebrafish

José Rino


Round Table

  • Clearing questions, troubleshooting

speakers from day 1 & 2, workshop organisers

Hands-On Workshop

July 11 - 13

The workshop will take place in three different groups. Each group is working with a different solution. The groups are limited to 4 persons / group. The allocation to the groups will be done by the organisers of the workshop accordingly to your field of work.


  • Group 1: ECi
  • Group 2: Cubic
  • Group 3: SmartClear

Program, July 11


Welcome Coffee & Registration


Group Organizsation


Hands-On Session 1:
Protocol Discussion & Solution Preparation

  • CUBIC L: solution preparation
  • ECi: dehydration 1
  • LC: prepare delipidation buffer-start incubation


Lunch Break


Lecture Session 1


Coffee Break


Hands-On Session 2:

  • Cubic L: photos
  • ECI: dehydration 2
  • LC : prepare machine and sample installation - start machine

Program, July 12


Hands-On Session 3:

  • ECi: sample in next dehydration solution
  • Cubic: prepare Cubic RA
  • LC: prepare Easy Index- incubate sample in Easy Index



Coffee Break



Lecture Session 2



Lunch Break


13:30 - 15:30

Hands- On Session 4:

  • Cubic: embedding and Cubic RA immersion
  • ECi: dehydration final step
  • LC: sample mounting


17:30 - 18:00

  • ECI: immersion in ECI


Program, July 13


Imaging Rotation: Organoids


Imaging Rotation: Mouse Tissue section




Imaging Rotation: Embryos


Concluding remarks

Watch the Recording

Lecture Session 1 & 2

The recording will follow soon.

Day 1 | July 11:
Day 2 | July 12:
Workshop Location

University of Basel

Spitalstrasse 41
4056 Basel
Room 07.Q4



Do you have questions? We will be happy to help!

Wolf Heusermann
+41 (0) 55 25 47 366
wolf .heusermann @zeiss .com

Department of Biosystems Science and Engineering



Jacques Paysan

Jacques started his career as a biologist with his diploma thesis at the MPI for Developmental Biology in Tübingen, and received his Ph.D. in 1995 from the University of Zürich. After his postdoc at the University of California San Diego (UCSD) he performed 11 more years of academic research in Neuroscience until he joined ZEISS as an application specialist for superresolution and lightsheet microscopy in 2007.

Daniel Reumann

Daniel is doing his PhD in the laboratory of Jürgen Knoblich in the Institute of Molecular Biotechnology Austria (IMBA) at the Austrian Academy of Science (OEAW) and is interested in understanding how brain regions start to interact with each other. For this, he started working on neuronal migration (particularly interneuron migration) and is now investigating how brain regions start to interact with each other, with a focus on the human dopaminergic system.

Maëva Luxey

Maëva is interested in the Development, Plasticity and Evolution of tetrapod limbs. She is developing whole-mount immunostaining to visualize the different component of the neuromuscular system in tetrapod limbs but also other proteins involved in limb patterning such as transcription factors and morphogens. She obtained her PhD in Molecular, Cellular and Developmental Biology from the University of Toulouse and worked as a postdoctoral fellow in the  McGill University (IRCM, Montreal). From 2017, she moved as a Project Leader in the laboratory of Patrick Tschopp (DUW, University of Basel) where she developed whole mount immunostaining and light sheet imaging.

Brian Nguyen

Brian is developing tools to maximize the applicable scope of LifeCanvas technologies. He received his PhD in Mechanical Engineering from the University of Toronto and conducted postdoctoral training at McGill University. In his research career, Brian has developed technologies to increase experimental throughput and provide new ways of analyzing samples.

José Rino

José graduated in Technological Physics Engineering from Instituto Superior Técnico, Technical University of Lisbon in 1999 and joined the lab of Prof. Maria Carmo-Fonseca at the Faculty of Medicine, University of Lisbon in the same year for his PhD, which was focused on the study of dynamics and interactions of nuclear proteins with quantitative photobleaching microscopy.José's postdoctoral research, carried out at the Instituto de Medicina Molecular (IMM) in the lab of Prof. Carmo-Fonseca, focused on applying quantitative microscopy methods to study mRNA biogenesis. José is currently Head of the Bioimaging Unit at the Instituto de Medicina Molecular João Lobo Antunes.