Advanced Lightsheet Imaging Center

Full service lightsheet imaging platform, from sample clarification to 3D VR visualization.

ALICe images

Who we are

ALICe is a full-service imaging platform that integrates a series of innovative fluorescence microscopy tools into a single pipeline. The platform images whole organs at high temporal or spatial resolution and allows 3D data exploration and analysis in a virtual reality (VR) environment.

We are a multidisciplinary team including physicists, neuroscientists, biologists and engineers.

The center is based at Campus Biotech and is under the scientific supervision of Professor Anthony Holtmaat (UNIGE), Professor Christian Lüscher (UNIGE) and Professor Grégoire Courtine (EPFL).

The ALICe Team. From L to R: Dr. Laura Batti, Dr. Stéphane Pagès, Audrey Tissot, Dr. Gilles Reymond, Dr. Corinne Brana.
Credit: Newton Cho – Courtine Lab (EPFL) and microscopy staff.

Our capabilities

ALICe includes the latest tools and technologies:

  • Tissue clearing
  • Imaging tools for large cleared samples
  • Workstation and software for 3D big data exploration and analysis
  • VR tools to interactively explore and analyze 3D datasets

Microscopy facility staff are available to help develop tailored solutions as required.

Tissue Clearing

We offer a tissue clarification service based on the CLARITY protocol. Two X-CLARITY tissue clearing systems from Logos Biosystems are available to researchers.

We have recently expanded our service to support users with existing DISCO-based clarification protocols.

Imaging with mesoSPIM

This custom built lightsheet microscope, developed in Fritjof Helmchen’s lab at the University of Zurich (UZH), is optimized for large scale screening of cleared samples at cellular resolution at high temporal resolution (10 min for a whole mouse brain). For more details see the mesoSPIM datasheet.

Find out more at at Campus Biotech developed by Fabian Voigt in Fritjof Helmchen’s Lab (UZH).

Imaging with Clarity Optimized Light-sheet Microscope (COLM)

This custom built lightsheet microscope (originally developed by Raju Tomer in Karl Deisseroth’s Lab – see is optimized for large scale clarified tissues. It offers neuroscientists a unique opportunity to capture high spatial resolution (diffraction-limited lateral resolution), whole brain fluorescence images without perturbing neuronal architecture. For more details, see the COLM datasheet.

Clarity-Optimized Lightsheet Microscope at Campus Biotech (modified from original Raju Tomer’s design).

Imaging with LSM-880 clarity module

We offer a specific module for imaging cleared tissue sections or organoids using Zeiss LSM880 confocal microscope.

A custom-built tissue holder combined with a clarity objective and sensitive detectors allow researchers to scan their cleared samples at high spatial resolution in a confocal system.

3D and VR large data-set exploration

We provide high end and efficient software solutions for 3D lightsheet data visualization and analysis, and exploration in a virtual reality environment.

FIJI, Terastitcher, Imaris, Arivis and Syglass are included in our workstations.


The VISTO VR integrated volumetric visualization and analysis tool.

How we work

ALICe is a pay for service platform – available to anyone from both academia and industry, worldwide.

You can submit your details in the application form.

Application form

Main contacts:

ALICe scientific coordinator: Stéphane Pagès, PhD

ALICe microscopy facility manager: Laura Batti, PhD

If you would like to find out more, please contact us:

ALICe images

A selection of representative images from the Wyss Center’s lightsheet microscopes:

ALICe images


Publications by the ALICe team:
Cell Reports, 2020, Neuroinflammation-Associated Aspecific Manipulation of Mouse Predator Fear by Toxoplasma gondii
Nature Methods, 2019, The mesoSPIM initiative: open-source light-sheet microscopes for imaging cleared tissue
Nature neuroscience, 2018, Cortico-reticulo-spinal circuit reorganization enables functional recovery after severe spinal cord contusion
Proceedings of the Lightsheet Microscopy Workshop, 2018, edited by the ALICE team and published as a Frontiers Research Topic: Lightsheet Microscopy: from technological developments to prospective applications

Publications that include data from ALICe:
Human Brain Mapping, 2020, Hippocampal segmentation for brains with extensive atrophy using three-dimensional convolutional neural networks 
Nature, 2018, Required growth facilitators propel axon regeneration across complete spinal cord injury
Journal of Neural Engineering, 2018, Multilayer 3D electrodes for neural implants
Nature, 2018, Stochastic synaptic plasticity underlying compulsion in a model of addiction


Meet the ALICe team presenting at these events

RISE Imaging opening meeting – IGBMC, 2020

12th FENS Forum of Neuroscience, 2020

CTLS 2020, Lisbon

mesoSPIM workshop March 2020, Zurich

Light Sheet Microscopy Conference 2019

BioAlps Networking Day 2019

Brainhack Geneva

7th Swiss Microscopy Core Facility Day

International European Light Microscopy Initiative Meeting, 2019

March 2018, Campus Biotech, Geneva
Wyss Center lightsheet microscopy workshop (First Edition)

April 2019, Irchel Campus, UZH Zürich
Swiss Light-sheet Microscopy Workshop (Second edition)

Where we are

We are based at Campus Biotech, Geneva.

ALICe is embedded in the Wyss Center’s Microscopy Facility, part of the Preclinical Neuroscience Platform (PNP), at Campus Biotech.

brain imaging
Credit: Microscopy Staff and Holtmaat Lab, UNIGE

Get in touch

We welcome informal enquiries.

Contact Stéphane Pagès or Laura Batti to find out more.

Contact us