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.
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.
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 mesoSPIM.org
Imaging with Clarity Optimized Light-sheet Microscope (COLM)
This custom built lightsheet microscope (originally developed by Raju Tomer in Karl Deisseroth’s Lab – see tomerlab.org) 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.
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.
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.
ALICe scientific coordinator: Stéphane Pagès, PhD
ALICe microscopy facility manager: Laura Batti, PhD
A selection of representative images from the Wyss Center’s lightsheet microscopes:
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
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.