State-of-the-art advanced lightsheet imaging center
Lightsheet microscopes can reveal the 3D anatomy of entire small organs. They image brain tissue down to individual neurons and offer unprecedented maps of nervous system structure and function.
ALICe, the Advanced Lightsheet Imaging Center, integrates a series of innovative fluorescence microscopy tools in a single pipeline to image whole organs with custom-built microscopes at high spatial and temporal resolution.
The multidisciplinary ALICe team unites expertise from physics, cell biology, neuroscience and engineering, and joins forces with research teams around the world to image and draw insights into the central and peripheral nervous systems, innervation of organs including the brain and heart as well as human brain samples. Another focus area is brain and spinal cord organization for researchers working to restore movement after paralysis or to investigate neuronal networks involved in cognition, pleasure and drug addiction.
Unlike traditional microscopy in which specimens are cut in slices with a blade before being viewed on a slide under a microscope, lightsheet microscopes optically slice samples with a sheet of light. This optical sectioning captures slivers of image without damaging the sample. The images are then combined to reconstruct a detailed three-dimensional image of a whole organ or specimen.
The ALICe pipeline
ALICe’s capabilities cover the entire pipeline, from sample preparation to image capture and post-processing. A variety of samples can be imaged from organoids to whole organs, labelled with genetically encoded fluorescent proteins or immuno-labeled with fluorescent antibodies.
1) Sample preparation: Tissue clearing for entire large samples
2) Custom-built lightsheet image acquisition: high spatial and temporal resolution imaging
3) Image and data analysis including 3D data-set exploration in virtual reality
Building connections, one cell at a time
Prof. Holmaat, Unige"Recent advances in microscopy have propelled the neurosciences into the era of connectomics, now allowing us to study single neurons with their synaptic connections in the whole brain."
Prof. Daniel Huber, Unige"The work at ALICe allowed us to reveal the distribution and anatomy of sensory receptors with unprecedented resolution and specificity. I was stunned by the quality of the images."
Prof Fyhn - UiO"Never before have we been able to visualise and quantify, in-depth, neuronal populations within the entire brain as we can now."
Mar 2021 Frontiers in Synaptic Neuroscience
Output-specific adaptation of habenula-midbrain excitatory synapses during cocaine withdrawal, Clerke, J., Preston-Ferrer, P., Zouridis, I.S., et al.*↗
Jan 2021 Nature
Neuroprosthetic baroreflex controls haemodynamics after spinal cord injury, Squair, J.W., Gautier, M., Mahe, L. et al.↗
Jan 2021 Frontiers
Mass Generation, Neuron Labeling, and 3D Imaging of Minibrains, Govindan, S., Batti, L., Osterop, S., et al.*↗
Dec 2020 (preprint)
DEVILS: a tool for the visualization of large datasets with a high dynamic range, Guiet, R., Burri, O., Chiaruttin, N., et al.↗
Sep 2020 arXiv (preprint)
Quantifying the effect of image compression on supervised learning applications in optical microscopy, Pomarico, E., Schmidt, C., Chays, F., et al.*↗
Jul 2020 Gene Therapy
Maximizing lentiviral vector gene transfer in the CNS, Humbel, M., Ramosaj, M., Zimmer, V. et al.↗
Jan 2020 Cell Reports
Neuroinflammation-associated aspecific manipulation of mouse predator fear by toxoplasma gondii↗
Dec 2019 Nature Communications
Multimodal image registration and connectivity analysis for integration of connectomic data from microscopy to MRI, Goubran, M., Leuze, C., Hsueh, B. et al.↗
Sep 2019 Nature Methods
The mesoSPIM initiative: open-source light-sheet microscopes for imaging cleared tissue, Voigt, F.F., Kirschenbaum, D., Platonova, E. et al.↗
Mar 2019 Front. Neuroanat - Research Topic
Light Sheet Microscopy: from technological developments to prospective applications↗
Apr 2018 Nature Neuroscience
Cortico-reticulo-spinal circuit reorganization enables Ffunctional recovery after severe spinal cord contusion↗
Study contributes to our understanding of how cocaine withdrawal affects brain circuits
The results could help clinicians understand addiction and enable people to better manage substance withdrawal.Collaboration
Shining a light on neurodegenerative disorders
Could a ray of light stop rogue proteins in their tracks and slow the spread of neurodegenerative disease in the brain? EPFL and the Wyss Center are set to find out.Collaboration
Peeking inside ‘mini-brains’ could boost understanding of the human brain in health and disease
Revealing details of the internal structure of ‘mini-brains’ could help accelerate drug studies and may offer alternatives to some animal testing.Collaboration