Microscopy

Overview

The facility provides state-of-the-art imaging equipment and expertise for the most demanding research projects from subcellular events to cell dynamics in organs. We also offer support and courses for students and researchers.

Manager

Diego Morone
diego.morone@irb.usi.ch
+41 58 666 7039

Equipment

Confocal and Super-resolution microscope
- Leica Stellaris 8 STED FLIM is a fully equipped confocal and super-resolution microscope, with flexibility to acquire whole-mount tissues and organoids, tissue and organoid slices, or fixed and live cells. Spectral scanning and lifetime capabilities allow the separation of fluorophores with overlapping emission spectra. Super-resolution STED 3D module can down to 50 nm resolution (XY). Fluorescence lifetime (FLIM) module provides reliable FRET and ion sensing quantifications.
  
  Key technical features
  – 405 nm laser
  – White Light Laser with all laser lines 440-790 nm
  – Confocal objectives 10x, 40x, 63x
  – 5 Power HyD photon counting detectors
  – Transmitted light brightfield
  – Piezoelectric Z-stage for fast 3D live imaging and tissue reconstructions
  – Galvo and resonant scanner 8 kHz
  – STED module with depletion lasers 660nm and 775nm for super-resolution up to 50 nm in all axis, highly-corrected 100X/1.4 oil and 93X/1.3 glycerol objective with motorized collar
  – FLIM module
  – FRAP module
  – Leica deconvolution module
  – Spectral scans both in excitation and emission
  – Eppendorf Femtojet injector
- Leica Stellaris 5, is a routine confocal microscope with motorized stage for acquisition of fixed tissues and organoids and fixed cells. Spectral scanning and lifetime capabilities allow the separation of fluorophores with overlapping emission spectra. Microscope integrates a deconvolution module for improving resolution.
  
  Key technical features
  – 405 nm laser
  – 448 nm laser
  – White Light laser with all laser lines 485-790 nm
  – Objectives from 4x to 63x
  – 5 Power HyD photon counting detectors
  – Transmitted light brightfield and DIC
  – Motorized stage
  – Piezoelectric Z-stage for fast tissue reconstructions
  – Leica deconvolution module

Wide-field microscopes
- Molecular Devices ImageXpress Micro 4 is a fast wide-field automated microscope for high-content screens and long-term live imaging in plates. It can acquire a 96-well plate with 3 colors in about 15 minutes, has a room-temperature robot for loading plates and supports automated analysis.
  
  Key technical features
  – 5 fluorescence channels
  – Transmitted light brightfield and phase contrast
  – Objectives from 4x to 40x
  – Automated stage with autofocus system
  – Incubator for long-term live imaging
  – Room-temperature loading robot for automated acquisition of up to 45 plates
  – Image segmentation and quantification modules integrated in the software
- Nikon Eclipse E800 upright widefield microscope is a simple and easy fluorescence microscope.
  
  Key technical features
  – 4 channels
  – Transmitted light
  – Objectives from 4x to 100x
  – Ds-Fi3 RGB and monochrome camera
  – Manual stage
- Leica Thunder is a versatile widefield microscope with a motorized stage and live cell imaging support. With Thunder deconvolution algorithms it provides gentle illumination and optical sectioning capabilities close to confocal microscopy.

Light-sheet microscope
- Bruker TruLive 3D is an an open-top, multi-chamber light sheet microscope for fast 3D reconstruction of organoids. It can follow multiple samples over the course of many days, tracking growth, cell-to-cell dynamics and interactions. Its flexibility in changing the magnification, its fast 3D acquisition speed and the integration of a precise photomanipulation laser for optogenetics and photoablation make it a very versatile platform for live 3D imaging.

Key technical features
– Imaging lasers 405, 488, 561, 642 nm
– Photomanipulation laser two-photon 920 nm
– Sheet thickness from 1.5 µm to 2.2 µm
– Magnification changer from 12.5x to 50x
– Uniform illumination module
– Destriping module
– Mosaic module
– Sample tracking module
– Python-controllable API for feedback microscopy

Multi-photon microscope
- LaVision BioTec TriM Scope II combines an upright and inverted microscope equipped with two tunable pulsed NIR lasers and OPO for multi-color simultaneous imaging on up to 5 channels.

Key technical features
– 2 Chameleon Coherent tunable lasers 690-1040 nm
– Coherent OPO 1000-1300 nm
– Double-headed upright and inverted
– 3 EOMs for photomanipulation
– Objectives 4x to 100x
– 5 GaAsP detectors for each side
– Incubator
– Python-controllable API for feedback microscopy

- Microscopy4d remote analysis workstation for demanding image analysis tasks and 3D analysis.
  Key technical features
  – 2 AMD Epyc CPUs
  – 512 GB RAM
  – 2x Nvidia A10 GPUs
- Igea10 remote analysis workstation for analysis of HCS data, imaging cytometry data and for 2D image analysis with open-source software.
  Key technical features
  – Intel Xeon Gold
  – 64 GB RAM
  – Nvidia A400 GPU
  
  Analysis WorkstationsWorkstation with Wacom tablet for manual image segmentation tasks and VR goggles for visualization of complex 3D images and time lapses. Key technical features
- – 2 XEON E5 CPUs
  – 256 GB RAM
  – Nvidia Quadro A400 GPU
  – Wacom tablet
  – Meta Quest VR goggles
- MetaXpress Powercore server for batch analysis of HCS data
- Linux server with NVIDIA RTX 2060 GPU.

With these systems, we can perform most cell and tissue imaging procedures, such as mosaic reconstructions of tissues and organoids, STED, fast live-cell and organoid imaging, FRAP, photoconversion, FLIM-FRET, and 3D reconstruction on unclarified and clarified tissues. Images with these techniques can also be combined with Electron Microscopy micrographs in Correlative Electron Microscopy (CLEM).

Support

Assistance in experimental design
Individual training on all instruments
Assistance during the whole imaging workflow, from the acquisition to image analysis
Support on image analysis, deconvolution, and 3D reconstruction
Software used for image analyses:
- Open software: ImageJ/FIJI, R, CellProlifer, napari, ilastik, QuPath
- Commercial software: Autoquant X3, MATLAB, MetaXpress, Imaris, arivis Pro with VR module.

Courses

Theoretical foundations of microscopy for biological applications
Fundamentals of Image analysis
Modern Advanced Confocal Microscopy, jointly organized with the University of Bern
Image Restoration in Light Microscopy, jointly organized with the Universities of Bern and Fribourg

The facility is also open to collaborations, such as the development of new tools, techniques and analysis software. An example is LysoQuant.

Istituto di Ricerca in Biomedicina

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