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Microscopy platform

The objective of the Microscopy Platform is to provide the appropriate tools to carry out the observation of both fixed and live samples. By using brightfield or fluorescence ("widefield" or confocal) microscopes, we are able to analyze the morphological and structural characteristics of cells, tissues, subcellular organelles and non-biological samples (e.g. nanoparticles), as well as to carry out different types of functional tests (e.g. protein-protein interaction, endocytic processes, calcium fluxes, etc.).


  • Cross-section of frozen specimens.
  • Selection of tissue structures by laser microdissection.
  • Conventional fluorescence microscopy.
  • Multidimensional widefield microscopy (equipped for mosaic capture and live experiments).
  • Confocal microscopy (available for both fixed samples and live cell experiments).

UAT staff offers training in the independent operation of the equipment, assistance during the performance of experimental techniques, as well as support in experimental design and in interpretation and analysis of the images.

You can contact us at:


  • Sample preparation:
    • Precise sectioning of frozen tissue (cryostat) for subsequent dyeing and observation.
    • Isolation and recovery of cellular and subcellular structures by laser microdissection.
  • General applications of wide-field microscopy:
    • Analysis of structural and morphological features of cells and tissues. In particular, the Thunder multidimensional microscope allows:
      • "Time-lapse" acquisition for live cell imaging (slow and fast dynamics).
      • Multidimensional acquisition: multichannel serial acquisitions [XYZ tn].
      • Fast acquisition and mosaic reconstruction, useful for large sample sizes.
      • Computational clarification method: generation of high-resolution/high-contrast images of thick samples with instantaneous removal of image blurring due to defocusing.
  • Confocal microscopy applications (in vitro/in vivo):
    • Linear analysis of spectral mixtures in samples labeled with various fluorochromes.
    • Functional studies of cell dynamics (in vivo): endocytosis, calcium fluxes, cell contraction, cell cycle, etc.
    • Colocalization analysis, with a particularly useful high-resolution imaging option (lateral resolution up to 120 nm).
    • Reconstruction of three-dimensional structures (thick tissue slices, spheroids, organoids) with high-resolution mosaic acquisition images (XY) and Z-stacks.
    • "High screening counting" for quantitative or colocalization studies where statistical information and high resolution are required.
    • High-resolution analysis of subcellular structures, and exosomes.
    • Imaging of nanoparticles.


  • Preparation of samples:
    • Leica CM3050 cryostat. Precise sectioning (from 0.5 to 300 μm) of frozen samples (self-service).
    • Leica LMD 6000 laser microdissection system. Technical specifications are available here.
  • Conventional fluorescence microscopy combined with digital cameras and image acquisition software.
    • Olympus BX61 upright microscope (for slides). Technical specifications are available here.
    • Leica DM-IRB inverted microscope (for cell culture/slide holder). Technical specifications are available here.
  • Thunder Imager 3D Cell Culture multidimensional widefield microscope (Leica).
  • Main applications: the capture of temporal dynamics in live cells, mosaics, and acquisition of three-dimensional samples with instantaneous out-of-focus signal processing and/or deconvolution. Technical specifications are available here.
  • Confocal microscopy:
    • Olympus FV1000 spectral confocal microscope (Olympus). Technical specifications are available here.
    • Zeiss LSM980 spectral confocal microscope equipped with 32-channel spectral detector, AiryScan 2 super-resolution detector, and incubation system for live experiments. Technical specifications are available here.
  • Three offline workstations for image viewing and processing, accessible both on-site and remotely. Open source software (Image J/Fiji) and generic commercial software (Imaris), as well as specific software from different commercial houses (Olympus Fluoview, Zeiss ZEN and Leica LAS X, with different analysis modules).