Light Microscopy Facility

The Advanced Light Microscopy Facility (ALMF) provides a collection of state-of-the-art light microscopy equipment and image processing tools, from standard wide-field microscopes to confocal microscopy systems, covering most of light microscopy applications.

The unit has the mission of providing service to researchers from CABIMER and associated laboratories as well as to visitors from other research institutes. We also contribute for the development of research projects and promote the cooperation between groups.

The unit is equipped with two confocal microscopes, one of which is designed for in vivo purposes, with 5 laser lines, an optional resonant scanner, a heating incubator and a humidifier column for efficient CO2 administration if required. The other confocal system, with 3 laser lines, is optimized for image acquisition of specimens, fixed or not, that do not required a specific environmental incubation.
Shortly, the facility will provide an offline unit with great capacity for processing, quantification and analysis of images, 3D simulation, video preparation, etc.
Additionally, the ALMF is developing a laser microdisection/microablation workstation, which will be available to users soon.

The facility is also equipped with a wide-field fluorescence inverted microscope for live imaging, with a heating stage and incubator, and CO2 supply. This system is connected to a Hamamatsu ORCA-ER camera for image acquisition.

This unit offers advisement for the manipulation and preparation of the specimens, fluorophores to choose, labels, markers, optimization of image acquisition, etc., and also for the processing, quantification and posterior analysis if required.

Services provided

  • Assisting all CABIMER groups and visitors through the microscopic imaging process: project planning, sample preparation, microscope selection and use, image processing and quantification using specific softwares, presentation, data transfer and storage.

Available applications

Laser Scanning Confocal microscopy
  • Multichannel fluorescence imaging + transmission imaging
  • 3D imaging and reconstruction
  • Multidimensional in vivo timelapse experiments
  • Fluorescence Recovery After Photobleaching-FRAP
  • Fluorescence Loss In Photobleaching-FLIP
  • Photoswitching
  • Photoactivation
  • Fluorescence localization analysis
  • Fluorescence Resonance Energy Transfer-FRET
Widefield microscopy
  • Multichannel fluorescence imaging + transmission imaging
  • Multidimensional  imaging and deconvolution
  • in vivo timelapse experiments
Microdissection microscopy (under development)
  • In vivo microdissection/microablation: Laser tweezers and Laser scissors
Offline processing unit (soon available)
  • Colocalization analysis
  • Granularity
  • Cell cycle studies
  • Apoptosis analysis
  • Particles tracking
  • Intensity histograms and graphics
  • Video preparation/in vivo analysis
  • Multichannel intensity quantification for advanced microscopy (FRAP, FLIP, FRET)


Microscopy equipment in Cabimer


Specimen requirements

Biological specimens are manipulated by researchers, using different protocols of fluorescence labelling in both: in vivo time-lapse imaging and fixed specimens, which are treated through inmunofluorescence techniques.

In order to choose the best fluorescent markers for your experiment, there are different websites where you can check the excitation and emission spectra and decide the best combination of markers for your experiment and according to our equipments:


Specimens to be observed by confocal microscopy should be flattened and mounted in fluorescence free medium with a coverslip of 0.17mm or No. 1.5 thickness; to optimize the sample to the objectives working distance, and reduce spherical aberrations.

In the case of observation of live cultured cells, the samples should be contained in a glass bottomed dish, with 0.17mm or No. 1.5 glass thickness, and in a red-phenol free culture medium.
Glass bottomed dishes for life imaging can be provided by the Microscopy unit.

Functioning of the Microscopy Unit:

If you require to use any of our confocal microscopes, please make a booking contacting the Responsible of the Unit (include here the link), giving your name and contact telephone. Bookings should be done at least 48 hours in advanced.

The external use booking for the confocal microscopes is from 15 to 17 hours on Wednesdays each week. In all cases, the Responsible of the unit will control the microscope and software when assisting external users.

If you require using any other equipment, please contact the Responsible of the unit.