Laser Confocal and Multidimensional in vivo Microscopy Facility provides scientific-technical support on any topic related to optical microscopy  with "samples size from centimeter to nanometer. 

Since 2013 Facility has been granted with the ISO9001 certificate by AENOR 9001:2015:" Technical  assistance in the acquisition of confocal  microscopy of fixed samples images, using microscopy equipment TCS SP5 and TCS SP8 STED 3X. IQNetES-0286-2009_2023-12-26.pdf

In addition, facility belongs to the Spanish Network of Advanced Optical Microscopy (REMOA)

        THE MAIN SERVICES offered by the Microscopy Unit to to the scientific community are: 


  • Adquisition images in different scan modes: XY, Xt, XYZ, XZY, XYZʎ, XYZt
  • 3D Reconstruction
  • FRAP analysis (Fluorescence recovery after photobleaching),
  • FRET analysis (Förster resonance energy transfer) and another dynamic analysis.
  • Photoconversion
  • Colocalization analysis. Super-resolution by STED in the confocal LEICA TCS SP8 STED 3X

             Multidimensional Microscopy fluorescence Advanced System for in vivo studies

  • Multidimensional acquisition of images in X,Y,Z,t and ʎ. Equipped with a wide range of fluorescence filters spanning whole visible spectrum from UV to near IR. Being fully motorized in temporal acquisition.
  • FRET (Förster resonance energy transfer) studies with CFP_YFP tandem.
  • Calcium in vivo studies with FURA and other dynamic studies.
  • Motorized applications: Mark & Find enables the user to define multi position experiments to observe a large number of cells within one experiment. Is particularly useful for studying dynamic processes in live cells. And the Tile Scan feature allows the acquisition of overview images of the specimen with multiple channels and in three dimensions.
  • Protein colocalization in vivo with high spatial and temporal resolution. Hamamatsu camera Orca Flash 4.0 LT has an effective number of pixels of 2048 x2048 with a cell size of 6,5 µm x6,5 µm, and a minimum frame rate of 30 frames per sec (30 fps), and can even reach values above 1000 fps. In addition, it has attached an image splitting optics (W-VIEW GEMINI), which provides one pair of dual wavelength (GFP/mCherry) images separated by a dichroic mirror. Simultaneous image acquisition of dual wavelength images allows you protein colocalization studies, high speed ratio metric imaging and other multiple fluorescence applications. Acquisition software Metamorph (Molecular Dynamics)
  • The facility is equipped with a high capacity storage system for digital images, which is password-accessible from any other workstation connected to the CIB intranet
  • The facility also hosts an independent image workstation equipped with different  software, including Metamorph offline (Molecular Devices), for image analysis and data output

THUNDER Imager 3D Tissue microscope.

Directed microscope with scanning stage for fluorescent imaging of 3D tissue sections. Real-time computational clearing and specific deconvolution algorithms for thick and thin samples.


  • Stereo Microscope Leica MZ16F with color camera Leica DFC490. Transmitted and fluorescence light.
  • CCD Digital Camera Leica DFC 350 FX coupled with a light microscopy Zeiss Axioplan with phase contrast technique and incident light fluorescence.
  • CMOS Digital Camera Hamamatsu Orca Flash 4.0 LT coupled an inverted  microscopy Leica DMIRE2 with DIC and incident light fluorescence.
  •  Confocal Laser Scanning Microscope (CLSM) LEICA TCS SP8 STED 3X fitted with UV Laser 405 nm and White Light Laser freely tunable excitation from 470-670 nm (1 nm steps).  AOTF (Acousto-Optical Tunable Filter) – AOBS (Acousto-Optical Beam Splitter) System. Scanning stage for motorized stage applications. Control temperature, CO2 and humidity system for p35, p60 petri-dish and standard slide.
  •  Confocal Laser Scanning Microscope (CLSM) LEICA TCS SP5 fitted with eight excitation lines (405, 457, 477, 488, 496, 514, 543, 633 nm) from UV, Ar and HeNe lasers and AOTF (Acousto-Optical Tunable Filter) – AOBS (Acousto-Optical Beam Splitter) System. Scanning stage for motorized stage applications.
  • Widefield Multidimensional Microscopy System Leica AF6000 LX for live cell imaging (epifluorescence and transmitted light). It consists of an inverted Leica DMI6000B microscope and an incubation chamber equipped with CO2 and temperature controls. System equipped with CCD Hamamatsu 9100-O2.  Scanning stage for motorized stage applications.
  • Widefield Microscope DMi8 Leica  with Orca-Flash 4.0 LT Digital CMOS camera, this one fitted with an image splitting optics (W-VIEW GEMINI), which provides one pair of dual wavelength (GFP/mCherry) images separated by a dichroic mirror onto a single camera. Software for acquisition and análysis Metamorph. tª Control.
  • THUNDER Imager 3D Tissue microscope. Directed microscope with LED and two CMOS cameras Leica: K5 for fluorescence and Flexacam C3 for histology. Scanning stage. Objectives: 1,25X, 20X, 40X y 63X. Phase contrast and fluorescence with filters for UV, GFP, Y3 and Y5.
  • CellASIC™ ONIX Microfluidic Platform delivers breakthrough control for live cell analysis experiments by combining the highest precision controls, maximum functionality, and simplified user operation for demanding long-term perfusion experiments. Its can be used with yeast, bacteria and animal cells. 

Fluorochromes: Furthermore, there are various conjugated fluorescent antibodies available for the users at reduced price. Fluorochromes.pdf



If the client belongs to the Biological Research Center (CIB), they must make the reservation on the intranet calendar : with the credentials of the CSIC intranet according to the following  FACILITY RULES.pdf    RATES.pdf

Customers outside the CIB will contact the service by email or telephone. The service person who picks up the message will make the reservation on the intranet calendar. They must also provide a series of data to fill in the Service Provision Offer, which will be sent to them from the Center's administration.

eMail:  Phone: 918373112 ext. 442801 or direct line: 911098001

Schedule is from Monday to Wednesday, from 8 a.m. to 5 p.m., on Thursday from 8 a.m. to 3 p.m. and on Friday from 8 a.m. to 2 p.m.