Core Facilities

CRG/UPF Advanced Light Microscopy Unit

Unit Structure

Timo Zimmermann
Raquel Garcia Olivas, Arrate Mallabiabarrena, Xavier Sanjuan (UPF)
Raul Gomez (since May 2013)
Thomas Pengo (associated)


The Advanced Light Microscopy Unit (ALMU) of the CRG and UPF serves as a core facility for high-end light microscopy for PRBB researchers. A range of instruments with unique capabilities fully covers the spectrum of advanced imaging applications from thick tissue reconstruction to fast in-vivo imaging to the sensitive detection of very faint signals of single molecules. The staff of the facility provides advice in the initial experiment planning, training of the researchers on the instruments and assistance with the subsequent data analysis. It is the aim of the facility to provide a link for the biological questions of researchers to the full capabilities of advanced light microscopy at the organismic, cellular and molecular level. Methods available in the facility include super-resolution microscopy by stimulated emission depletion (STED) and Ground State Depletion Imaging Microscopy (GSDIM), optical sectioning (single photon and multi-photon microscopy), spectral imaging, in-vivo time-lapse imaging, Total Internal Reflection Fluorescence (TIRF) Microscopy and methods for the study of molecular properties and interactions like Fluorescence Correlation Spectroscopy (FCS), Fluorescence Lifetime Imaging Microscopy (FLIM), Fluorescence Resonance Energy Transfer (FRET) detection and Fluorescence Recovery after Photobleaching (FRAP). Additionally, dedicated software packages for data visualization and analysis are available for 3D rendering, particle tracking and image analysis.

In 2013, the total booked microscope usage time of the unit reached 16,800 hours in more than 5,000 separate bookings. This corresponds to approximately seven hours of daily usage on the bookable microscope systems plus many additional hours on equipment without mandatory booking and on special equipment. During the year, 128 users from 26 CRG research groups and 34 users from 17 UPF-CEXS groups have used the unit. Additionally the unit was used by 39 users from 20 groups of other PRBB institutes and for six projects from external visitors. On average, 93 investigators use the unit every month.

During the year a pulsed UV laser cutting/ablation device (Rapp Optoelectronics) was added to an existing microscope. The image-based screening capability was increased through the integration into the unit of a specialist for screening and automation and a fully automatic screening microscope. Image processing inside the unit was significantly extended through the addition of a processing specialist as well as additional dedicated workstations and software. The unit also currently hosts a Lightsheet Z1 system from Carl Zeiss Microimaging Spain.

The unit organized in October a three-day workshop on “Applied Super-resolution Microscopy” for 20 international  participants and with three invited speakers that are leaders in the field. The course was substantially supported by the Photonic Sciences Institute (ICFO) in the framework of the Barcelona Super-Resolution Light Nanoscopy Alliance (SLN@BCN). All members of the staff are frequently participating as speakers and instructors in masters courses from the CRG and UPF, as well as in conferences and microscopy courses both at the PRBB as well as at other institutions, nationally and internationally.

Selected Publications

  1. Grünberg R, Burnier JV, Ferrar T, Beltran-Sastre V, Stricher F, van der Sloot AM, Garcia-Olivas R, Mallabiabarrena A, Sanjuan X, Zimmermann T, Serrano L.
    “Engineering of weak helper interactions for high-efficiency FRET probes.”
    Nat Methods, 10(10):1021-7 (2013).
  2. Carvalho A, Menendez DB, Senthivel VR, Zimmermann T, Diambra L, Isalan M.
    “Genetically Encoded Sender-Receiver System in 3D Mammalian Cell Culture.”
    ACS Synth Biol, 2013 Dec 20. [Epub ahead of print]
  3. Mitrovic S, Nogueira C, Cantero-Recasens G, Kiefer K, Fernández-Fernández JM, Popoff JF, Casano L, Bard FA, Gomez R, Valverde MA, Malhotra V.
    “TRPM5-mediated calcium uptake regulates mucin secretion from human colon goblet cells.”
    Elife, 2:e00658 (2013).