Core Facilities


CRG/UPF: Advanced Light Microscopy Unit

Timo Zimmermann
Raquel Garcia Olivas, Arrate Mallabiabarrena, Xavier Sanjuan (UPF)
Raul Gomez
Thomas Pengo (associated, until 10/2014)


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, Fluorescence Recovery after Photobleaching (FRAP) and confocal and widefield screening microscopy. Additionally, dedicated software packages for data visualization and analysis are available for 3D rendering, particle tracking and image analysis.

In 2014, the total booked microscope usage time of the unit reached 18,300 hours in approx. 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, 120 users from 28 CRG research groups and 52 users from 27 UPF-CEXS groups have used the unit. Additionally the unit was used by 33 users from 13 groups of other PRBB institutes and for projects from external visitors. On average, 88 investigators use the unit every month.

The ALMU was one of the few sites worldwide that performed beta-testing of the latest 3D STED technology for Leica Microsystems. The unit also hosted the first Lightsheet Z1 system from Carl Zeiss Microimaging Spain for the first half of the year. The unit was involved in several additional tests of not yet released microscopy equipment.

During the year, several custom procedures were implemented for automated image-based screening using confocal or widefield microscopy. These include an intelligent screening/machine learning software solution for ImageXpress microscopes, automatic large object localization in a primary scan with subsequent detail acquisition and high-resolution high-throughput screening of multiwell plates using oil immersion objectives.

Another focus was put on increasing the available offer of image processing solutions and expertise, specifically for localization-based super-resolution microscopy and image databases.

All members of the staff are frequently participating as speakers and instructors in master courses from the CRG and UPF, as well as in many conferences and microscopy courses both at the PRBB as well as at other institutions, nationally and internationally. A specific highlight among these activities was the extremely well attended public discussion round on the content of biological images that was held as part of the successful “Tree of Life” exhibition of microscope images taken at the CRG and displayed at the Palau Robert in Barcelona.