Advanced Digital Microscopy

Advanced Digital Microscopy Core Facility

IRB Barcelona

c. Baldiri Reixac, 10-12. E-08028 Barcelona

tel: +34 93 40 34647,

microscopy(at)irbbarcelona.org

The Advanced Digital Microscopy is a Core Facility unit of the IRB Barcelona.

It was Inaugurated in January 2009 and offers 24/7 access and support to 12 state-of-the-art and conventional imaging instruments for Life Science research, from high content imaging in widefield, confocal/multiphoton and super resolution microscopy, to emerging techniques for cell manipulation and lightsheet-based 3D imaging.

Access to Advanced Light Microscopy

ADM supports on average 150-180 users per year from IRB Barcelona and external entities, i.e. public Institutions in Barcelona and private companies. In brief, ADM offers 24/7 access to laser scanning spectral and multiphoton microscopy, spinning disk confocal microscopy, fully automated widefield and confocal screening, TIRF, laser manipulation (FRAP, laser nanosurgery, photoactivation), fluorescence macroscopy and stereoscopy, micromanipulation and microinjection, Lightsheet fluorescence Microscopy (SPIM) from macro- and micro- resolution, Fluorescence Lifetime Imaging (FLIM) and Time-correlated Single Photon Counting (TCSPC) confocal Microscopy (including derivatives e.g. FCS, FCCS, FLCS etc...), Super Resolution Imaging (PALM/STORM, SIM, Airyscan).

Service

ADM assists scientists throughout the full process of microscopy experiments: design projects, teaching techniques, introducing the use of instruments, processing data and analyzing images, assist scientists in interpreting and shaping final results.

ADM is responsible for the maintenance of the instruments, in close collaboration with industry partners, to provide non-stop services, 24/7.

Since 01-01-2010, ADM has served 130 different research groups and over 890 different users, for an average usage of >16.000 hours /year.

Methods & Technology Development

We develop and give access to highly specialized instruments, which are either not commercially available or perform beyond standards of existing commercial systems, e.g. laser nanosurgery for living cells and organisms, Lightsheet Fluorescence Microscopy both for living organisms (SPIM) or for large samples (MacroSPIM, e.g. optically cleared organs, tumors).

Highlights:

- ADM offers a unique Lightsheet-based system dedicated to 3D-Imaging of full transparent organs and tumors.

- ADM developed ‘Intelligent Imaging’ with the Leica HCS Matrix-CAM software module for confocal imaging and MicroManager for epi-fluorescence.

- ADM currently develops OPM: Oblique Plane Microscopy, for the deep and high-throughput imaging of living organoids.

Past collaborations with the following partners: Leica Microsystems, Cytoo, Izasa (Nikon distributors in Spain), Acquifer Gmbh.

Bioimage Analysis

ADM is very active in Image Processing and Analysis to address existing gaps in the panel of available open source and commercial software for Image processing. We focus on developing custom software tools tailored to the the specific needs of our scientists and to accelerate/improve the outcome of microscopy experiments. We also develop signal processing tools and data analysis routines to address the new challenges brought by the large amounts of data generated by high-throughput and 3D Imaging.

funded by the EU COST framework, COST Action CA15124

A New Network for BioImage Analysts: NEUBIAS

IRB Barcelona, together with other 14 institutions in Europe, has constituted a new network of BioImage Analysts through the award of a COST Action under the competitive call of 2015.

The Action started activities on May 3rd, 2016. IRB Barcelona acts as Grant Holder for the Action, which has established a series of activities for the development of BioImage Analyst professionals in Europe, for a period of 4 years.: 15 Training schools in 4 years for over 400 trainees, 10 workshops, development of online tools and repositories, a program of 50 transnational staff exchanges, textbooks, etc...

ADM played a leading role in the establishment of the following resources:

biii.eu: The Bioimage Informatics Index, an crowd-sourced repository, aimed to exhaustively catalogue all tools and workflows for Bioimage Analysis.
BIAFLOWS: A repository to benchmark and reproducibly deploy Bioimage analaysis workflows.
NEUBIAS Academy: An intense series of 20 bleeding-edge live webinars by Bioimage Analysis experts, that accompanied the scientific community during the pandemics confinement in April-June 2020, with over 10.000 registrations in 9 weeks, and 21.000 views on our NEUBIAS Youtube channel.
NEUBIAS F1000R Gateway: Launched in March 2020, this new publication platform will collect advances in Bioimage Analysis: articles, posters, Slides, more...

In 2019, the Action counts with over 250 members in 43 countries in Europe and beyond (including Australia, USA, Singapore, Brazil). The action is extended until October 2020.

More information at www.neubias.org

Access to Technology, Networks

EUROBIOIMAGING

2019: Eurobioimaging is now Eurobioimaging-ERIC

ADM takes part in EuroBioImaging, a large‐scale pan‐European research infrastructure project on the European Strategy Forum on Research Infrastructures (ESFRI) Roadmap, aiming at constructing a network Infrastructure for Biomedical and Life Science Imaging.

ADM participates in 2 Nodes, expected to start activity soon:

- B-MIN: Barcelona Mesoscopic Imaging Node, together with the CRG and ICFO.

- B-LIVIN: Barcelona Live and Intravital Imaging Node, together with the University of Barcelona and the CRG.

In the 1^st Open Call for Euro-BioImaging Nodes, more than 220 imaging facilities from 19 different European countries submitted 71 applications for expressing their interest to become part of Euro-BioImaging. The Interim Board has nominated 28 Nodes candidates in 2015.

REMOA

ADM is an active and founding member of the Spanish Network of Advanced Light Microscopy (REMOA: Red Española de Microscopia Óptica Avanzada), whose first founding meeting was hosted by IRB Barcelona in March 2011.

In 2016, REMOA joined efforts with its homologous network in Portugal PPBI, to convert the conference into SPAOM: Spanish and Portuguese Advanced Optical Microscopy meetings series. Check the past and future meetings here.