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Molecular Imaging Platform IBMB

The Molecular Imaging Platform (MIP) has been set up as a co-operation between the Molecular Biology Institute of Barcelona (IBMB) and the Barcelona Science Park (PCB). We offer a collection of state-of-the-art light microscopy systems and techniques and provide assistance with all aspects of image acquisition and analysis, ranging from advice on imaging experiments to microscopy training or project collaboration.

Available applications

  • Automated Wide-Field Microscopy/High content screening
  • Live 3D imaging/On-line computational clearing
  • Laser Scanning Confocal Microscopy
  • Multiphocal High-Speed Confocal Microscopy
  • Multiphoton Microscopy/laser cutting/spectral imaging
  • Fluorescence Correlation & Cross-correlation Spectroscopy
  • Total Internal Reflexion Fluorescence
  • Superesolution SRRF-stream
  • Image processing and analysis
image_presentation

Modus operandi

  • The Platform is accessible 24 hours a day from Monday to Sunday to researchers at IBMB and other PCB and outhouse institutions and companies.
  • We provide System Introductions on a regular basis, where you will be taught in both theoretical and practical aspects of the different image acquisition techniques.
  • The equipment can be operated on a self-service mode. Booking permissions are only granted to autonomous users who have been introduced to the systems.
  • For further information contact the MIP manager at erabmc@ibmb.csic.es or mip@ibmb.csic.es

Location

You can find us at the PCB Helix building, base floor PBA07. C/ Baldiri i Reixac 15-20, 08028 Barcelona.

GENERAL EQUIPMENT

THUNDER IMAGER 3D LIVE CELL (LEICA MICROSYSTEMS)

Thunder Imager is a new generation widefield technology for fast 3D optical sectioning of fixed and live specimens, from cells up to large tissues, embryos and organoids. Together with a super fast integrated hardware, the Thunder algorithms remove the out-of-focus light in real time, thus opening real new possibilities in high-content applications. Our Thunder system has been appointed as reference machine, the first of its kind in Spain, based on a collaboration agreement with Leica Microsystems.

Specifications:

Download specifications

HIGH SPEED AND SUPER-RESOLUTION DRAGONFLY 505 (ANDOR)

Dragonfly 505 is a high speed & sensitivity multimodal confocal microscope whose applications range from live cell widefield and confocal imaging to single molecule localization, and from TIRF to whole embryo and thick tissue imaging. It delivers real time visualization for rapid specimen inspection, in parallel to GPU driven deconvolution to maximize resolution and throughput.

State subprogramme for Research Infrastructures and Scientific-Technical equipment Co-financed by the European Regional Development Fund (ERDF) with a grant of 614.919,65€

     

LSM780 CONFOCAL & MULTIPHOTON MICROSCOPE (CARL ZEISS)

The Zeiss Lsm780 is a confocal system with exceptional sensitivity. The GaAsP detector achieves 45% quantum efficiency compared to the 25% of conventional PMT detectors, and is capable of photon counting. The system´s illumination/detection design allows for simultaneous acquisition of up to ten dyes. The new optical design, the electronics concept and the user-friendly software make this confocal system fast, efficient and easy to use. In addition, the system is configured for Fluorescence Correlation Spectroscopy (FSC) and equipped with a MaiTai Deepsee IR laser for Multiphoton Microscopy (MPM).

Specifications

Download specifications

State subprogramme for Research Infrastructures and Scientific-Technical equipment Co-financed by the European Regional Development Fund (ERDF) with a grant of 614.919,65€

     

TCS-SP5 CONFOCAL MICROSCOPE (LEICA MICROSYSTEMS)

The SP5 TSC confocal system provides a highly efficient spectral detection, which together with the AOBS (Acousto-Optical Beam Splitter) enables the simultaneous imaging of up to 4 different wavelengths at high resolution. The system covers a wide range of confocal applications, including a number of other advanced techniques such as FRAP, FRET, FLIP and Photoconversion, which are facilitated by user-friendly wizards designed to the purpose.

Specifications

Download specifications

Users manuals

Quick Start LAS AF
Sequential Scanning in LAS AF
Viewer Tools in LAS AF
Draw ROIs
Scan ROIs
Removing Crosstalk Notes
Lambda Scan in LAS AF
Intensity loss compensation in Z-stacks
Time lapse in LAS AF
Dye Separation in LAS AF
FRAP with TCS SP5
FRET with TCS SP5
Photoconversion with TSC SP5
Live Data Mode (LDM)

AF7000 MOTORIZED WIDEFIELD MICROSCOPE (LEICA MICROSYSTEMS)

The Leica AF6500 wide-field system offers a flexible platform for a wide range of conventional fluorescence applications, from routine imaging and documentation to high-speed live cell imaging. It is equipped with temperatura and CO2 control and uses the same easy-to-use software platform shared by the Leica confocal systems.

Specifications

Download specifications

E600 EPIFLUORESCENCE MICROSCOPE (NIKON)

Our Nikon E600 upright microscope is equipped for basic routine examinations of cells and tissues, It specifically includes high NA immersion objectives, phase contrast optics, basic epifluorescence filters and an Olypues DP72 color digital camera specially suited for immunohistochemistry experiments.

Specifications

Download specifications

PCB agreement *: It guaranties free access to the Leica TCS SP5 confocal microscope, the Leica wide-field AF7000 microscope, the epifluorescence microscope NikonE600 and the 64-bit workstations, under the SCC self-service regime, introductions granted. The remaining equipment will be charged at the internal PCB pricelisted above.

General discounts: All users will benefit from a 50% discount during the overnight slots (11pm to 8am).

Non IBMB user´s may additionally include technical assistance (32.90 euros/hour).

Safety rules during pandemic

Become a user

Registration

  • Registration is required to obtain booking autonomy.
  • To become a registered user Click Here, fill in the form and submit it.
  • Applications lacking lab extension and institutional e-mail address will not be processed.
  • Please note that you will not receive any automatic e-mail notification after submission of the form, you will have to contact the facility staff.
  • Registration does not provide access to the on-line booking application until permissions are granted.

Introductions and Permissions

  • We provide Introductions to all the systems on a regular basis. You can choose a date in our Introductions Calendar and send a request to erabmc@ibmb.csic.es.
  • The Nikon E600 microscope and the imaging workstations do not require permissions.

Access to the Booking Application

External Users

  • External researchers should request an authorization to enter the PCB premises during non-working hours. Send a request to erabmc@ibmb.csic.es.

User guidelines

Here are some general guidelines we follow in order to make every day’s work smooth and efficient. If you need any special requirements or have any useful suggestions please contact us directly.

General

  • Registration and Introduction to the systems by the Unit staff are compulsory for every user, either novice or advanced.
  • If you cannot remember how to operate a system you were already introduced to, ask the stuff team for advice.
  • Please do not enter in the facility any samples that are potentially hazardous or classified over S1 safety group.
  • If you publish or present any work made or processed in any of our systems, please acknowledge this facility.

Before you start

  • Wipe off dust and smear from the lens and the sample cover slip using lens tissue (soaked in ethanol if required).
  • When environmental control is needed, make sure you have switched on temperature controller at least 30 min in advanced.

While working

  • Check which immersion media are required for each lens you use, before you add any medium (oil, glycerol, water, air). If you don’t know, ask the facility stuff.
  • Clean immersion media from lenses with a dry lens tissue every time you change slides. Slides should also be cleaned by a dry kim wipe.
  • Use moderate amounts (1 drop=50 µl) of immersion media. Immediately remove immersion media spilling over the objective rim.

 After you have finished

  • Clean immersion media from every lens you used with a dry lens tissue.
  • Always check up the reservations page to see whether somebody is booked after you.
  • If you are last user of the day, switch off the equipment (fluorescence lamps, lasers, microscope controllers, cameras, softwares, PCs), according to the instructions provided by the facility stuff. Cover the microscope (if applicable) and clean up the microscope bench from any residues (including dangerous glass coverslips and slides pieces).
  • Pay especial attention to the “system switch off” on Fridays; please make sure the lasers and fluorescence lamps are not left on over the weekend.
  • Incidences should be reported to the unit stuff, either in person or by e-mail. Writing incidences in the logging sheet is not a guarantee of efficient assistance.

Booking Guidelines

  • Booking of the microscope before use is mandatory, even if it is not being used by anybody else.
  • Logging sheets (at the microscope) should be filled up and signed after your session.
  • If you have booked the system and do not need to use the slot, delete your booking.
  • If you delete a booking on a saturated system (SP5), please send an e-mail to the cancellations list provided by the facility stuff. You can request us to be included in the cancellations notification list (or deleted from it).
  • If you delete the last booking on the day, ensure that the system is switched off (the previous user might not know that you are going to delete your booking).
  • Try to set long time-lapse experiments during nights and weekends, especially if the system is saturated (remember to switch off devices not needed during time lapse like the HBO lamp on confocal systems).
  • If you would like a long experiment to be saved by the next user, please contact him/her and get to an agreement.
  • Indicate in the booking application whether you will use temperature control during your session.

Data transfer and storage

  • When you save data locally, store it in a folder prepared to that purpose (normally it will be local hard disk D, folder “Users” or “Data”). Do not store data on the C: system hard disk, it may damage the system and reduce working memory.
  • Transfer you data as soon as possible to avoid data loss, local hard disks will be automatically deleted in 15 days. Please remember that external memories/pendrives are not allowed due to the risk of viruses. Use the servers designated to that purpose.

Servers

Data will be automatically deleted in all MIP computers in 15 days, according to creation date. In order to transfer your files, use the servers below (no external memories are allowed)

“Caballa” PCB Server

Data will be stored in the server for 1 week, after that time they will be automatically deleted

How to get permissions

How to connect

Windows users

  • Go to “My pc” and write in the address bar: \\caballa.adm.pcb.ub.es 
  • Click on the folder “microscopy”
  • Insert your user name as: adm\username
  • Type your password

Mac users

  • Finder/Go/Connect to Server,  write in the address bar:
    smb://caballa.adm.pcb.ub.es 
  • Insert your user name as: adm\username
  • Type your password
  • Click on the folder “microscopy”

Please disconnect from server once you have finished

Warning: do not click on “remember my password”, otherwise access will be blocked for other users !!!

MIP FTP Server

Only data acquired at MIP is allowed on this server. Users will need to delete their own data to manage their storage space

How to ask for credentials

How to connect

Using windows 

  • Go to My PC and write in the address bar: ftp://161.111.236.17
  • Write the provided username and password in the form

Using Filezilla client (installed in all the facility computers).

  • Open Filezilla and write the host (161.111.236.17), username and password.
  • Click “Quick connect”
  • Before transferring your files, select the transfer default action “overwrite file”, to prevent files getting stuck in the queue

E. Rebollo publications list: https://bit.ly/2WbVguw

Open source code imaging contributions at https://github.com/MolecularImagingPlatformIBMB

MIP publications during 2019-2020

FoxO Maintains a Genuine Muscle Stem-Cell Quiescent State until Geriatric Age. García-Prat, Laura, Eusebio Perdiguero, Sonia Alonso-Martín, Stefania Dell’Orso, Srikanth Ravichandran, Stephen R. Brooks, Aster H. Juan, et al.  Nature Cell Biology 22, no. 11 (November 2020): 1307–18. 


Multimerization of Zika Virus-NS5 Causes Ciliopathy and Forces Premature Neurogenesis. Saade, Murielle, Diego S. Ferrero, José Blanco-Ameijeiras, Elena Gonzalez-Gobartt, Marco Flores-Mendez, Victor M. Ruiz-Arroyo, Elena Martínez-Sáez, et al. Cell Stem Cell 27, no. 6 (December 3, 2020): 920-936.e8.


Culture and Differentiation of Human Hair Follicle Dermal Papilla Cells in a Soft 3D Self-Assembling Peptide Scaffold. Betriu, Nausika, Claire Jarrosson-Moral, and Carlos E. Semino. Biomolecules 10, no. 5 (28 2020).


Unravelling the Distinct Contribution of Cell Shape Changes and Cell Intercalation to Tissue Morphogenesis: The Case of the Drosophila Trachea. Casani, Sandra, Jordi Casanova, and Marta Llimargas. Open Biology 10, no. 11 (n.d.): 200329.


Stress Granules Display Bistable Dynamics Modulated by Cdk. Yahya, G, AP Pérez, MB Mendoza, E Parisi, DF Moreno, C Gallego, and M Aldea. BioRxiv, January 1, 2020, 2020.05.08.083782.


Lactate Promotes Cardiomyocyte Dedifferentiation through Metabolic Reprogramming. Ordoño, Jesús, Soledad Pérez-Amodio, Kristen Ball, Aitor Aguirre, and Elisabeth Engel. BioRxiv, January 1, 2020, 2020.07.21.213736.


EEF1A2 Controls Local Translation and Actin Dynamics in Structural Synaptic Plasticity. Mendoza, Mònica B., Sara Gutierrez, Raúl Ortiz, David F. Moreno, Maria Dermit, Martin Dodel, Elena Rebollo, Miquel Bosch, Faraz K. Mardakheh, and Carme Gallego. BioRxiv, January 1, 2020, 2020.10.20.346858.


Cell Intercalation Driven by SMAD3 Underlies Secondary Neural Tube Formation. Gonzalez-Gobartt, Elena, José Blanco-Ameijeiras, Susana Usieto, Guillaume Allio, Bertrand Benazeraf, and Elisa Martí. BioRxiv, January 1, 2020, 2020.08.24.261008.


A Fraction of Barrier-to-Autointegration Factor (BAF) Associates with Centromeres and Controls Mitosis Progression. Torras-Llort, Mònica, Sònia Medina-Giró, Paula Escudero-Ferruz, Zoltan Lipinszki, Olga Moreno-Moreno, Zoltan Karman, Marcin R. Przewloka, and Fernando Azorín. Communications Biology 3, no. 1 (August 19, 2020): 454.


A SMAD1/5-YAP Signalling Module Drives Radial Glia Self-Amplification and Growth of the Developing Cerebral Cortex. Najas, Sonia, Isabel Pijuan, Anna Esteve-Codina, Susana Usieto, Juan D. Martinez, An Zwijsen, Maria L. Arbonés, Elisa Martí, and Gwenvael Le Dréau. Development (Cambridge, England) 147, no. 13 (July 13, 2020).


Mechanical Coordination Is Sufficient to Promote Tissue Replacement during Metamorphosis in Drosophila. Prat-Rojo, Carla, Philippe-Alexandre Pouille, Javier Buceta, and Enrique Martin-Blanco. The EMBO Journal 39, no. 3 (03 2020): e103594.


Proteostasis Collapse Halts G1 Progression and Delimits Replicative Lifespan. Moreno, David F., Kirsten Jenkins, Sandrine Morlot, Gilles Charvin, Attila Csikász-Nagy, and Martí Aldea. Elife. 2019 Sep 13;8:e48240.


PHF2 histone demethylase prevents DNA damage and genome instability by controling cell cycle progression of neural progenitors. Pappa S, Padilla N, Iacobucci S, Vicioso M, Álvarez de la Campa E, Navarro C, Marcos E, de la Cruz X, Martínez-Balbás MA.  2019. Proc Natl Acad Sci USA;116, 19464-19473.


Anti-Siglec-1 Antibodies Block Ebola Viral Uptake and Decrease Cytoplasmic Viral Entry. Perez-Zsolt, Daniel, Itziar Erkizia, Maria Pino, Mónica García-Gallo, Maria Teresa Martin, Susana Benet, Jakub Chojnacki, et al. Nature Microbiology 4, no. 9 (2019): 1558–70.


3D + Time Imaging and Image Reconstruction of Pectoral Fin During Zebrafish Embryogenesis. Nguyen, Hanh, Jaume Boix-Fabrés, Nadine Peyriéras, and Elena Kardash. Molecular Biology (Clifton, N.J.) 2040 (2019): 135–53.


Automated Macro Approach to Quantify Synapse Density in 2D Confocal Images from Fixed Immunolabeled Neural Tissue Sections. Rebollo, Elena, Jaume Boix-Fabrés, and Maria L. Arbones. Methods in Molecular Biology (Clifton, N.J.) 2040 (2019): 71–97.


Automated Macro Approach to Remove Vitelline Membrane Autofluorescence in Drosophila Embryo 4D Movies. Boix-Fabrés, Jaume, Katerina Karkali, Enrique Martín-Blanco, and Elena Rebollo. Methods in Molecular Biology (Clifton, N.J.) 2040 (2019): 155–75.


Coincidence Analysis of Molecular Dynamics by Raster Image Correlation Spectroscopy. Moreno, David F., and Martí Aldea. Methods in Molecular Biology (Clifton, N.J.) 2040 (2019): 375–84.


Competition in the Chaperone-Client Network Subordinates Cell-Cycle Entry to Growth and Stress. Moreno, David F., Eva Parisi, Galal Yahya, Federico Vaggi, Attila Csikász-Nagy, and Martí Aldea. Life Science Alliance 2, no. 2 (April 1, 2019).


Dendritic Cells From the Cervical Mucosa Capture and Transfer HIV-1 via Siglec-1. Perez-Zsolt, Daniel, Jon Cantero-Pérez, Itziar Erkizia, Susana Benet, Maria Pino, Carla Serra-Peinado, Alba Hernández-Gallego, et al. Frontiers in Immunology 10 (2019): 825.


Evolutionary Conserved Canonical BMP Activity Controls Cortical Neurogenesis. Najas, Sonia, Isabel Pijuan, Anna Esteve-Codina, Susana Usieto, Juan D. Martinez, An Zwijsen, Mariona L. Arbonés, Elisa Martí, and Gwenvael Le Dréau. BioRxiv, January 1, 2019, 558486.


Fast Multiphoton Microscope Based on Polymer Ulenses Array Using a 3D Printed Mold. Zalvidea, Dobryna, Xavier Trepat, and Elena Rebollo. In 2019 Conference on Lasers and Electro-Optics Europe and European Quantum Electronics Conference (2019), Paper Cl_p_22, cl_p_22. Optical Society of America, 2019.


Proteostasis Collapse Halts G1 Progression and Delimits Replicative Lifespan. Moreno, David F., Kirsten Jenkins, Sandrine Morlot, Gilles Charvin, Attila Csikász-Nagy, and Martí Aldea. BioRxiv, January 1, 2019, 648287.


β-Catenin Tumour-Suppressor Activity Depends on Its Ability to Promote Pro-N-Cadherin Maturation. Herrera, Antonio, Anghara Menendez, Blanca Torroba, and Sebastian Pons. BioRxiv, January 1, 2019, 571810.


Altered Cytoplasmic Maturation in Rescued in Vitro Matured Oocytes. Ferrer-Vaquer, A, M Barragán, A Rodríguez, and R Vassena. Human Reproduction 34, no. 6 (June 4, 2019): 1095–1105.

Publications 2015-­2018

Publications 2012-­2014

 

Collaboration Agreement with Leica Microsystems (2019-2020).

Collaborative agreement to help promote and use the Leica Thunder 3D Live Cell, as reference machine in Spain.

PTA2018-016150-I

2018 Aids for recruiting Technical Support Personnel (PTA)
State Programme for the Promotion of Talent and its Employability
Ministry of Sciences, Innovation and Universities (MICIU)
Co-financed by CSIC

EQC2018-004541-P

Supply and Installation of a High Speed and Super-resolution Imaging Platform
CPV code: 38515000-8
Ministry of Sciences, Innovation and Universities (MICIU)
StateSubprogramme for Research Infrastructures and Scientific-Technical equipment
Co-financed by the European Regional Development Fund (ERDF)
S&T Manager: E. Rebollo

CSIC1501/18
Supply and Installation of a High Content & Performance Microscope Extension
CPV code: 38519000-6
Spanish National Research Council (CSIC), within the Exceptional Support Fund Programme
S&T Manager: E. Rebollo.

PTA2016-12597-I
2016 Aids for recruiting Technical Support Personnel (PTA)
State Programme for the Promotion of Talent and its Employability
Ministry of Economy and Competitiveness (MINECO)

PEJ-2014-A-41034
Scientific Service TechnicianPosition, financed by the National Youth Guarantee System
Ministry of Economy and Competitiveness (MINECO)

CSIC13-4E-2065
Spectral confocal microscope for single molecule detection and 2-P nano-spectroscopy.
CPV code: 38515000-8
Ministry of Economy and Competitiveness (MINECO)
State Subprogramme for Research Infrastructures and Scientific-Technical equipment.
Co-financed by the European Regional Development Fund (FEDER)
S&T Manager: E. Rebollo

EXPLORA2012- BFU2011-15229-E
Insights into Stem Cell Biology through the development of New Imaging Technology.
Ministry of Economy and Competitiveness (MINECO), within the EXPLORA Programme.
PI: E. Rebollo.

Collaboration Agreement with Carl Zeiss (2011-2013).

Collaborative agreement to help promote and use the Spectral Confocal LSM780 system in Catalunya.

Collaboration Agreement with the Barcelona Sciences Parc.

This Platform has been set-up as a co-operation between the Molecular Biology Institute of Barcelona (IBMB) and the Barcelona Sciences Park (PCB), which ensures general services and maintenance for those systems covered by the PCB common services regime.

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