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MOLECULAR IMAGING PLATFORM

The Molecular Imaging Platform (MIP IBMB-PCB) has been set up as a co-operation between the Molecular Biology Institute of Barcelona (IBMB) and the Barcelona Scientific Park (PCB). It offers a collection of state-of-the-art light microscopy equipment, including high-resolution and high-speed confocal microscopy, multiphoton microscopy, automatized wide-field imaging, fluorescence correlation spectroscopy and image processing tools.

Available applications

  • Automated Wide-Field Microscopy
  • Laser Scanning Confocal Microscopy
  • Spinning Disk Confocal Microscopy
  • Multiphoton Microscopy
  • Fluorescence Correlation Spectroscopy
  • Image processing and analysis

Modus operandi

  • The AFMU is accessible 24 hours a day from Monday to Sunday, and welcomes in-house groups from IBMB and PCB as well as external researchers.
  • 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 should be operated on a self-service mode. Booking permissions are only granted to autonomous users who have been introduced to the systems.
  • The Head of the Unit is Elena Rebollo. If you need any further information please click here.

Other activities

  • We organize every year a Digital Image Processing course. Click here.

Location

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



Elena Rebollo Arredondo
  • Elena Rebollo Arredondo. PhD.
  • IBMB-CSIC
  • C/ Baldiri Reixac 15
  • 08028 Barcelona, Spain
  • Phone: +34 93 402 0249 / +34 93 402 0837
  • E-mail: erabmc@ibmb.csic.es

Head of the Platform



Past students

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.
  • Undergraduate and master students will work under the supervision of autonomous users from their labs, they will not be granted registration neither permissions.

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 two routine epi-fluorescence microscopes 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.
Room & Equipment

Zeiss Lsm780 Confocal & Mutiphoton Microscope

Zeiss780MP_FotoWeb(1).png

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

Leica TCS-SP5 Confocal Microscope (Leica Microsystems, Wetzlar, Germany)

SP5_web_reduced.jpg

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

User Manuals

Spinning disk confocal microscope (PerkinElmer Ultraview ERS)

Images-Spinning_web.jpg

The PerkinElmer UltraVIEW system (PerkinElmer Life Sciences Inc., MA, USA) is a Yokogawa (Yokogawa Corp. Japan) Nipkow Spinning Disk Confocal System. It uses a spinning disk with multiple pinholes to achieve confocality (e.g. the rejection of out-of-focus light). Emission light from the sample passes through the pinholes to generate a confocal image of the sample that can be detected with an EMCCD (Electron Multiplification Charge-Coupled Device) camera. Spinning disk confocal systems have 2 main advantages over conventional Laser Scanning Confocal Microscopes (LSCM):

  • Higher imaging speed: up to 360frames/sec compared to 0.5-1 frames per second in a LSC
  • Lower photo-toxicity: around 5 times less than a LSCM, probably due to the fact that the system splits the laser light into thousands of minibeams.

It is specially suited for live 4D imaging of fast cellular processes and for FRAP (fluorescence recovery after photobleaching) and related experiments.

Specifications

User Manual

Leica AF6500 widefield microscope

AF7000_fotoweb.jpg

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

Nikon E600 microscope

Upright microscope fitted with a digital camera.

Objectives 4x  0.13NA Plan Fluor

10x 0.30NA Plan Fluor

20x 0.50NA Plan Fluor

40x 0.75NA Plan Fluor

60x 1.40NA Oil Plan Apo

100x 1.30NA Oil Plan Fluor

Camera DP72 (Olympus)

Color digital camera

Leica DM IRBE (Leica Microsystems)

DMIRBE_01(2).jpg

The DM IRBE microscope is a versatile inverted scope used for a wide range of applications. It is ideally suited for basic examinations of cells and tissues, but can also be implemented for more sophisticated demands such as micromanipulation, microinjection, microdissection or confocal microscopy. Our DMIRBE is equipped with long distance working objecives, phase contrast optics, basic epifluorescence filters and a cool snap CCD camera (photometrics) for basic acquisition of transmission and fluorescence images.

Specifications

User Manuals

It is not allowed to plug in any USB memories into the Microscopy Unit computers. There are two servers you an use:

  • PCB Server (CABALLA).  For all PCB members. It allows access to group´s folders. Images will be stored in the server for 1 week, after that time they will be automatically deleted.
  • IBMB Server.  Only for IBMB members. It allows access to personal folders. Users will need to delete their own images.

How to access CABALLA:

1. You first need to get permissions:


2. Then you can connect either way:

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
IMPORTANT NOTE: do not click on "remember my password", otherwise it will be blocked for other users !!!

How to access the IBMB FTP Server

1. User Registration: 

  • Send an email to lfminf@ibmb.csic.es to request a user/password in the server. You will need to attach the authorisation of your group PI. 

2. How to connect: 

A. Go to My PC and write in the address bar: ftp://161.111.236.25
  • Write the provided username and password in the form.
  • Move files from your folder in the computer to the server.
  • To finish, just close the window.
B. You can also transfer files using an Ftp client. Filezilla client is installed in all the facility computers.
  • Open Filezilla and write the host 161.111.236.25, username&password and click "Quick connect"
  • You will enter in your personal folder. Move files from your local hard drive to the server.
  • To finish, just close the window.

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 DNA structure directs positioning of the mitochondrial genome packaging protein Abf2p. Chakraborty A, Lyonnais S, Battistini F, Hospital A, Medici G, Prohens R, Orozco M, Vilardell J, Sola M. Nucleic Acids Res. 2016 Nov 29.

Transcriptional Elongation Regulator 1 Affects Transcription and Splicing of Genes Associated with Cellular Morphology and Cytoskeleton Dynamics and Is Required for Neurite Outgrowth in Neuroblastoma Cells and Primary Neuronal Cultures. Munoz-Cobo JP, Sanchez-Hernandez N, Gutierrez S, El Yousfi Y, Montes M, Gallego C, Hernandez-Munain C, Sune C. Mol Neurobiol. 2016 Nov 14.

Leader Cells Define Directionality of Trunk, but Not Cranial, Neural Crest Cell Migration. Richardson J, Gauert A, Briones Montecinos L, Fanlo L, Alhashem ZM, Assar R, Marti E, Kabla A, Hartel S, Linker C. Cell Rep. 2016 May 31;15(9):2076-88.

Delamination of neural crest cells requires transient and reversible Wnt inhibition mediated by Dact1/2. Rabadan MA, Herrera A, Fanlo L, Usieto S, Carmona-Fontaine C, Barriga EH, Mayor R, Pons S, Marti E. Development. 2016 Jun 15;143(12):2194-205.

Nucleosome architecture throughout the cell cycle. Deniz O, Flores O, Aldea M, Soler-Lopez M, Orozco M. Sci Rep. 2016 Jan 28;6:19729.

Cold Temperature Induces the Reprogramming of Proteolytic Pathways in Yeast. Isasa M, Suner C, Diaz M, Puig-Sarries P, Zuin A, Bichman A, Gygi SP, Rebollo E, Crosas B. J Biol Chem. 2016 Jan 22;291(4):1664-75.

Autophagy maintains stemness by preventing senescence. Garcia-Prat L, Martinez-Vicente M, Perdiguero E, Ortet L, Rodriguez-Ubreva J, Rebollo E, Ruiz-Bonilla V, Gutarra S, Ballestar E, Serrano AL, Sandri M, Munoz-Canoves P. Nature. 2016 Jan 07;529(7584):37-42.

EZH2 regulates neuroepithelium structure and neuroblast proliferation by repressing p21. Akizu N, Garcia MA, Estaras C, Fueyo R, Badosa C, de la Cruz X, Martinez-Balbas MA. Open Biol. 2016 Apr;6(4):150227.

Aberrant epigenome in iPSC-derived dopaminergic neurons from Parkinson's disease patients. Fernandez-Santiago R, Carballo-Carbajal I, Castellano G, Torrent R, Richaud Y, Sanchez-Danes A, Vilarrasa-Blasi R, Sanchez-Pla A, Mosquera JL, Soriano J, Lopez-Barneo J, Canals JM, Alberch J, Raya A, Vila M, Consiglio A, Martin-Subero JI, Ezquerra M, Tolosa E. EMBO Mol Med. 2015 Oct 29;7(12):1529-46.

Inntags: small self-structured epitopes for innocuous protein tagging. Georgieva MV, Yahya G, Codo L, Ortiz R, Teixido L, Claros J, Jara R, Jara M, Iborra A, Gelpi JL, Gallego C, Orozco M, Aldea M. Nat Methods. 2015 Oct;12(10):955-8.

Development of tailored and self-mineralizing citric acid-crosslinked hydrogels for in situ bone regeneration. Sanchez-Ferrero A, Mata A, Mateos-Timoneda MA, Rodriguez-Cabello JC, Alonso M, Planell J, Engel E. Biomaterials. 2015 Nov;68:42-53.

HIV-1 immune activation induces Siglec-1 expression and enhances viral trans-infection in blood and tissue myeloid cells. Pino M, Erkizia I, Benet S, Erikson E, Fernandez-Figueras MT, Guerrero D, Dalmau J, Ouchi D, Rausell A, Ciuffi A, Keppler OT, Telenti A, Krausslich HG, Martinez-Picado J, Izquierdo-Useros N. Retrovirology. 2015 May 07;12:37.

Using iPS Cells toward the Understanding of Parkinson's Disease. Torrent R, De Angelis Rigotti F, Dell'Era P, Memo M, Raya A, Consiglio A. J Clin Med. 2015 Mar 30;4(4):548-66.

Gastrin-stimulated Galpha13 Activation of Rgnef Protein (ArhGEF28) in DLD-1 Colon Carcinoma Cells. Masia-Balague M, Izquierdo I, Garrido G, Cordomi A, Perez-Benito L, Miller NL, Schlaepfer DD, Gigoux V, Aragay AM. J Biol Chem. 2015 Jun 12;290(24):15197-209.

Deciphering the genetic programme triggering timely and spatially-regulated chitin deposition. Moussian B, Letizia A, Martinez-Corrales G, Rotstein B, Casali A, Llimargas M. PLoS Genet. 2015 Jan;11(1):e1004939.

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Identification and functional analysis of healing regulators in Drosophila. Alvarez-Fernandez C, Tamirisa S, Prada F, Chernomoretz A, Podhajcer O, Blanco E, Martin-Blanco E. PLoS Genet. 2015;11(2):e1004965.

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