Optical Spectroscopy Platform

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  • Physical Sciences

Irantzu Llarena Conde Email: illarena@cicbiomagune.es Telephone no.: +34 943 00 53 41

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Contact with Platform Manager, by email external.services@cicbiomagune.es or check the services here.


The optical Spectroscopy platform offers a wide range of techniques to characterize physico-chemical properties of biomaterials and biosurfaces. Training, assistance for experimental procedures and data interpretation are provided to support researchers. The platform is equipped with the following systems:

Scanning confocal fluorescence microscopes, Raman confocal microscope, epi-fluorescence microscope for in vivo imaging, dark filed microscope, flow cytometer, UV-Vis-NIR spectrophotometers and fluorimeters, FT-IR and Raman spectrophotometers, circular dichroism, differential scanning calorimeter and isothermal titration calorimeter.



Confocal Fluorescence Microscope Zeiss LSM 880 Airyscan and MaiTai DeepSee
The microscope is equipped with three Ar laser excitation sources (458, 488 and 514 nm), DPSS (561 and 590 nm) and HeNe (633 nm). It is coupled to a MaiTai DeepSee multiphoton laser, with variable excitation range (690 to 1040 nm). It has two PMT photomultiplier type detectors, one standard and one with high sensitivity in the infrared range, as well as a GaAsP detector for detection in the visible spectrum. All three spectral detectors can be used simultaneously in confocal image acquisition. The Airyscan module is an array of detectors that allows measurements with high lateral resolution of 150 nm and axial of 400 nm, on the 488 channels. It also has a BIG-2 detector module, composed of two GaAsP detectors for high sensitivity multiphoton measurements. Allows for fluorescence correlation and cross-correlation spectroscopy measurements.

Confocal Fluorescence Microscope Zeiss LSM 510 Meta
The microscope is equipped with three lasers which cover the following excitation wavelengths (458, 477, 488, 514 nm), DPSS 516nm and HeNe 633nm, been possible to use all of them simultaneously. A wide range of long pass and band pass filters are configured in different channels before signals reach PMTs detectors. Equipment is also set up with a ConfoCor 3 spectroscope. It's used for fluorescence correlation spectroscopy, whereas the beam is parked in a sample, which might consist of a solution or a cell, fluorescence fluctuations are recorded and analysed by the so-called correlation function. Acquisition and analysis of LSM image and Confocor is controlled by Zen software. Microscope is also fitted with a FLIM (Fluorescence lifetime imaging) unit from Becker&Hickl Gmbh equipped with a pulsed diode laser of 405nm excitation wavelength, which can be set to 20, 50 or 80MHz repetition rate. SPCM software set up parameters and allows multidimensional data analysis.

Confocal Raman microscope (Renishaw inVia Raman Reflex)
The Raman microscope collects fingerprint spectra of materials and molecules. In combination with the motorized x,y,z scanner stage with 112 mm x 73 mm lateral travel distance 2D Raman images can be measured and chemical composition maps be created in standard or confocal mode achieving higher lateral and axial resolution. A humidity cell (GenRH) is available and can be used for living cell samples or samples requiring defined environment and inert gas atmospheres. The macro sampling kit facilitates Raman measurements of liquid, solids and powders. Raman microscope (Leica) is coupled to three different lasers for excitations at 532 (green), 633 (red) and 785 nm (NIR) and equipped with an internal Si calibration source and a video camera. The spectrometer features two front-illuminated Peltier-cooled CCD cameras and gratings of 1800 and 1200 grooves/mm providing high spectral resolution (1 cm-1) and a 600 grooves/mm grating optimized for 532 and 633 nm for low resolution. The streamline option allows fast sample scanning at high spectral resolution and polariser/analyser kit available for the three excitation wavelengths enable polarised-Raman measurements. Latest 4.4 Wire software update controls the system and can be used to data analysis, processing, and presentation.

Portable Raman spectrometer (B&W Tek iRaman)
The portable spectrometer is a compact instrument designed for Raman spectra measurements of macroscopic samples and materials in form of liquids, gel, powders and solids. The spectrometer is equipped with a 300 mW 785 nm laser and operates in the spectral range from 175 to 3200 cm-1 with spectral resolution of 3.5 cm-1 featuring patented CleanLaze technology for laser stabilization with a line width of 0.3 nm and a thermoelectrically cooled linear 2048-pixel array detector. Laser light is coupled to the probe BAC 100 and collected signal outcoupled through optic fibres. The probe can be mounted on a manual x,y,z stage and has a spot diameter of about 85 mm (in focus) at 5.6 mm working distance. BWSpec4 software is used for data acquisition and analysis.

Cell Observer microscope (Zeiss Axio Observer)
The epifluorescence microscope, cell observer, allows quantitative and qualitative analysis of fast and slow processes in live cells under biological conditions. The equipment incorporates Colibri LED illumination system and fluorescence lamp, which allow combination of fluorescence imaging with different brightfield imaging modes as DIC and phase contrast.  Microscope is fitted with an EMCCD camera and incubator for the exact control of temperature, CO2 and humidity. Motorized stage allows Z-stack acquisition, multilocation measurements and full specimen reconstruction (tile scan) Zen blue software controls image acquisition, processing and analysis.

Dark-field microscope (Nikon Eclipse Ti-U)
The dark-field microscope is an inverted microscope allowing light scattering imaging within the wavelength range of 400 and 900 nm in solid crystals and thin films, assemblies and colloidal or polymer suspensions. The microscope features Ti-DH Pillar illuminator 100W, bright-field (air) and dark-field condensers (air with numerical aperture 0.8-0.95 and oil with numerical aperture 1.2-1.43), polarizers for incoming and outgoing light, several neutral density filters, color video camera (Coolpix) and is equipped with a motorized sample holder. RS image software is used for data acquisition.

Flow Cytometer (BD FACSCantoII)
Flow cytometry using light scattering and multicolour emission detection allows the physico/chemical characterization of cells and microparticles, performing up to 8 colour detection simultaneously. The optics of the BD FACSCanto II system consist of an excitation source with up to three lasers, a blue (488-nm, air-cooled, 20-mW solid state), a red (633-nm, 17-mW HeNe) and a violet (405-nm, 30-mW solid state). Laser excitation optics illuminate the flow cell containing the sample and collection optics direct light scatter and fluorescence signals through spectral filters to the PMTs detectors. The carousel automatically loads up to 40 12x75-mm tubes for predefined measurements. FACS Diva software controls the setup, acquisition of flow cytometer workstation. WinMDI and FlowJo analysis software are available for further analysis of the data.

Spectrofluorometer (Edinburgh FS5)
It allows to acquire emission, excitation and synchronous spectra from ultraviolet to near-infrared UV-NIR between 200 and 1650 nm. It also allows to record the kinetic profile at multiple wavelengths, perform polarization and fluorescence anisotropy measurements in liquid samples, thin films and solids. It has an integrating sphere that allows measurements to be made to determine the fluorescence quantum yield and acquire diffuse reflectance spectra. The system allows the characterization of fluorescence and phosphorescence lifetimes, for this purpose it uses high intensity pulsed LEDs (340 and 405nm) and pulsed xenon lamps respectively. The system is controlled by the Fluoracle software.

Spectrophotometer UV-vis-NIR (Varian Cary 5000)
The spectrophotometer is a double-beam instrument operating within the wavelength range between 175 and 3300 nm offering biochemical analysis (including kinetics, thermal denaturation/renaturation), quantitative analysis and wavelength scanning. The available multi-cell holder compartment is coupled to a water bath and a Peltier-cooler allowing temperature-controlled measurements within the range from 263 to 373 K. The solid sample holder enables UV-vis-NIR absorption measurements on thin films. The spectrometer features double out-of-plane Littrow monochromator, dual-sided 1200 lines/mm (for UV-vis) and 300 lines/mm (for NIR) grating, R928 photomultiplier tube (for UV-vis) and cooled PbS photocell detector (incorporated PbSmart technology, for NIR), tungsten halogen visible source, deuterium arc UV source and Hg lamp for wavelength accuracy validation and fits Schwarzchild coupling optics, variable and fixed slits (spectral bandwidth limits from 0.01 to 5 nm for UV-vis and from 0.04 to 20 nm for NIR). CaryWinUV software is used to control the measurements, data acquisition, processing and analysis.

Circular Dichroism Spectropolarimeter (CD Jasco J-1500)
Allows measurements of absorbance, circular and linear dichroism from ultraviolet to near-infrared UV-NIR (180 and 1600 nm); It also allows to measure the fluorescence and rotational scattering fluorescence. It I equipped with a Xe light source (power 150 W), Peltier temperature control and an integrating sphere for measurements of samples with high light scattering from solids, either by reflection or by diffuse reflectance. The system is coupled to an ATS-429L automated titration system. The system is controlled with Spectra Manager II software.

Fourier Transform Infrared Spectrophotometer (FT-IR – Bruker Invenio-X)
Allows light absorption analysis of solid, liquid or gel samples, in the transmission range between 30 and 15.500 cm-1 and an accessory to measure in attenuated total reflectance (ATR) mode. The equipment has a software selection system for the three detectors: InGaAs, DLaTGS and DLaTGS. The system is controlled by the OPUS 9 software. A hydraulic press is available for the compression preparation of tablets.

Differential Scanning Calorimeter (DSC Nano III 6300)
Nano-Differential Scanning Calorimeter III measures absolute heat capacities of macromolecules in dilute solution, it can be used to study the thermal denaturation stability and structure, with as little as 50 μg. It’s design for the study of biological samples in aqueous media.
The instrument is a power compensation design using a completely solid-state thermostat and is equipped with fixed platinum cylindrical cells. Scan rates up to 2°C/min. in both the heating and cooling directions, an operating temperature range of -10 to +130°C and baseline repeatability of ±0.4 μcal/C @ 1°C/min.

Isothermal Titration Calorimeter (VP-ITC MicroCal)
VP-ITC (Isothermal Titration Calorimeter) measures heat evolved or absorbed in liquid samples as a result of mixing precise amounts of reactants, allows the study of molecular interactions, binding affinity, structural information and kinetics. A pair of identical coin shaped cells is enclosed (1.4ml cell/volume). Temperature differences between the reference cell and the sample cell are measured, calibrated to power units. Spin rates range is 0 to 1000 rpm. The temperature operating range is 2°C to 80°C. Measurements are run with VP viewer 2000-ITC software.

Microscale thermophoresis, MST – Nanotemper Monolith. It allows to measure the dissociation constants (Kd) of proteins in aqueous solution or of cellular lysates by adding serial dilutions of the ligand. Is equipped with two red and blue fluorescents channels, that allows to analyse protein concentrations between nM and mM working in a temperature range between 20 and 40 °C.


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