SESAME IR beamline is in full service

Beamline Portrayal

The Infrared beamline is the first completely new beamline at SESAME that has been successfully designed and simulated to allow the Synchrotron Radiation Infrared Microspectroscopy (SR-µFTIR) and imaging, using a Fourier Transform Infrared (FTIR) interferometer. It was scheduled as a DAY-1 beamline, with a reliable capacity to address the diverse requirements of the Infrared scientific community, compared to the laboratory-based Globar Infrared sources. The potential applications will cover a wide range of research fields, including Life Sciences, Biomedical Diagnostics, Environmental Science, Surface and Material Science, Archaeology, Cultural Heritage, Art restoration, Geology, and many others.

The beamline has been designed to transport Infrared radiation to the experimental end station with the minimum aberrations. To ensure the optimum beam delivery, the optical set up delivering the Synchrotron radiation emitted in the infrared range from a bending magnet of the storage ring SESAME has been considered and examined using simulation software packages such as SRW and SPOT X.

IR Dipole chamber (Bending Magnet)
IR Dipole chamber (Bending Magnet)

Following the Conceptual Design Report (CDR), Infrared worldwide experts of different Synchrotron facilities had evaluated the Technical Design Review (TDR). The review provides comprehensive details of the beamline design and management of the complete project.

Beamline Status

The IR beamline was designed and implemented in the framework of the SESAME collaboration agreement with the French Synchrotron Facility, SOLEIL.

The beamline components were fabricated in France (Gavard Company). The installation, commissioning, and coupling of the beamline end station with the Synchrotron radiation was completed in February 2018 with the first IR beam recorded in April 2018. The beamline went into operation and hosting users in November 2018.

Nevertheless, since 2014 till date, and thanks to the presence of the beamline end station (FTIR spectrometer coupled to the IR microscope), infrared research using a Globar Infrared source is successfully achieved at the SESAME Infrared Laboratory.

Significance of the Infrared Synchrotron Sources

IR microspectroscopy is a vibrational technique that is non-destructive and which is exhibiting a strong interest at synchrotron facilities. It combines the spatial resolution of a microscope together with the high chemical sensitivity of the IR spectrometer. In addition to the SR-IR source broad spectral emission and the wavelength characteristics, Infrared Synchrotron sources provide advantages in its brightness/brilliance (about 1000 times brighter) with a signal-to-noise ratio that cannot be achieved by the conventional sources. The mid-infrared region of 2.5-25 µm (4000-400 cm-1) is very informative on the microscopic scale (a few tens of micron resolution). This is mainly because most of the existing molecular groups have their vibrational energies in this spectral range.

Moreover, the spatial resolution is no longer controlled by the geometrical aperture size, but rather by the numerical aperture of the optical system and the wavelength of the light. Therefore, the spot size is set to diffraction limit (~ 3 to 10 µm) in confocal geometry. An optical system used in diffraction limit geometry may use less than 1% of the light emitted from a conventional source whereas Synchrotron sources are optimally matched.

Based on that significance, numerous advances have been made in diverse scientific fields, and the research has resulted in huge number of publications in highly specialized journals, with an important impact at the international level. Examples are shown in the figure below.


Beamline Photon Source

The science mission in all the Synchrotron facilities defines performance goals reaching from the mid-IR (2.5–25μm) to the Far-IR (25–1000μm) regions, SESAME IR-beamline has been designed with a maximum acceptance opening angle of 39 mrad (H) x15 mrad (V) that will utilize infrared Synchrotron emission of the two main sources of radiation; the edge radiation (ER) and the constant field of the bending magnet (BM).


Beamline Technical Specification

The beamline has been designed to produce a dual beam in the experimental floor, which enables serving in the future, two independent end stations. One end station will be made operational at initial development step of the beamline. With the expected growth in user demand, and in diversity of scientific applications, a second end station will be easily implemented, without redesigning any component of the initial set up. An easy mirror swapping is planned to allow the simultaneous operation of the two modes/end stations.

With the appropriate exploitation of the synchrotron source brightness (collection, accurate propagation until the sample), the beamline has the following specifications:

  • Optimum optical performances in the Mid-IR
  • Good performances in the Far-IR –THz domain (down to 200μm wavelength). * Exploiting this feature is not fully optimized at this stage of operation
  • The beamline design has been optimized to provide the following modes of operations, together with excellent detectors’ performance
  • Point-by-Point IR microspectroscopy analysis at diffraction-limited spatial resolution in confocal geometry (ideally for dual aperture l/2NA with 2 μm < λ < 25 μm, where N.A. is the Numerical Aperture)
  • IR imaging by raster scanning the sample

Beamline Design (Schematic)

The Synchrotron Infrared beamline is composed of three sub-systems:

  1. Beam extraction
  2. Optical system for beam steering and transport
  3. End-station Instruments (i.e. spectrometers, microscopes)

Beam coupling with the FTIR spectrometer via the matching box

The coupling box, positioned after the exit of the beam from the last KBr window and before the spectrometer, allow reshaping the divergent beam, rectangle, in a more or less squared beam, collimated. This collimated beam enters the interferometer, and can be moved in X, Z direction, and tilted in order to optimize the coupling and fitting with the Schwarzschild of the microscope.

Experimental Station [Instrumentation, set up and accessories]

Being designed for optimum performance from the near- to the far-IR, a suite of single and array detectors equip the end stations to cover the whole IR range. The wide range of applications call for a versatile suite of sample environments and sampling methods coupled with off-line facilities for sample preparation and handling as well as data analysis.


The end station is equipped with 8700 Thermo Scientific© FTIR spectrometer coupled with Thermo Scientific © Nicolet Continuuμ IR-microscope.














The end station is equipped with 8700 Thermo Scientific© FTIR spectrometer coupled with Thermo Scientific © Nicolet Continuuμ IR-microscope

Data formats and Analysis software

OMNIC© version 9 is used for data collection and data analysis. Single spectra are saved as OMNIC Spectrum files. 2D infrared maps files are saved as OMNIC map files (.map). OMNIC Multiple files contain all spectral and x-y spatial information for a two dimensional grid map, plus related captured video images.

Following data analysis packages are available for use on the off-line data analysis at SESAME PCs.

  1. The Unscrambler v 10.5
  2. CytoSpec v 1.3.02
  3. Orange (Open Source Software)

Opportunities and Applications of Infrared Microspectroscopy

IR spectroscopy is among the most powerful analytical techniques available to the scientists nowadays being a fast tool to get important information about the chemical compounds of practically any sample in practically any state may be studied. Sample preparation is perhaps the most critical part in successful infrared Microspectroscopy experiments, but since there are a number of ways to use the microscope, sample preparation can be done also in variety of ways.

Applications cover a wide range of research fields, including life and material science, biochemistry, microanalysis, polymers, archaeology, geology, cell biology, biomedical diagnostics, pharmaceuticals and drug design, environmental science, and forensic investigations. Examples are listed below.

Biology, Biomedicine: Single cells, human and animal biological tissues, bacterial identification, etc.
Archeology: Ancient manuscripts, human remains, mummies, and ancient cosmetics, etc.
Geology: Inclusions in minerals, Interfaces, archaeological minerals, soil, etc.
Thin Films: Analysis and chemical imaging of thin films, protection layers, etc.

Possible techniques of FTIR spectroscopy/microscopy include:

  1. ATR Spectromicroscopy
  2. Grazing incidence angle
  3. Fluorescence illumination:
    • Wide Band Blue Fluorescence Cube 450-480nm
    • Wide Band Green Fluorescence Cube 510-550nm
    • Wide Band UV Fluorescence Cube 330-385nm
  4. Reflection
  5. Transmission


  1. TE Cooled DLaTGS Detector with KBr Window (12,500-350 cm-1)
  2. DLaTGS Detector with Polyethylene Window (700-50 cm-1)
  3. Room Temperature InGaAs Detector for NIR (12.000-3.800 cm-1)
  4. 50um MCT-A Detector (11.400-700 cm-1)
  5. MCT-B Detector (11.700-450 cm-1)

Sample Environment:

Microscope coupled to a Fourier transform IR spectrometer bench Simultaneous fluorescence measurement, ATR and glazing incidence objectives.

The simplest way to collect infrared spectra is in the transmission mode, in this mode, thin samples are generally needed, 5 to 30 µm is the typical thicknesses for the transmission measurements, polymers, biological tissues and geological and organic materials can be studied in this mode.

The second most common technique of recording infrared spectra is the reflection mode. In reflection mode, the infrared beam penetrates the sample, then reflects off from the substrate, returns to the sample and passes back through the illumination objective, Samples studied in reflection are normally have high reflective properties, or polished samples which cannot be cut by microtome to a thin section.

Highly reflective substrates have commonly thickness of coating material approximately of 1-10µm. The flat and smooth sample surfaces are important requirements in this mode to avoid scattering. Irregular surfaces reduce the collection efficiency, and produce oscillations in the background of the spectra. In special cases, irregular surfaces can be pressed to adjust the slope of the sample with respect to the incident light, and to make the surface of the sample parallel to the microscope stage.

Attenuated total reflection is a technique that probes the near-surface region of materials. Materials that are not reflected and cannot be cut into thin sections, such as liquids, semi solids, and pliable solids, like rubber and plastic, can be analyzed using an ATR technique. This method works well with samples that are too opaque or too thick for standard transmission methods.

The sample is placed in contact with a crystal of high refractive index such as ZnSe, Ge, or diamond. Total internal reflection occurs along the crystal-sample interface. The IR beam entering the crystal is totally internally reflected within the crystal. The beam creates an evanescent wave, which projects orthogonally into the sample in intimate contact with the ATR crystal. Some of the beam absorbed by the sample and the reflected radiation return to the objective.

Grazing incidence sampling in FTIR spectroscopy is a useful technique for measurement of thin films on highly reflective substrates. The technique is often used for sub-micron thick coating substrates. Films that are typically less than 1µm thick can get benefits from the technique. The basics of the technique involve measurements of the reflected beam from a sample surface at a given angle of incidence. Using Schwarzschild objective, that contains a beam mask, transmits only the grazing incidence rays onto the sample.

  1. Transmission mode:
  2. Reflection mode:
  3. Attenuated total reflection (ATR):
  4. Grazing incidence angle:


Person Position Email Address
Gihan Kamel IR Beamline Principal Scientist
Ahmed Refaat IR Beamline Scientist