Mass spectrometers and preparation systems

These system are used for routine measurements of:

  1. Clumped isotopes of carbonate minerals and CO2 (Hagit Affek)

  2. Compound specific (e.g. DMS,  petroleum)  δ34S analysis at the picomole level by gas chromatography (GC) and high resolution multi-collector inductively-coupled plasma mass spectrometry (MC-ICP-MS) (Alon Amrani)

  3. Dust and soil phosphate δ18O  (Alon Angert)

  4. Organic δ13C and water δ18O (Eugenie Barkan

  5. Δ17O and δ18O of Oand H2O (Boaz Luz)

Computer cluster for modeling of atmospheric and oceanic Processes

The cluster comprises 192 Haswell i7 2.7GHz processors arranged in eight cores of 24 processors each, with each core containing 128GB. In addition, a separate 16-core, 512GB machine is available for big-data processing (Haim Garfunkel, Hezi Gildor).

Clean laboratory


The clean laboratory is used to prepare samples with pico- to nano-molar levels of trace metals for concentration and isotopic composition analyses. Laboratory room surfaces are made of non-corrosive, acid resistant, metal free plastic materials (including floors, cabinets, and benches). It has a monitored positive pressure air supply with HEPA filtration, and has its own clean water supply. The laboratory is composed of several separated working spaces with different degrees of contamination-control, which serve different purposes.

Several analytical instruments, located in a next-door analytical laboratory, are used for the analysis of samples that were prepared in the clean laboratory.

Analytical equipment:

(1) Inductively Coupled Plasma Mass Spectrometer (ICP-MS; Agilent 7500cx) for analysis of trace metals.

(2) Inductively Coupled Plasma Optical Emission Spectrometer (ICP-OES; Analytic Jena PlasmaQuant PQ9000 Elite) for analysis of major and minor elements.

(3) Direct mercury analyzer for solid, liquid and gas samples (Milestone DMA-80).

(4) Multi Collector Inductively Coupled Plasma Spectrometer (MC-ICP-MS; Neptune, Thermo – shared w/ A. Amrani) for the analysis of isotopic ratios (Sr, Pb, Nd, U, Fe, Cu, Mo).

(5) X-Ray Fluorescence spectrometer (XRF; Bruker Tracer III–V handheld XRF) equipped with a SiPIN Detector and excitation source of X-ray-tube Rh target live time count.

(6) Micro-balance (Mettler Toledo MX5) an ultra-sensitive analytical balance (±1 mg).

   (7) Auto-siever (GA-6 Gilsonic) for size separation equipped with 10mm, 20mm, 63mm, 75mm, 125mm, 250 mm sieves. 


clean lab_Yigel Erel_1.png


Clean laboratory_Yigal_Erel2.png

Magnetometer and shielded room

The magnetically shielded room is used for sensitive paleomagnetic experiments, and houses a fully automated superconducting rock magnetometer for magnetic measurements and characterization (Ron Shaar).

Electron Probe Micro-analyzer (EPMA)

electron probe  



Omri Dvir   - Instrument supervisor

Electron Probe Microanalyzer (EPMA) Lab at the Hebrew University of Jerusalem,
Fredy and Nadine Department of Earth Science

In our lab, we have a JEOL Superprobe JXA-8230. SEMs are built mainly for imaging
samples using SEI or BSEI detectors. An EPMA is designed for chemical analysis of the
characteristic X-Rays emitted from a sample when probed by an electron beam. An
EPMA can quantify elemental concentration using electron dispersive spectroscopy
(EDS) and wavelength dispersive spectroscopy (WDS) to detect and count
characteristic X-Rays emitted from a sample. There are pros and cons to using the
EDS and WDS detector (mainly time and the necessity of experience using the
techniques). We will be happy to discuss these in person.

Imaging options in the EPMA:

-Back scattered electron imaging (BSEI) is sensitive to the mean electron density
(atomic weight). Back scattered electrons ate a form of elastic scattering in which
incoming incident electrons are bounced back off the sample to hit the detector.
(Electrons scattered by Coulombic interaction with the charge of the atomic nucleus
aka Rutherford scattering.)
-Secondary electron imaging (SEI) reveals the sample's topography due to the
variation in SE production at different tilt angles. Secondary electrons are ejected
from the k-shell by inelastic scattering interactions with the electron beam. They
originate within a few nanometers of the surface.
-Cathodoluminescence- Promotion of valence band electron to conducting band can
emit photon of electromagnetic radiation in the visible light region.

Chemical analysis in the EPMA:

-EDS Detector: Energy dispersive spectroscopy counts the number and energy of X-
Rays emitted from a specimen. The energy spectrum of the X-Rays characterizes the
atomic structure of the emitting element.
-WDS Detector: Wavelengthe dispersive spectroscopy counts the number of X-Rays
of a specific wavelength diffracted by a crystal. In contrast to EDS, WDS detectors
only count the X-Rays of a single wavelength at one time that characterize the
atomic structure of the emitting element.
For more information see the following website:


Atomic force microscope

The instrument is mainly used for studying water-rock interaction at the nano-scale. Nanomechanical properties and magnetic properties of geological materials are also routinely measured (Simon Emmanuel).

Confocal microscope

The microscope is used for live imaging of biomineralization in calcifying organisms (mainly foraminifera and corals), and allows imaging of fluorescence at a cellular level (Jonathan Erez).

Scanning Electron Microscopy (SEM)



Instrument supervisor: Omri Dvir    


The SEM can be used to examine surface details of solid materials. Internal surfaces

can be exposed by sectioning or fracturing. It is equipped with an energy dispersive

spectrometer which permits qualitative and quantitative compositional analysis.

Image analysis software permits detection, measurement and analysis of features of


  • Secondary electron imaging (morphology and surface topography)
  • Backscattered electron imaging (compositional contrast and phase distribution)
  • Digital image collection, enhancement and analysis
  • Elemental recognition and phase identification
  • Quantitative compositional analysis
  • Digital x-ray maps and linescans
  • Analysis of particle samples

JEOL JSM6400 Digital SEM with:

  • EDS (oxford) Energy Dispersive X-ray Analyzer

Neev Center for Geoinfomatics

The Neev Center for Geoinfomatics came into existence around 2011-12 as a result of several coalescing circumstances. These were:

1) The presence of an appropriate space due to the removal of an ancient mass spectrometer operated together with the Geological Survey of Israel (GSI);

2) The beginning of construction of the new location of the GSI  only 400 m from the IES;

3) The decision of the Israel Government to invest in a state-of-the-art research vessel, the R/V Bat Galim, fully equipped for the full gamut of marine geophysical, geological, and oceanographic research;

4) The experience of the international networking associated with the ICDP Dead Sea Deep Drilling Project in 2010-11.


In light of the above, Prof. Amotz Agnon approached Dr. John K. Hall, retired from the GSI in 2006, about becoming the Godfather of what would become the Center. He was told that there was interest in establishing a HUJI Center for Ocean Research, and that Shlumberger had already provided seven licenses to their Petrel seismic data processing software. Dr. Hall was weirdly enticed by this proposal, because as a GSI Division Head he had been responsible for the recently removed mass spectrometer, but had never visited it, and also by the fact that his first university job at RPI had been to help build their mass spectrometer in the summer of 1961.

Dr. Hall's background was a natural for a Godfather. Having a BSc in Geophysics from RPI, he had acquired a PhD in Marine Geophysics from Columbia's Lamont-Doherty Geological Observatory in 1970, after three years of primarily seismic work at sea at Woods Hole Oceanographic Institution (WHOI). Hall had done his doctoral work in the Arctic from a drifting ice station, with mostly home-built equipment and hand-crafted computer programs. He was the first geophysicist at the GSI, and as a marine scientist concentrated primarily on mapping the offshore.

When shown around the numerous labs at the IES by Prof. Yigal Erel, Hall was impressed by what Dr. Rotstein cited (in the 2013 Evaluation) as HUJI's "current distribution of disciplines, in which geochemistry appears to be over represented and overwhelmingly dominant". Dr. Hall had been somewhat of an outlier at the GSI during his 35 years there, compiling the bathymetry of the SE Med, Kinneret, Dead Sea, and Red Sea, as well as the Black and Caspian Seas and Persian Gulf, and producing the 25 m digital Terrain Map (DTM) of Israel and its immediate neighbors over a 6 year period from 1987-1993.

This spatial, rather than pinpoint orientation towards earth science (geochemical analyses of micro-specimens or vertical analyses of isotopes, composition, and paleontology from a single core or borehole) is now one of the driving forces behind the Neev Center. Little Israel itself features some 20,200 km2 of land, while the area of Israel's Mediterranean EEZ is over 17,000 km2, with ~600 km2 in the Dead Sea, ~445 km2 in the Kinneret, and ~34 km2 in the Red Sea. Thus the breadth of the land and its adjacent areas, probably to the limits of our Arabian plate, should be the subject of its studies and expertise.

The timing of of the Neev Center's inauguration was fortuitous in view of suggestions from the Committee for the Evaluation of Geology and Earth Science Study Programs in early 2013 to modernize and augment the spatial aspects of the programs in the Institute.

The Center now features the following:

1) Computers. The original seven powerful PC computers with large monitors and extensive disk space have now grown to ten work-stations. They are attached to a Center LAN, the HUJI network, and their own mass storage. An extra-large flat-screen is set up for lecture and video viewing.

2) Computer Software. The Center has seven current Schlumberger PETREL licenses for working with 2D profiles and 3D seismic cubes from the oil and gas companies. The new Midland Valley’s MOVE is available for stratigraphic and structural modeling. Golden Software programs Surfer, Grapher, Voxler, and Didger are available. A license is available for a large lidar analysis package used for terrestrial lidar. For digitizing there is Able Software's r2v, and various version of Global Mapper up to GM15. QPS's CARIS HIPS/SIPS can deal with multibeam bathymetry and sidescan sonar data, while multiple types of grids and cross-sections can be manipulated by Fledermaus.

3) Legacy data scanning. Today's graduate students look to the web for much of their legacy knowledge. In the earth sciences, this is a tremendous quantity of analog data on maps, logs, reports, bulletins, slides etc. The Center hosts a Contex IQ4490 large format (110 cm) scanner, an A3 flatbed scanner, and a Fujitsu ScanSnap duplex auto color selection scanner for paper documents. For permanent archiving of legacy slides. there is a Nikon CoolScan 5000 ED slide scanner with SF-210 mounted slide feeder offering 14 bit color at 4000dpi.

4) Camera equipment. The Center has a DJI Phantom 3 Pro drone with gimbaled HD and 4K video and still camera. Various GoPro camera are available for documenting field work. Software is available for video editing, and Agisoft can be used to produce 3D models from oblique drone photos.

5) Field equipment. Together with other universities the Center now fields a Geometrics Seismic Reflection system with 96 geophones for shallow seismic studies. Other equipment such as Geometrics Cesium marine magnetometer and high resolution Klein 4500 sidescan sonar are sometime available via the IOLR. Upgraded GPS navigation and lidar imaging systems are contemplated. Also a marine metal detector.

6) Library. New books from geophysical scientific societies such as GSA, EAGE, AAPG, SEG, and Geological Society of London are regularly acquired. Other books on remote sensing and satellite navigation and global topography are acquired as they appear. The Center also hosts the results of some 10 years of scanning of materials from the 100m of shelf space and 22 map cabinets (8 drawers each)in Dr. Hall's home library. The fifty years of journals from this library are now at Haifa University's Charney School of Marine Sciences, and the marine geological and geophysical books and maps at the Hall Map Archive at the IOLR in Haifa. These scans together with constant additions from the GSI library holdings are also available on the disk storage of the Neev Center. Data sets for the entire globe are also archived at the Center. Land topography and ocean bathymetry  sets range from the GEBCO 2014 and SRTM-Plus Bathy world grids at 30sec and finer. Regional sets such as EMODNet and MediMap Group are also available. Land grids at 1 sec (30m) from ASTER 2 and SRTM v3 are kept up to date, with efforts to acquire finer datsets as the satellites obtain them. LANDSAT 15m imagery for the world are also keyed into the 30m topographic sets.

7) Poster and map distribution. The Neev Center is frequented by students and personnel from the 7 MERSI (Mediterranean Sea Research Center of Israel) universities and institutes. Printed legacy posters, books, and postcards produced by Dr. Hall of Israel's topography, geology, bathymetry etc. are available at the Center.

8) Connection to the marine world. The new R/V Bat Galim will be used to carefully study the offshore seafloor. Multibeam sonar operators will be needed for cruises up to 8 days in length, so that a cadre of student sonar operators should be available. The new attitude to bathymetric swath data is that availability of grids should be limited to those who collect and analyze the data. The initial assumption is that a pool of up to 20 trained operators should be able to provide 3 people available for three watches per day for such cruises. Knowledge of multibeam operation and data analysis should also provide needed work in the offshore industry as ships continue to be equipped for swath survey. Despite what world maps suggest, only 12% of the oceans (71% of Earth) are mapped.

9) Connection to the GSI. Dr. Hall's retirement in 2006 basically ended the GSI's hands-on connection to marine geophysical work at sea. It is hoped that Neev Center students will continue this connection. For instance one student today is working on the shallow waters of the Red Sea as mapped from satellite imagery.

10) A nice place for students. The Neev Center provides a friendly workplace, with Expresso coffee machine, refrigerator, color printer, and other amenities.


A Note on David (Bibi) Neev (Rabinovich): The Center is named for Dr. David Neev, former Palmach and Haganah intelligence officer, Oil Commissioner, author with K.O. Emery of the main bulletin on the Dead Sea, and founder of the GSI's Marine Geology Division. Dr. Neev hired Dr. Hall, unseen, over the telephone in 1969. The two of them worked together in studies of the regional and global tectonics, and initial seismic surveys of the Mediterranean and Dead Seas. Together with Leslie Greenfield, Dr. Neev worked up the Tamar gas field prospect for Yossi Langotsky. Now in his nineties, Dr. Neev hopes that the Neev Center will continue to influence the success of geophysics in Israel and its offshore.



From the Evaluation, 2010

The IES has a close working relationship with the Geological Survey of Israel, which has broadened both research and educational opportunities and led to “the whole being greater than the sum of its parts” for both institutions. The move of the Geological Survey to the Givat Ram campus will afford even greater opportunities for collaboration in research and for shared infrastructure, likely allowing for instrumentation opportunities now not currently feasible for the individual institutions. This connection will also make it even easier than it is already for Geological Survey scientists to engage in teaching in the IES and amplify further their professional opportunities and development.

The discovery of oil in the eastern Mediterranean offers a range of possibilities that might benefit the IES, Hebrew University, the Geological Survey, and Israel at large. We endorse the approach being taken by the IES, with a possible emphasis on geophysics, of supporting individuals as they see opportunities in their own research programs to benefit from and contribute to this. Moreover, the university level goal of embedding these opportunities in a larger, coordinated university‐wide set of activities in energy‐related science also appears wise. We also endorse IES’s efforts to pursue educational opportunities connected with these discoveries (e.g., an M.Sc. in fossil fuels; enhancing teaching in geophysics), including its exploration of collaborations with other Israeli universities in these teaching programs. Likewise, we also endorse IES’s engagement in inter‐university research activities (especially the new marine sciences program centered at the University of Haifa, which can ensure engagement of the Hebrew University with national efforts in this area). Finally, recognizing the importance of the Eilat facility, the review committee endorses the university’s intention to maintain this valuable educational and research resource.

Laser Ablation ICP-MS Laboratory

RESOlution ASI SE laser
RESOlution ASI SE laser


Omri Dvir   - Instrument supervisor

The Laser Ablation (LA) ICP-MS facility performs direct analyses of virtually any material. The LA-ICP-MS technique is particularly useful for in-situ analyses of trace elements for applications requiring understanding of the spatial variation of elemental content within the sample.

The laboratory currently operates an Agilent 7500 quadrupole ICP-MS and ASI (SE) Resolution 193 nm excimer Laser Ablation systems covering a wide range of specific applications, the high-energy UV laser ablation (LA) system produces craters in the sample ranging in size from 2 microns to 100 microns. The ablated material then swept from the sample cell directly into the plasma of the ICP-MS. The ablated material then ionized similarly to any liquid sample aerosol (for more information on ICP-MS). The LA system is fully computer controlled with a real-time video imaging system capable of reflected and transmitted light (polarized light available) viewing. The system can programmed to ablate continuous lines, spots or a variety of more complex ablation patterns. (for more information on LA-ICP-MS).

Samples intended for LA-ICP-MS can be prepared in a variety of routine ways. The lab routinely accept thin sections, thick sections, microprobe round mounts or small samples. For specific sizes, please contact to the laboratory staff.

Quantitative LA-ICP-MS analyses are possible if the following criteria:

  1. The sample must be of somewhat known and must be known or assumed to be of known major element composition.
  2. The sample must be of matrix of which a calibration standard reference material (SRM) of close matrix match is available.

The technique is capable of determining many trace elements down to low ppm and even ppb levels, although absolute detection levels are highly element, sample matrix and spot size dependent.

The LA-ICP-MS lab has been involved in a wide variety of studies involving geological, biological, environmental and material science related samples.

Current analytical instruments:


State-of-the-art 193nm excimer laser ablation system for in-situ sampling of solid materials. The system offers controlled ablation of geological materials at spot sizes ranging from 2 to 100um at energy densities up to >20 J/cm2.


Our workhorse quadrupole mass spectrometer for trace element analyses in a wide range of matrices and for U-Th-Pb isotope analyses by laser ablation.


  • Trace element analysis in various samples such as geological, biological archeological and Industries.
  • U-Th-Pb isotope analysis of zircon and rutile.
  • Powders analysis.
  • Metal analysis.
  • Air filter analysis.
  • Food Industries analysis.