Equipment
University of Ljubljana
Faculty of Medicine
Center za klinično fiziologijo
MR tomograf Philips Achieva 3.0T TX d Stream
Philips Achieva z multi-transmit tehnologijo ter nadgradnjo z digitalizacijo signala v samih tuljavah, omogoča zajemanje visoko resolucijskih slik ob hitrejšem/vzporednem zajemu in z odlično kvaliteto. Naš MRI sistem je opremljen s širokim naborom tuljav in podporno opremo za raziskovalno snemanje. Zato lahko poleg visokoresolucijskih strukturnih slikanj nudimo tudi natančna difuzijska slikanja, hitra visokoresolucijska funkcionalna slikanja BOLD modalnosti, podrobnejša slikanja žil z metodami perfuzije, fazne kontrastnosti ter časa pretoka. Philips tomografi so priznani tudi bo najboljših spektroskopskih meritvah ravni metabolitov tako v možganih kot drugje v telesu. Tomograf je bil inštaliran leta 2013 ter nadgrajen leta 2020.Infrastructural Center – Biomedical Center for Microscopy
No | Equipment name (equipment location) | Use |
1 | Transmission electron microscope Philips CM100, (IBC FM) | Analysis of cell ultrastructure, display of immunolabeled molecules in cells and in extracellular matrix |
2 | Scanning electron microscope, TESCAN, (IBC FM) | Analysis of cell membrane surfaces and structures and the structures in extracellular matrix |
3 | Fluorescent microscope Axioscope Zeiss with Apotome attachment, (IBC FM) | Three-dimensional analysis of the distribution of fluorescently labeled molecules in cells and extracellular matrix |
4 | Freeze-fractioning device, (IBC FM) | The apparatus enables the preparation of samples for the analysis of larger surfaces of the plasma membrane and intracellular membranes. The FRIL method enables labeling of molecules by showing their distribution across the membranes |
5 | Cryoultramicrotome Leica EM FSC, (IBC FM) | Microtome for cutting ultrathin sections of frozen samples for cryoelectron microscopy and immuno-gold labelling. |
6 | High pressure freezing device HPF (IBC FM) | Device for quick freezing of biological samples at high pressure. |
7 | Fluorescence microscope Eclipse TE300 (Nikon), (IBC FM) | Analysis of the distribution of fluorescently labeled molecules in cells and extracellular matrix |
8 | Laboratory equipment for cell cultures (laminaries, incubators) (IBC FM) | Sterile work with cell cultures (BSL2) |
9 | Transmission electron microscope JEM-1400 Plus (IMI FM) | Analysis of cell ultrastructure, display of immunolabeled molecules in cells and intercellular space, electron tomography (3D tomography of cell ultrastructures) |
10 | Transmission electron microscope JEM-1200 (IP FM) | Analysis of cell ultrastructure, display of immunolabeled molecules in cells and extracellular matrix |
11 | Confocal microscope/TIRF/Rescan (IBF FM) | Three-dimensional analysis of the distribution of fluorescently labeled molecules in cells and extracellular matrix. |
Biotechnical Faculty
IC MBV Oddelek za biologijo
| Field-emission scanning electron microscope FE-SEM JSM-7500F (Jeol) | A high-resolution scanning electron microscope with a cold-field emission source of electrons (cold FEG), which enables observation of the surfaces of sensitive biological samples with nanometer resolution.
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| Mikro-CT Neoscan N80 | The N80 X-ray micro-tomograph enables X-ray analysis and spatial (3D) reconstruction of native animal and plant specimens. It operates in the range of 40 to 100 keV and achieves a resolution of in a micrometer range. The system is upgraded with a cooling and heating sample stage, allowing observations of frozen objects and analysis of the temperature effect on samples in situ.
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| AxioImager Z.1 microscope with Apotome system (Zeiss) | The light microscope enables observations by various illumination techniques (bright and dark field microscopy, differential interference contrast (DIC), phase contrast) and epifluorescence. The microscop is upgraded by the Apotome system, which enables 3D and time-lapse analysis of samples.
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| Motorized fluorescent stereomicroscope SMZ25 (Nikon) | The stereomicroscope enables observation of objects in size range between a few tenths of a millimeter to a few centimeters, isolated animal and plant organs and tissues, bacterial and fungal cultures, and larger tissue slices by various regimes of illumination. These include brightfield illumination by transmitted light, oblique contrast, the dark field illumiation, classic surface illumination and epifluorescence. In addition, stereomicrscope enables image capture without parallax, with motorized movement in the z-axis, as well as image composition with extended depth of field and surface reconstruction in 3D.
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Chair of Botany and Plant Physiology, Dept of Biology
1. Sample preparation
- Cryostat (Leica CM3050)
- Vibrato (Precissionary)
- Two-chamber thermo-block for freezing in propane or isopentane cooled with liquid nitrogen
- Lyophilizer (alpha Christ)
- Lyophilizer (ScanVac, Labogene)
2. Data analysis using synchrotron light based techniques:
- Analysis of XRF spectra: Software PyMCA, GeopixeII,
- Analysis of FTIR spectra: Software Opus
- image analysis with multivariate statistical tools (PCA, NNMA): PyMCA, Orange, R-platform
Veterinary faculty, Universtiy of Ljubljana
Center for Microscopy and Image Analysis
Equipment | Purpose of equipment |
Inverted Leica multispectral laser scanning confocal microscope (Leica Microsystems, Heidelberg, Germany) with separate workstation with image analysis software Imaris. | Three-dimensional localization of the distribution of fluorescently labeled molecules in cells and in the intercellular space. |
Stereo Microscope Stemi 508 KMAT (Zeiss) equipped with Microscopy Camera Axiocam and ZEISS imaging software ZEN. | Evaluate, sort, select or dissect eggs, larvae or embryos and use micromanipulators for injection. |
Microscope (Eclipse Ni-UM, Nikon). Tissue processor Tissue-Tek embedding station,Gemini AS automated slide stainer and automated glass coverslipper ClearVue (Thermo Scientific). | Equipped with digital camera (DS-Fi1, Nikon) and software for image analysis adapted for histological samples (NIS-Elements BR 4.60). |
Conventional electrophysiological technique Two-electrode voltage clamp (TEVC) and two-microelectrode oocyte voltage clamp technique in combination with microscopy. | Device for measuring ion currents through cell membranes of excitable cells and device for measuring ion currents through individual ionotropic receptors. |
Cell culture laboratory | Cell culture facilities (registered closed system for working with GMOs; safety level 1). |
Tristar 3 Multimode Reader – Berthold Technologies | Measurements of luminescence, fluorescence and absorbance as well as FRET, BRET2 and nanoBRET signals. The system includes two automatic injectors (range 10 to 100 µl), temperature control (5 – 42°C), monochromator (measuring range 200 – 1000 nm) and detection module for AlphaScreen tests. |
Registered experimental animal facilities (IPV) | Equipment for breeding laboratory rodents (cages, racks, acclimatized rooms, washing facility). |
Registered experimental animal facilities (IPV) | Equipment for behavioral analyses in mice with stereotaxic equipment (various labyrinths, system MotorMonitor for monitoring spontaneous activity, software package Anymaze for analyses of behavioral tests). |
National Institute of Chemistry
Department of Analytical Chemistry
LA-ICP-MS
Laser ablation (LA) system (Photon Machines Analyte G2) hyphenated with (a) inductively coupled plasma elemental mass spectrometer (ICP-MS) (Agilent Technologies 7900 ICP-MS) or with (b) inductively coupled plasma time-of-flight elemental mass spectrometer (ICP-TOF-MS) (Nu Ametek, Vitesse).
- list of services for which the equipment is available: (i) 2D/3D elemental (bio)imaging, and (ii) in-situ single-particle (SP) elemental analysis for the needs of nano(bio)metallomics, including sizing and counting, based on the LA-SP-ICP-MS detection mode.
- list of projects/programs related to EuBI/SiMBiON: P1-0034, “Analytics and chemical characterization of materials and processes”.
Figure. LA-ICP-MS (left) and illustration of the silver nanoparticle size distribution analysis (right) in root cross-sections of sunflower using LA-single-particle-ICP-MS detection mode.
Jožef Stefan Institute:
F5 – Department of Solid-State Physics, Prof. Dr. Igor Serša
100 MHz MRI system for imaging of medium-sized samples and MR microscopy
- 2.35 T horizontal superconducting magnet with a bore of 30 cm
- Tecmag Apollo spectrometer
- gradient system for imaging of medium-sized samples with gradient strength up to 20 mT/m
- RF probe for imaging of medium-sized samples with a diameter of 15 cm
- gradient system for MR microscopy with gradient strength up to 250 mT/m
- RF probes for MR microscopy 10, 15, 20, 25 mm in diameter
- diffusion probe with gradient strength up to 6 T/m
400 MHz MRI system for MR microscopy
- 9.4 T vertical superconducting magnet with 94 mm opening
- Tecmag Redstone spectrometer
- gradient system for MR microscopy with gradient strength up to 800 mT/m
F2 – Department of Low and Medium Energy Physics
X-ray Analytical Microscope (Micro-XRF) Horiba XGT-9000
Micro X-ray fluorescence spectroscopy is an imaging technique based on excitation of the sample with a photon beam of X-ray light of energy 50 keV and diameter 15 m and detection of characteristic X-ray fluorescence rays during raster scanning of the sample. It enables the localization of elements in various solid samples: biological tissues, geological materials, metals, artifacts of cultural heritage. With the XGT-9000 instrument, it is possible to scan samples from a few mm to 15 cm.
Micro-PIXE
Analytical method of excitation of characteristic X-rays during target irradiation with protons PIXE (Proton Induced X-ray Emission) is based on the detection of characteristic X-ray spectral lines emitted by the sample when it is bombarded with protons with energy in the MeV range. Protons are accelerated in a tandem accelerator, and the focused beam is moved in the form of a raster over the selected part of the sample. The beam is focused with quadrupole lenses to a diameter of 700 nanometers (hence the name micro PIXE), this is also the lateral resolution with which elemental or molecular distributions in the sample are measured.
MeV-SIMS
Secondary ion mass spectrometry with primary heavy ions of energies in the MeV range (MeV – SIMS) is a technique used to analyze the molecular composition of solid surfaces and thin films through the use of a focused primary ion beam that knocks secondary ions out of the sample. These are then analyzed through the mass/charge ratio, which is measured with a time-of-flight mass spectrometer. With this, the elemental, isotopic or molecular composition of the surface can be determined to a depth of 1 to 2 nm. The method is particularly useful for imaging of large molecules in biological tissues. Cl-35 ions with an energy of 5.8 MeV are most often used for the primary ion beam, focused down to 700 nm of diameter.
Nacionalni inštitut za biologijo
IC MBV in IC Planta
Naziv osnovnega sredstva | Uporaba |
Presevni elektronski mikroskop CM 100 (Philips), kamera BioScan 792 in kamera Orius SC 200 | |
Aparatura za pripravo mrežic za presevno elektronsko mikroskopijo: naprševalec za ogljik z enoto glow discharge in QSG (Leica EM ACE200) | |
Presevni elektronski mikroskop Talos L120C, kamera Ceta (Thermo Fisher) | Presevni elektronski mikroskop je specializiran za opazovanje bioloških vzorcev |
Krioultramikrotom Leica EM U |
IC Planta
Presevni elektronski mikroskop Talos L120C
Presevni elektronski mikroskop (transmission electron microscope, TEM) (Talos L120C) je specializiran za opazovanje bioloških vzorcev, čemur so optimalno prilagojene njegove karakteristike, ki so velik kontrast, visoka ločljivosti pri širokem razponu povečav, hitro pregledovanje slike preparata na zaslonu ter zajem in obdelava slik z visoko ločljivostjo. Navedene karakteristike omogočajo vizualizacijo izredno širokega spektra bioloških vzorcev, to je vse od izoliranih makromolekul, virusov in bakterij do notranje zgradbe celic gliv, rastlin, živali in človeka.
Tematike raziskav in analiz, za katere se uporablja presevni elektronski mikroskop Talos L120C, so izjemno raznolike, saj ga uporablja veliko število različnih uporabnikov za raziskovalno delo na zelo raznovrstnih področjih raziskav, različne aplikacije v delo za podjetja, kot podporo državnim in vladnim organom in resorjem ter za pedagoško delo.
TEM Talos L120C je v večinski lasti Nacionalnega inštituta za biologijo, solastnika pa sta še Oddelek za biologijo Biotehniške fakultete Univerze v Ljubljani in Kemijski inštitut.
Presevni elektronski mikroskop (Philips CM100)
Presevni elektronski mikroskop (transmission electron microscope, TEM) (Philips CM100) je opremljen z dvema digitalnima kamerama BioScan 792 (Gatan) in Orius SC200 (Gatan) ter programsko opremo DigitalMicrograph za obdelavo slik.
Presevni elektronski mikroskop Philips CM 100 se uspešno uporablja tako v bazičnih kot tudi aplikativnih bioloških raziskavah, saj s svojo ločljivostjo omogoča analizo celične ultrastrukture. Za raziskave bioloških vzorcev se uporabljata v glavnem dve metodi. Metoda negativnega kontrastiranja je primerna za opazovanje delcev v suspenziji, kot so virusi, bakterije, makromolekule (proteini, nukleinske kisline, liposomi). Druga metoda omogoča opazovanje rastlinskih, živalskih in človeških tkiv na nanometrskem nivoju, to je na nivoju ultrastrukture. Vključuje fiksacijo tkiv, vklapljanje v smole in rezanje ultratankih rezin. S TEM Philips CM 100 se izvajajo analize strukture in imunolokalizacija v različnih bioloških vzorcih.
Presevni elektronski mikroskop Philips CM 100 je v skupni lasti Nacionalnega inštituta za biologijo in Oddelka za biologijo Biotehniške fakultete Univerze v Ljubljani.
Konfokalni stereomikroskop Leica TCS LSI
Konfokalni stereomikroskop (Leica TCS LSI) omogoča neinvazivno opazovanje fluorescence v vzorcih. Posebnost tega mikroskopa je širok spekter povečav, saj omogoča povečave od 0,7x (vidno polje velikosti 16 mm) vse do 20x. Zaradi tako širokega obsega povecav je mogoče opazovanje tako večjih objektov kot tudi posameznih celic. Stereomikroskop omogoča tudi precejšnjo delovno razdaljo, kar pomeni da lahko pod objektiv postavimo tudi večje objekte (na primer rastline v lončkih). Ena ključnih prednosti konfokalnega stereomikroskopa pred sorodnimi tehnikami je tudi možnost opazovanja intaktnega tkiva ali organa, kar skrajša čas analize in bistveno povečalo relevantnost rezultatov.
Medicinska fakulteta Maribor
| Oprema | Maksimalna dostopnost za zunanje (%) | |
| 1 | Mikroskop na atomsko silo (AFM) | 20% |
| 2 | Kriostat (naročen, dobava v februarju) | 20% |
| 3 | Nanotomograf (NanoCT, dobava v aprilu) | 10% |
Univerzitetni klinični center Maribor
| Equipment | Maximum availability for external users (%) | |
| 1 | FMRI device | 10% |
| 2 | Optical microscope | 10% |
Biograph mCT PET/CT scanner
PET/CT scanner combines the advantages of functional nuclear medicine imaging (PET scanner) and morphological radiology (CT scanner) in a single device. Precise information obtained from the scan leads to a greater possibility of earlier diagnosis and a more accurate treatment strategy, ultimately leading to a better patient outcome.
The design of the Biograph mCT scanner addresses the need for future success. The bore diameter of 78 cm and the tunnel length of 135 cm, as well as the table capacity of 227 kg, allow for the examination of a heavier population and easier patient positioning while offering space for additional therapeutic procedures and helping to increase patient comfort.
The large opening and short tunnel help reduce patient discomfort. The water-cooling component, which reduces the need for noisy fans and over-cooling by air conditioning, creates a calmer environment. In-bed physiological devices and well-placed controls make it easier for technicians to position the patient. The Biograph mCT is designed as a true dual-modality scanner, integrating the best capabilities of PET and CT into one compact system. It was installed in July 2015 with all related equipment.
MRI 1,5 T: Siemens Magnetom Sola
The MAGNETOM Sola represents the pinnacle of 1.5T MRI technology, enabling high-quality and individualized examinations. It is the first 1.5T MRI device with biometric technology that automatically adapts to patient biovariability, allowing for higher quality and faster examinations, which is particularly important for oncology patients. The device also enables the optimization of patient appointments and increases work efficiency. It has a wide range of hardware and software options, including a wide range of coils and a pump for contrast application. It was installed in June 2020, when the premises were also renovated.
EPIQ 7 Ultrasound Machine
The Philips EPIQ 7 ultrasound machine belongs to the highest class of ultrasound machines. The xMATRIX technology offers all image capture modes (2D, 3D/4D, Live xPlane, Live MPR, MPR, Doppler, Colour Doppler and CPA) in one transducer. MaxVue high-definition display brings extraordinary visualization of anatomy with 1,179,648 additional image pixels compared to a standard 4:3 display format mode, enhances ultrasound viewing and provides 38% more viewing areas to optimize the display of dual, side/side, biplane, and scrolling imaging modes. It has a wide range of probes.
Surgical microscope Zeiss Kinevo 900
KINEVO 900 is an innovative, high-performance robotic visualization system that combines features such as: next-generation motion assistance, on-demand digital 4K visualization capabilities and the QEVO integrated micro-viewing tool. Advanced features include intraoperative fluorescence visualization, an integrated endoscopic examination tool, ocular imaging and a new robotic platform for visualization and three-dimensional (3D) display of images on a 4K monitor, enabling operation in an exoscopic mode.
FacSymphony A3 flow cytometer
It is a multi-parameter flow cytometry using an ultra-quiet VPX electronic system, powerful lasers and highly sensitive photomultipliers. It is a powerful tool that allows the scientist to conduct in-depth research. The instrument offers the ability to identify and analyze characteristic phenotypes in heterogeneous populations, analyze 30 parameters in up to five lasers and use new dyes with improved brightness and gradation characteristics.
CT Siemens Somatom Drive
It is a second-generation high-performance dual-energy CT machine with two Straton MX Sigma X-ray tubes and two Stellar Infinity detectors. Unique 10 kV tuning levels, the metal filter, Turbo-Flash option, customizable 4D spiral, fast integrated interface with a fast 3D camera, powered by artificial intelligence. It was installed in May 2020, with all the associated equipment, a pump for contrast application, along with the renovation of the premises.
X-ray angiography Philips Azurion
It is a state-of-the-art, latest-generation bi-planar angiography device equipped to perform the most demanding minimally invasive interventional radiology and neuroradiology procedures. It has the latest hardware platform and software. It was installed in June 2020, along with an extensive renovation of the premises and all the related equipment.
Infrastructure Research Center of the University of Maribor
University Center for Electron Microscopy
JEOL JSM-IT800SHL
The JEOL JSM-IT800SHL is a multi-purpose FE-SEM offering both high-resolution observation and the capability to conduct various types of analysis, incorporating an in-lens Schottky Plus field emission electron gun (FEG), a Super Hybrid objective Lens (SHL), as well as a new electron optical control mechanism (New Electron Optical Engine: Neo Engine). The electron optical system equipped with an in-lens Schottky Plus field emission gun can deliver a finely focused electron beam even with large irradiation currents, with quickly acquired high accuracy results, including element analysis with EDS, EBSD and Soft X-ray. A high-resolution observation and analysis of a wide variety of specimens from metals, biological specimens to nano materials are possible. The SHL is especially useful for the observation of magnetic materials and analysis such as EBSD measurement. The equipped Soft X-Ray Emission Spectrometer (SXES) is an ultra-high resolution spectrometer consisting of a newly-developed diffraction grating and a high-sensitivity X-ray CCD camera. In the same way as EDS, parallel detection is possible, and 0.3 eV (Fermi-edge, Al-L standard) ultra-high energy resolution analysis can be performed, surpassing the energy resolution of WDS. With the high energy resolution, chemical state analysis mapping can be performed.
FEI Sirion 400 NC
The FEI Sirion 400 NC electron microscope is a high-resolution electron microscope with Field Electron emission, which enables extremely high magnifications (up to a million times, with a high resolution of 1 nm). A feature of this research equipment is its suitability for both engineering materials and biological samples.
FEI Quanta 200 3D
FEI Quanta 200 3D is an environmental Scanning Electron Microscope with a tungsten cathode for an electron source (formation of an electron beam with heat emission). The microscope has the name “environmental” because it allows working at different pressures and at 100% humidity. Conditions for observing different samples are obtained by adjusting the pressure in the chamber. ESEM-mode microscopy is, thus, suitable not only for conductive materials such as metals and metal-coated materials, but also for moist, volatile, and soft materials without prior preparation, which is particularly important for the Food and Chemical industries. Another special feature of this equipment is a focused ion beam FIB SEM (the ion gun on the SEM Quanta microscope), which allows not only SEM observation of the surface, but also surface treatment and analysis of the microstructure below the surface.
We perform procedures for optimal sample preparation for Electron Microscopy and examinations, along with examination and classification of nanoparticles of metal compounds. We also review and participate in the classification of “rare earth” compounds with cobalt, which are the basis for the fabrication of strong magnets.
For the last several years, we have been investigating and inspecting precious metal alloys used in jewellery, for dental prosthetics and industry regularly.
Admission of Slovenia to the European network of Euro-BioImaging infrastructure centres
The Slovenian Consortium of Infrastructure Centres (SiMBioN) dealing with biomedical and biochemical imaging, of which the University Centre for Electron Microscopy (UCEM) of the Faculty of Mechanical Engineering of the University of Maribor is also a member, was founded in 2018 under the coordination of the University of Ljubljana, Faculty of Medicine. The vision of this Consortium was to bring together groups using different imaging methods with the aim of an interdisciplinary approach to the analysis of biological and medical samples.
In order to work more successfully with infrastructure centres across Europe, the Consortium has launched an initiative to join the European network of Euro-BioImaging infrastructure centres. With the support of the Ministry of Education, Science and Sport, the decision to join was made by the Government of the Republic of Slovenia, who committed to the obligations of the Member States of Euro-BioImaging. The application for Slovenia’s membership was considered by the Board of Directors of Euro-BioImaging, and at its session on 5 May, 2020, it accepted Slovenia as its full member.
Slovenia’s inclusion in Euro-BioImaging enables its researchers to access state-of-the-art equipment in the European infrastructure centres, participate in European infrastructure projects and participate in planning a vision for the development of European infrastructure in the field of Biomedical Imaging methods.
Upon Slovenia’s inclusion in the Euro-BioImaging organisation, an interview with the coordinator of the Slovenian consortium, Prof. Dr. Peter Veranič, is available on the web link:
https://www.eurobioimaging.eu/news/slovenia-joins-euro-bioimaging-eric-/.
UCEM operates within the Mechanical Engineering Research Institute (RIS) of the Faculty of Mechanical Engineering in Maribor, where equipment for optical and scanning electron microscopy and the preparation of various types of samples is available.
UCEM was established as the first infrastructural research center at the University of Maribor by a decision of the University Senate on 1 August 2005.
The founding members are:
– Faculty of Mechanical Engineering
– Faculty of Chemistry and Chemical Technology
– Faculty of Civil Engineering
The basic goal of the center is to enable the greatest possible access to research equipment for all teachers, students and researchers at the University of Maribor, other research institutions and the economy.
Scanning electron microscopy – SEM
At UCEM, we use three scanning electron microscopes for different samples:
Type of sample | Conductive | Non-Conductive | Damp | Dirty, greasy | Resolution |
FEI Quanta 200 3D | + | + | + | + | 3,5 nm at 30 kV (high vacuum) 3,5 nm at 30 kV (ESEM mode) 15 nm at 3 kV (low vacuum) |
FEI Sirion 400 NC | + | + | – | – | 1,0 nm at 15 kV 2,0 nm at 1 kV |
JEOL JSM-IT800SHL | + | + | – | – | 0,5 nm at 15 kV 0,7 nm at 1 kV 0,9 nm at 500 V |