Nodes
NEMI’s infrastructure comprises a distributed network of local EM Nodes and unique Flagship Nodes. These nodes offer state-of-the-art EM technologies that require specific expertise and expensive equipment. Our network enables comprehensive imaging across various length, resolution, and time scales, integrating with light microscopy and proteomics.
Amsterdam
Amsterdam UMC - Electron Microscopy Center Amsterdam (EMCA)
Description
The Electron Microscopy Center Amsterdam (EMCA) is a collaboration between all Amsterdam life science research institutes, including the Amsterdam UMC (AMC & VUmc), NKI, ACTA and NIN, and is housed at Core facility Cellular Imaging within the department of Medical Biology at the Amsterdam UMC, location AMC. At the EMCA the operators and researchers from the different universities and institutes work on the various TEM and SEM microscopes and have shared work-discussions. The shared equipment is paid for by the involved partners as well as by various other academic and industrial users and clients. As such we collaborate with most Amsterdam and various (inter)national research groups and have created an EM knowledge center in Amsterdam. We have long standing expertise in transmission electron microscopy (TEM), scanning electron microscopy (SEM), but also apply new developments such as combined light electron microscopy (CLEM), tomography, immunoEM, and Cryo-EM.
Contact
Techniques
Scanning Electron Microscopy (SEM)
Field Emission Scanning Electron Microscopy is an analytical technique used in biological and material science to investigate surface structures and their properties. The electron beam that hits the specimen at the bottom of the microscope generates secondary and back-scatter electrons. These electrons are detected by various detectors which are selective for these secondary or backscattered electrons. The microscope is equipped with a high resolution in-lens detector, a SE detector, and a backscatter detector.
Transmission Electron Microscopy (TEM)
- Immuno-EM: Immuno-Electron microscopy can be used to detect proteins in tissues or cells. Ultrathin sections can be decorated with 5, 10, 15 or 20 nm gold particles that specifically pinpoint the localization of an antibody and thus a protein of interest. This way subcellular, surface, endocytic proteins /markers can be detected to a resolution of 5 nm. Biological material will be mildly fixed and processed for ultra thin (60 nm) cryo-sections. The sections can then be immuno-labelled with antibodies that will be detected using gold particles. The analysis will be done using a transmission electron microscope. When a specific area needs to be identified, first thick sections (±250 nm) are immuno- fluorescent labelled and analyzed using a fluorescence microscope. Then ultrathin EM sections will be analyzed.
- Resin embedded TEM: This technique is broadly applied in cell biological research and diagnostic pathology. Biological (patient) material is fixed, dehydrated and stained with heavy metals (lead, uranium, osmium). After embedding in plastic resin, ultrathin sections are cut on a diamond knife and materials are analyzed using the TEM. With the electron dense counter- staining (positive staining) you can obtain an ultrasharp image with high contrast.
- Negative staining TEM: Negative staining can be used to obtain images of small particles in suspension. E.g. viruses, liposomes, membrane structures , protein complexes and purified complexes. It is needed to increase the contrast of biological materials as electrons will pass through and limited contrast is achieved. By using an e-dense solution surrounding the biological materials, contrast is created around the sample instead of in the sample, as in positively stained EM samples.
- Combined Light Electron Microscopy (CLEM): Image a sample in fluorescence microscopy and then image the same sample using electron microscopy to combine the images and localize fluorescence in TEM.
Equipment
TEM
- FEI Tecnai T12, G2 Spirit Biotwin,+ Veleta and Eagle
- FEI Tecnai T12, G2 Spirit Biotwin,+ Veleta
- Talos L120c, Ceta 16M camera, EDX detector (Quantax 200)
SEM
- Zeiss Sigma Field Emission
Preparation Equipment
- Plunge freezer
- Cryo-Ultramicrotome Leica FC6
- Ultramicrotomes Leica
- Carbon coater Leica Ace600
- Linkam CLEM cryo-holder
- Leica EM CPD 300
Extra Holders
- Multigrid holder
- Gatan cryo-holder
- Fischione cryo-holder
- Tomography holder and software
AMOLF Nanolab Amsterdam
Description
AMOLF NanoLab Amsterdam is a facility for materials fabrication and characterization down to the nanometer scale. It aims to provide state-of-the art opportunities in nano research, servicing the scientific and engineering community within the greater Amsterdam area. The AMOLF NanoLab is a partner in NanoLabNL (www.nanolabnl.nl), the Dutch national facility for nanotechnology research that provides a full-service and open-access infrastructure for R&D in nanotechnology. It offers access to a range of techniques for lithography, deposition, etching, and characterization. Its prime focus areas are metamaterials, nanophotonics, nanomechanics, quantum science and technology, and energy research. With respect to electron microscopy (EM), AMOLF NanoLab Amsterdam houses several scanning electron microscopes (SEMs) including a dual beam focused ion beam FIB/SEM. A new aberration-corrected transmission electron microscopy (TEM) will be installed in summer 2024. AMOLF has longstanding experience in developing and modifying EM equipment, which resulted in a collection of unique EM infrastructure and techniques as listed below. The AMOLF NanoLab Amsterdam acts as an open facility, with regional users including the University of Amsterdam, VU University Amsterdam, Utrecht University, ARCNL, and a number of industrial partners.
Contact
TEM Facility
AMOLF NanoLab Amsterdam
Techniques
Scanning Electron Microscopy (SEM)
SEM is an analytical and surface-sensitive technique. An electron beam is scanned over a sample and the generated secondary and backscattered electrons are used for imaging the sample with nanometer spatial resolution. Our SEMs are additionally equipped with specialized detectors such as Energy Dispersive X-ray Spectroscopy (EDS), Electron Backscatter Diffraction (EBSD) and Cathodoluminescence (CL) detectors.
Energy Dispersive X-ray Spectroscopy (EDS)
An EDS detector allows for chemical analysis of elements in the sample by measuring the energy of the emitted X-rays upon electron beam excitation. The X-ray energy is characteristic of the atomic structure of each element and can be used to distinguish and quantify the amounts of elements in the sample.
Electron Backscatter Diffraction (EBSD)
EBSD enables the analysis of a sample’s crystallographic microstructure by detecting the diffraction patterns of backscattered electrons after interacting with the atomic lattice of the sample. In this manner, the crystallographic orientation and grain boundary morphology can be determined. The AMOLF NanoLab Amsterdam EBSD detector is a Clarity system with a direct electron detector with very high sensitivity that allows for much lower beam current and beam voltage compared to standard EBSD. This enables damage-sensitive samples to be mapped (such as halide perovskite films).
Cathodoluminescence (CL)
CL is emitted light from the sample, which is generated by the electron beam. By scanning the electron beam in an SEM, CL maps with high spatial and spectral resolution can be measured. CL is useful in studying the local electronic structure and optical properties of materials.
Focused Ion Beam FIB/SEM
A focused ion beam is a nanofabrication tool used to mill samples by ion sputtering. A FIB is often used to prepare thin samples for TEM imaging by milling out a thin slice out of a sample that would otherwise be too thick for TEM imaging. The sample preparation process is often simultaneously imaged with a focused electron beam.
Time-resolved EM
EM measurements are normally static images. However, dynamic information on the sample is often required to gain insights into rapid physical, chemical or biological processes. In EM, fast dynamic information can be obtained by pulsing the electron beam by, for example, electrostatically chopping the stream of electrons into short electron pulses, so-called electrostatic beam blanking. In this manner, ultrafast imaging measurements and pump-probe experiments (e.g. pumping the specimen with a laser pulse and probing it with an electron pulse) can be performed. At AMOLF we have SEMs and a TEM that are equipped with such electrostatic beam blankers.
Transmission Electron Microscopy (TEM)
In a TEM the sample is generally imaged with highly energetic electrons allowing for high spatial resolutions down to the atomic scale. As opposed to SEM, the imaging occurs via transmitted electrons and therefore the specimen needs to be thin enough to be electron transparent. Next to imaging, a TEM is often equipped with a variety of different detectors providing complementary information about the sample.
○ In-situ TEM: A conventional TEM operates at room temperature under high vacuum conditions. In-situ techniques allow introducing application-relevant conditions like elevated temperatures or gas/liquid environments. This is often done via specific sample holders that incorporate electric contacts for heating and biasing or tiny chambers with gas and liquid flow.
○ Electron tomography: Conventional TEM provides 2D projection images of the sample. With electron tomography the characterization can be extended to 3D by acquiring a series of projection images under different tilt angles of the sample. Different methods exist to then reconstruct the 3D morphology from the series of 2D projection images. Electron tomography is often applied for quantification purposes and for highly anisotropic shapes.
○ Light excitation: To study photo-driven processes inside the TEM, light excitation of the sample is required. This can either be done via a dedicated sample holder or by inserting an optical window in the column itself. The latter has the advantage that the sample holder can be freely chosen and that light excitation can therefore be combined with other in-situ stimuli.
Equipment
SEM
- Dual beam FIB/SEM: FEI Helios Nanolab 600 (SFEG, Ga FIB, gas injector system for Pt, SiO2 and C deposition, plasma cleaner, CL spectrometer)
- FEI Verios 460 equipped with a SFEG source and STEM, EDS, EBSD Clarity and EBIC detectors
TEM
- JEOL NeoARM (to be installed in summer 2024): Cs corrected 200 kV (S)TEM, cold FEG, variety of detectors (HAADF, ABF, SAAF, EDS, OBF), fast beam blanker and dose modulator, laser incoupling unit, ASI CheeTah 3 direct electron detector
Extra TEM Holders
- Double tilt beryllium holder
- High tilt tomography holder
NKI
TBA
Delft - Delft University of Technology
Kavli Nanolab Imaging Center (KNIC)
Description
The Kavli Nanolab Imaging Center is part of the Kavli Nanolab Delft, one of the largest academic nanofabrication facilities in Europe. The cryo-EM facility of the Kavli Nanolab Imaging Center hosted at the Bionanoscience Department supports cryo-EM/ET activities of academic users across the TU Delft campus, other regional knowledge institutions and industrial partners of the Delft biotechnology and nanotechnology industries. Besides supporting cryo-EM related research activities, the TEM facility of KNIC also has a mission to advance cryo-EM technology through method development. The facility is housed in dedicated and modern lab space at VC-F level and has a humidity-controlled environment for cryo-EM sample preparation.
Contact
Techniques
- Cryogenic Electron Microscopy (Cryo-EM)
- Cryogenic Electron Tomography (Cryo-ET)
- Time-resolved Cryo-EM
- Cryo-EM/ET sample preparation
- Cryogenic Correlative Light and Electron Microscopy (Cryo-CLEM)
Equipment
- JEOL JEM3200 FSC EFTEM (300 kV FEG, in-column EF, Gatan K2 Summit DED & TVIPS XF416 CMOS cameras, TVIPS USG scan generator, liquid N2 + liquid He cooling)
- JEOL 1400+ TEM (120 kV LaB6, TVIPS F416 CMOS camera. Gatan 626 cryoholder and Gatan 910 cryo-tomography holder, tomography holder, EDS double tilt holder, Bruker Quantax EDS)
- Leica GP2 automatic plunge-freezing robot
- TFS Vitrobot Mark IV automatic plunge-freezing robot
- ZEISS Axio Imager Z2 + LSM 900 Airyscan2 cryo-confocal microscope
- LINKAM CMS196v³ cryo-correlative microscopy stage
- Glovebox clean station for low humidity cryo-EM/ET sample preparation/transfer
- Various custom-built prototypes for time-resolved cryo-EM sample preparation
- Leica Ultracut EMFCS ultramicrotome with cryogenic cooling unit
- Quorum GloQube Plus Glow Discharge System
- Cressington 208 sputter coater
- Instrumentation for nanofabrication and method development of MEMS-based cryo-EM sample preparation
Electron Nanoscopy of Quantum Materials
Description
The main scientific driver of our group is the understanding, controlling, and exploiting of the exciting physical phenomena arising in quantum materials such as two-dimensional (van der Waals) nanomaterials and assessing their potential for applications from optoelectronics to nanophotonics.
Contact
Techniques
Crafting new functionalities in two-dimensional materials
We combine advanced nanofabrication techniques from top-down (e.g. etching and lithography) to bottom-up (e.g. chemical vapor deposition) methods in order to develop novel strategies to fabricate a variety of morphologies in low-dimensional 2D materials and explore the resulting induced local electronic properties.
Electron microscopy to accelerate the understanding of two-dimensional materials
We exploit state-of-the-art electron microscopy and related techniques to unambiguously ascertain the underlying physical mechanisms leading to the remarkable phenomena emerging in quantum materials.
- High-resolution scanning transmission electron microscopy (HR-STEM)
- Electron energy-loss spectroscopy (EELS)
Machine learning for EELS data interpretation
Data analysis in EELS is powered by a dedicated Python machine learning framework, EELSfitter, developed in-house within our group. It makes it possible to access key properties of 2D nanomaterials such as modulation of the bandgap, dielectric function, dispersion relations, low-energy electronic states, excitons, and other collective excitations, and their direct correlation with structural features. This effort is carried out in collaboration with experts from Nikhef, the Dutch national institute for particle physics.
Quantum materials to quantum technologies: (CL)
Engineering the resulting functionalities of quantum nanomaterials has an immense potential to revolutionize both the way we think about fundamental material science as well as for technological applications in fields from nanoelectronics and nanophotonics to quantum communication and sensing.
Equipment
High-resolution scanning transmission electron microscopy (HR-STEM)
Electron energy-loss spectroscopy (EELS)
Van Leeuwenhoek Laboratory for Advance Imaging Research (VLLAIR)
Description
The Van Leeuwenhoek Laboratory for Advanced Imaging Research (VLLAIR) is a unique facility for collaboration between the Departments Imaging Physics, Quantum Nanoscience, and industrial parties. The lab has a clean and stable lab-climate and is fully transparent to increase and stimulate cooperation between scientists and public-private parties. Most of the instruments in the lab are prototypes with unique functionalities. These instruments will be further developed by researchers in our Departments in collaboration with external scientists and industrial partners for beta testing, application development, and evaluating the developments/improvements.
Contact
Techniques
- Scanning Electron Microscopy (SEM) – 0-30 keV energy
- Focused Ion Beam (FIB) Microscopy and Milling
- FAST-EM 64-Beam Scanning Electron Microscope
- Integrated Light and Electron Microscopy
- Integrated Light, Electron, and Ion Cryo-Microscopy
- Pulsed and Time-Resolved Scanning Electron Microscopy
- Energy-Dispersive X-ray Detection (EDX)
- Electron-beam Induced Deposition for Nanopatterning – various precursor systems available, including glovebox to fill gas injection systems
Equipment
SEM
- FEI Verios SEM with Delmic SECOM and customizable light microscopy optics
- Delmic 64-beam FAST-EM
- FEI Quanta FEG with fast beam blanker (pulsed electrons) and (customizable) advanced light optics excitation and detection
Keyence Digital Light Microscope
Microtome
FIB-SEM
- FEI Helios G4 CX FIB-SEM with lift-out system
- FEI Helios G3 UC FIB-SEM with EDX, gas injection systems, retrofittable cryo-fluorescence microscope with autogrid holder
- Several customized SEMs and FIB-SEMs for development and prototyping of new equipments
Gloveboxes
- Glovebox for filling gas injection systems
- Glovebox clean station for low humidity cryo-FM-FIB-SEM sample preparation/transfer
Eindhoven - Eindhoven University of Technology
Center for Multiscale Electron Microscopy (CMEM)
Description
The Eindhoven Center for Multiscale Electron Microscopy (CMEM) houses state-of-the-art electron microscopy (EM) instrumentation ideally suited for cryo, in-situ & 3D studies of molecules, materials, and processes across multiple length scales. At CMEM we integrate life and materials science approaches and develop innovative workflows for analysis in organic solvents, using ultrathin samples supported on graphene oxide, or in oxygen free conditions.
Contact
Techniques
- Cryogenic Transmission Electron Microscopy (Cryo-TEM) Analysis
- The samples are cooled within a millisecond to 183 degrees below zero, after which they can be imaged in their frozen native state.
- In-Situ EM Analysis of Materials and Processes
- 3D EM Analysis Across Length Scales
Equipment
TEM
- Glacios Cryo-TEM: equipped with a Falcon 4i direct electron detector, Cryo-STEM capabilities such as BF/DF & iDPC, and a full set of data acquisition and analysis software.
- Titan Themis for in-situ & 3D analysis: equipped with fast cameras (Ceta II and Falcon 3EC direct electron detector) and a liquid-phase holder,.
FIB-SEM
- Quanta3D Environmental FIB-SEM: equipped with heating/cooling stage, liquid-cell and nano manipulators.
Coherence and Quantum Technology (CQT)
Description
The research of the Coherence and Quantum Technology group focuses on collective effects in dilute, strongly interacting systems of high phase-space density: ultra-cold atoms, quantum gases and plasmas, and high-brightness electron, ion and atom beams.
Contact
Techniques
- Light-Matter Interaction: to reach the special experimental conditions needed for our research, atomic gases and charged particle beams are manipulated and controlled by coherent light-matter interaction, using both ultra-narrowband continuous-wave lasers and mode-locked femtosecond lasers, enabling a new class of experiments that are both ultracold and ultrafast.
- Development of (sub)nm focused ion beam (FIB) technology using laser-cooled ion sources, with Thermo Fisher Scientific.
- A program on ultracold source development and ultrafast beam manipulation for femtosecond electron microscopy & crystallography, also supported by Thermo Fisher.
- Ultra-bright, high-current electron source development for a new generation of high-brilliance X-ray sources, supported by EU Interreg, ASML and CERN.
- Development of a quantum simulator based on Rydberg atom lattices.
- Development of quantum theory of few-body systems to describe fundamental phenomena in ultracold atomic gases.
Equipment
Microscopy
- (Sub)nm focused ion beam (FIB) technology using laser-cooled ion sources
- Ultracold source development and ultrafast beam manipulation for femtosecond electron microscopy & crystallography
- Ultra-bright, high-current electron source development for a new generation of high-brilliance X-ray sources
- Development of a quantum simulator based on Rydberg atom lattices
Plasma and Materials Processing (PMP)
Description
The Plasma and Materials Processing (PMP) group has established an internationally leading position in the area of atomic scale processing, particularly in the preparation of nanolayers and nanostructures by means of methods such as (plasma-based) atomic layer deposition (ALD).
Contact
Techniques
- We aim to develop advanced atomic layer deposition and etching processes through in-depth understanding of the underlying reaction mechanisms. With this we try to enable future device technologies in nanoelectronics, photonics, photovoltaics and beyond.
- Atomic Layer Deposition (ALD)
- Atomic Layer Etching (ALE)
- We focus on the study of plasma conversion of gases, both through experiments and modelling.
- We experimentally study the plasma conversion in-situ, we develop at PMP (laser-based) diagnostics to measure densities of species both spatially and temporally resolved and apply these to different types of plasma, like glow, micro-wave and ns-pulsed discharges.
Processing of Low-Dimensional Nanomaterials
- We pioneer atomic layer deposition (ALD) for 2D nanomaterials synthesis.
- ALD is a scalable, low temperature preparation method for thin films which offers precise thickness control down to the sub-monolayer and can therefore be instrumental for the large area synthesis of 2D materials.
- The current focus of the group is on ALD of 2D transition metal dichalcogenides (2D-TMDs) for (opto)electronics and catalysis.
- We use plasma chemistry (plasma-enhanced ALD, PEALD) to control functionalities of the 2D-TMDs, such as morphology, materials phase and stoichiometry. By doping, alloying and by the formation of heterostructures we tune the electrical properties of the 2D TMDs, such as the charge carrier concentration and band gap.
- High-Resolution Transmission Electron Microscopy (TEM)
- DFT Simulations
Selective Atomic-Scale Processing for Nanoelectronics
- Thin film deposition and etching for applications in nanoelectronics, with a focus on selective processing for bottom-up fabrication of materials.
- Using the atomic layer deposition (ALD) and atomic layer etching (ALE) techniques as a starting point, novel approaches are developed to synthesize materials with atomic-level control.
Interfaces in Future Energy Technologies
- design and engineering of atomic-scale processed interfaces and thin films, which are key to promotion of selective charge carrier transport in energy devices, such as metal halide perovskite solar cells, tandem solar cells, (Li-ion) batteries and (electro-)catalysis.
Groningen
UMCG Microscopy and Imaging Center (UMIC)
Description
The University Medical Center Groningen (UMCG) Microscopy & Imaging Center (UMIC) provides equipment and analysis facilities for high-end microscopy.
Contact
Techniques
- Advanced Light & Electron Microscopy
- Standard Advanced Techniques (see equipment below)
- Spearpoints are implementation of a zebrafish model for disease that are typically analyzed using light sheet microscopy.
Innovation is in:
- Large-Scale Electron Microscopy
- Correlated Light & Electron Microscopy (CLEM)
- Creating tools to identify molecules and follow processes
- Label-free imaging with EDX (‘ColorEM’)
- Label-free imaging with Raman techniques
Equipment
See www.umic.info for an up-to-date list.
Electron Microscopy
- Zeiss Supra 55 – STEM
- TalosF200i – S/TEM
- DELMIC – FAST-EM
- ColorEM – EDX Oxford instruments
- ColorEM – Bruker
- Nanotomy – ATLAS Fibics/Zeiss
- Leica ICE – High pressure freezer
- Leica AFS2 – Freeze substitution
- Leica UC7 – Alexia Utramicrotome
- Leica UC7 – Sidonia Ultramicrotome
- Leica UC7 – Cryo-ultramicrotome
- Leica UC7 – ARTOS-ultramicrotome
- Leica VT1000s – Vibratome
- Leica –Sputtercoater ACE600
- Leica Tissue processor
Light Microscopy
- Zeiss LSM 780 NLO two photon CLSM
- Zeiss LSM 7MP two photon CLSM
- Zeiss CD7 /CLSM900 high content
- Zeiss LS7 Light Sheet
- Tissuegnostics TissueFaxs high content
- Leica Stellaris CLSM, Raman, Falcon
- Leica SP8X DLS light sheet & CLSM
- Leica SP8 CLSM
- Leica Laser microdissection
- Leica Thunder Live Cell 20 and infrared
- Leica DM 4000B fluorescence
- DeltaVision Elite for life cells
- IncuCyte S3A inside incubator
- IncuCyte S3B inside incubator
- Olympus BX50 (color, no fluorescence)
- CLEM – Delmic SECOM
Spatial Omics
Nanostring GeoMx DSP
- 10x Genomics Xenium (2024)
RUG - Zernike Institute for Advanced Materials (ZIAM)
Description
The Zernike Institute for Advanced Materials is one of the leading institutes in the field of materials science. Our goal is to design, build and connect nanostructured and (bio)functional materials to achieve unprecedented functionality.
Within ZIAM there is Nanostructured Materials and Interfaces
- Investigating the relation between nanostructure and functional properties of materials. Our research focus is on material structures, surfaces/interfaces, and surface interactions at the nanoscale. Our research interests include phase change materials, nanoclusters/nanoparticles, nanoresonators, surface forces, friction, and adhesion.
Contact
Techniques
Experimental facilities include:
- Scanning Probe
- Scanning Electron Microscopy (SEM)
- Transmission Electron Microscopy (TEM)
Equipment
AFM / Scanning Probe
SEM
TEM
RUG - Groningen Biomolecular Sciences and Biotechnology (GBB) institute
Description
The cryogenic electron microscopy (cryo-EM) group, headed by Assistant Prof. Alexander Belyy, is part of the Membrane Enzymology group and is embedded in the Groningen Biomolecular Sciences and Biotechnology (GBB) Institute. The group studies the actin cytoskeleton and molecular mechanisms of bacterial protein toxins. This interdisciplinary research combines structural data, determined by high-resolution single-particle cryo-EM, with the biochemical analysis of the target proteins.
Contact
Techniques
The modern electron microscopy (EM) labs are custom-designed and fully equipped for grid modifications, sample preparation, negative stain EM, and cryo-EM. For the extensive demand on image processing, we have several dedicated CPU and GPU clusters and a large data storage unit.
Equipment
Electron Microscopes
Three smaller and mid-level electron microscopes suitable for screening:
- CM100
- CM120
- T20
TEM
- FEI Talos Arctica Transmission Electron Microscope (TEM): equipped with an energy-filter, a phase plate, and a state-of-the-art K2 summit camera, providing the best set-up for high-resolution cryo-EM studies.
Leiden
Netherlands Center for Electron Nanoscopy (NeCEN)
Description
The Netherlands Center for Electron Nanoscopy (NeCEN) is an open access facility for high resolution cryo-electron microscopy of biological samples. A Titan Krios Transmission Electron Microscope (TEM) allows cost-efficient automated data collection for our customers.
Contact
Techniques
NeCEN gained Cryo-Focused Ion Beam (Cryo-FIB) micromachinery capabilities, allowing the production of thin sections of cryo-preserved material, i.e. whole vitrified cells, using a dual-beam SEM microscope. The removal of some sections of the sample by ablation thought the impact of heavy ions produces “windows” inside the cell. The remaining material, in the shape of wedges or lamellas, can be further explored by cryo-ET.
Equipment
TEM
- Screening Cryo-TEM (Talos L120C): a screening electron microscope is available (120 kV). The screening microscope is meant to be used to check and/or optimize specimen preparation conditions (sample concentration, ice thickness, grid quality) as the subsequent step after sample vitrification using a cryogenic plunger. Key features:
- LaB6 filament 120 keV
- Ceta camera
- SerialEM
- Krios 1: Titan Krios transmission electron microscope (TEM). Key features:
- X-FEG 300 keV
- K3 bioquantum
- EPU, Serial EM
FIB-SEM
- Aquilos 1 Cryo-FIB: dedicated instrument to prepare frozen, thin lamella samples from biological specimens for high-resolution tomographic imaging in one of our Titan Krios. Key features:
- CERES cryo Shield (DELMIC)
Leiden University - Institute of Physics - Physics of Quantum Materials
Description
In our lab, we investigate the physics and material properties of low-dimensional systems.
Contact
Techniques
- Low-Energy Electron Microscope (LEEM): called ESCHER. Due to its aberration correction, it has a record lateral resolution of 1.4 nm. Still, our research program aims far beyond pure microscopy. One of our goals has been to make LEEM a key measurement system in condensed matter physics research as a whole and to apply it specifically for research on Van der Waals materials, thin oxides and molecular.
- LEEM-Based Potentiometry (LEEP): allowing us to map potential differences in a 2D material under a voltage bias.
- Angle-Resolved Reflected-Electron Spectroscopy (ARRES): allows us to map the dispersion of unoccupied bands above the vacuum level with a very high cross section.
- Low-Energy Transmission Electron Microscope (eV-TEM): A novel form of transmission electron microscopy operating at very low energies, i.e. 0-100 eV (hence named eV-TEM)
- Optical Near-Field Electron Microscopy (ONEM): This new type of microscopy combines the best of optical microscopy (no damage to organic or biological structures) with the best of electron microscopy (a superb resolution). We have coined it ONEM (optical near-field electron microscopy).
- (Micro-)LEED
- Dark-Field Imaging
- (Micro-)ARPES
Equipment
Low-Energy Electron Microscope (LEEM)
- ESCHER
Low-Energy Transmission Electron Microscope (eV-TEM)
Leiden University - Institute of Biology
Description
The Briegel lab is part of the Institute of Biology at the Leiden University and the Centre of Microbial Cell Biology. We are interested in understanding how microbes sense and respond to their environment. How are the cells able to actively seek out their preferred environmental niches, how can they effectively evade toxins and predators, and how can they adapt to thrive in changing environments. In order to gain insight into the structure and function of the molecular complexes involved in these behaviors, we use cryo-electron tomography (cryo-ET).
Contact
Techniques
Cryo-Electron Tomography (Cryo-ET)
Cellular electron cryotomography allows the study of individual microbial cells in their native state and in three dimensions at macromolecular resolutions.
Equipment
We have access to the electron microscopes at NeCEN, the Dutch cryo-electron microscopy center located in the Biology Institute of the Leiden University.
- Talos L120C
- Aquilos cryo-FIB
- 2 TITAN Krios microscopes with state-of-the-art equipment for highest quality data collection
Fully equipped sample preparation laboratories:
- Leica instruments for sample freezing
- Large-volume preprocessing and correlative imaging
- Cryo-ultramicrotome
- High-pressure freezer (ICE)
- Thunder light microscope with cryo-stage and a cryo-plunger
LUMC - Koster Lab
Description
The aim of the Koster Lab Facility is to develop new (correlative light and electron) microscopy techniques, implement state-of-the-art microscopy techniques, and support clinical and pre-clinical science with microscopy techniques.
The Koster Lab Facility part comprises the Technical Focus Area (TFA) microscopy: the Electron Microscopy (EM) Facility, including the Microtissue Imaging Core and the Light Microscopy (LM) Facility. The aim of the EM and LM facility is to aid research with microscopy techniques by aquiring and maintaining electron and light microscopes and facilitating access to these apparatuses by education and technical support.
Contact
Techniques
Correlative Light and Electron Microscopy (CLEM)
Fixation techniques:
- Negative Staining
- Chemical Fixation
- Vitrification
- High-Pressure Freezing
Imaging Techniques:
- 2D Imaging and stitching
- Tomography
- Scanning Electron Microscopy (SEM)
- Sold Block-Face SEM
Equipment
SEM
- ZEISS GEMINI SEM 300: Field Emission Scanning Electron Microscope (SEM) for imaging of micro-structures. The microscope is equipped with the Gatan 3View system to image 3D ultrastructure using serial block-face imaging. Furthermore, the system is also equipped with the Zeiss Atlas V system to allow the imaging of serial sections in a non-destructive manner.
TEM
- FEI TECNAI 20 FEG with ICORR: a 200 kV Transmission Electron Microscope (TEM) equipped with a Gatan 2001 energy filter with a 2k x 2K CCD camera, a Gatan US 4000 4k x 4K CCD camera, and an FEI iCorr integrated light microscope for cryo- correlative light-electron microscopy (Cryo-CLEM).
- FEI T12 SPIRIT BIOTWIN: a 120 kV TEM with a LaB6 filament and a FEI Eagle 4k x 4K CCD camera to record high contrast images. The microscope has in-house developed software for automated scanning of specimen grids, and is equipped for cryo-electron microscopy and tomography.
- FEI T12 SPIRIT TWIN with ILEM & STEM: The FEI Tecnai 12 Twin is a 120 kV TEM with a LaB6 filament and an FEI Eagle 4k x 4K CCD camera and is equipped with a integrated laser scanning microscope (iLEM) for correlative light-electron cryo-microscopy and a Fischione HAADF STEM detector. Like the other TEMs, this microscope runs in-house developed software for automated scanning of specimen grids and can perform cryo-electron microscopy and tomography.
Other Microscopes
- ZEISS AXIO IMAGER with LINKAM FREEZING STAGE: The Zeiss Axio Image M2 is equipped with the Linkam CMS196M cryo correlative microscopy stage, which is controlled by Zeiss Zen software. It is specifically setup for automated cryo-CLEM imaging. It is capable of performing automated multi-color, z-stack recording, and recording tile-scan overviews.
- LEICA DM RXA with LINKAM THMS600 CRYOSTAGE: The Leica DM RXA is a development microscope, specifically used to develop super-resolution light microscopy on cryo-samples. To that end, it is equipped with a Linkam THMS 600 freezing stage, 100x dry objectives (NA of 0.75 and 0.9), three laser lines (405, 488 and 532 nm) and a sensitive CMOS camera (PCO Edge 4.2). Acquisition and read-out is being done with home-written software specifically designed for super-resolution image acquisition.
Maastricht - Maastricht University
Maastricht Multimodal Molecular Imaging Institute (M4I)
Description
Maastricht Multimodal Molecular Imaging Institute (M4i) is a state-of-the art international institute that brings together a powerful palette of innovative molecular imaging technologies. Its mission is to perform fundamental, instrumentation and applied studies in molecular imaging as part of a translational, synergistic, interdisciplinary research programme that attracts top researchers from across the world.
Contact
Techniques
M4I Division of Imaging Mass Spectrometry (IMS)
Developing and applying state-of-the-art mass spectrometry based molecular imaging approaches for nanomedicine and biomedical research, including mass spectrometry as a diagnostic and prognostic tool for personalized medicine in oncology, neurology and cardiovascular medicine.
Division of Nanoscopy Infrastructure
Cryo-electron microscopy is the only way to study cellular processes close to the in vivo situation. In order to do so, we have implemented a full workflow, starting with life cell imaging of cells or tissues followed by rapid cryo-fixation to preserve the structure. Cryo-light and Cryo-electron microscopy will resolve the 3D structure at nm resolution by means of electron tomography.
Equipment
IMS – Mass Spectrometry
- 9.4T MALDI/ESI SolariX Fourier Transform Ion Cyclotron Resonance imaging mass spectrometer
- 7T LTQ-FTICR system for ambient ionisation and imaging
- LAESI DP-1000 ambient imaging system of Protea Biosciences
- Bruker Ultraflex III ToF/ToF MALDI molecular imager with an IonPix Camera
- A Bruker RapiFlex TissueTyper
- A MS/MS enabled Bruker Rapiflex TissueTyper
- A Bruker MALDI-ToF Biotyper for microbial screening
- Physical Electronics NanoTof V Tandem MS SIMS system for high resolution SIMS equipped with a Bismuth, C60 and Argon Cluster sources
- A Physical Electronics TRIFT II for SIMS imaging with a Gold source
- TRIFT II based mass microscope for direct ion imaging with MALDI and C60-SIMS
- Waters 8K MALDI/ESI Synapt G2Si system for ion mobility enabled high resolution molecular imaging
- Waters 32K MALDI/ESI Synapt G2Si system for ion mobility enabled high resolution molecular imaging and MRM
- Waters MALDI Synapt HDMS system for conformational molecular imaging
- A Waters Xevo q-ToF system equipped with a DESI source for ambient ionization based imaging
- A Waters Xevo-q-ToF system equipped with a REIMS source for the development of intraoperative diagnostics
- A Waters HEPA filtered Xevo q-ToF systems system equipped with a REIMS source for research on intraoperative diagnostics
- A Waters TQS-micro triple quad with DESI-MRM capabilities.
- A Thermo Scientific q-Exactive HF system with a nano-LC system
- A Thermo Scientific Orbitrap Elite with a Spectroglyph MALDI imaging source for high resolution imaging MS
- A SimulToF MALDI Linear ToF imaging system
- An LCT q-ToF system modified for native MS and fitted with a high molecular weight IonPix Camera
Sample Preparation
- A fully equipped sample preparation facility, including cryosectioning, staining, analytical microscopes, matrix deposition and coating devices such as:
- Advion Triversa Nanomate system
- Several matrix deposition systems. ImagePrep, SunCollect and HTX sprayer
- 2 Cryo-microtomes for imaging MS
- Mirax histology scanner
- Leica optical research microscope with UV fluorescence imaging module
- ChIP spotting robot for LC-MALDI
- Virtual laboratory based image processing and analysis tools, including tissue classification and correlation software and protein data basing tools
- Large scale data storage and cluster computing facilities
Nanoscopy
- CorrSight
- Scios DualBeam
- Tecnai Arctica
- Ultramicrotome Leica EM UC7
- Cryochamber Leica EM FC7
- Leica EM AFS2
- Combined iCorr fluorescence light microscope module and the FEI Tecnai electron microscope
Nijmegen
Radboudumc Electron Microscopy Center
Description
The Radboudumc Electron Microscopy (EM) Center was established in 2019 by Dr. Anat Akiva and Prof. Nico Sommerdijk as part of the Radboudumc Technology Centers (RTC) Microscopy within the Radboud University Medical Center in Nijmegen, The Netherlands. The center supports users in the application of electron microscopy in life sciences, employing both standard techniques and the most advanced imaging and analysis strategies. Its special focus areas include 3D volume imaging, correlative light and electron microscopy, and cryo-electron microscopy, where efforts are made to advance techniques and methodologies beyond the state-of-the-art. Through a recently awarded NWO-Groot project, the center also serves as a National Facility for liquid-phase EM of biological materials (BIOMATEM).
Contact
Techniques
Cryo-TEM of Plunge-Frozen Samples
Samples are frozen in a vitrified amorphous ice layer to preserve (bio)nanostructures in their near native hydrated state. One can achieve (sub)nanometer-scale resolution with 2D cryoTEM imaging, and/or cryo-electron tomography. Additionally, energy dispersive X-ray spectroscopy (EDS) for elemental composition and electron diffraction under cryogenic conditions are also available.
Liquid-phase (LP) Electron Microscopy (EM)
LP-EM allows the direct visualization of samples in their liquid environments with nanometer spatial resolution and (sub-)second temporal resolution. Samples can be encapsulated in graphene liquid cells using the VitroTEM Naiad, or enclosed within a Denssolutions Stream liquid cell holder for precise fluid flow and temperature control. The Talos F200C G2 TEM is equipped with a unique light source mounted inside the column, providing light pulses for initiating processes inside the microscope.
Scanning Electron Microscopy (SEM) (cryo & room temperature)
EBSD enables the analysis of a sample’s crystallographic microstructure by detecting the diffra
Scanning Electron Microscopy (SEM) captures high-resolution images that contain information about the surface topography of the sample and can be used to examine dry specimens or those preserved in a hydrated state through rapid freezing (cryoSEM). Composition information of the sample can also be obtained through back-scattered signal imaging and Energy Dispersive X-ray Spectroscopy (EDS).
ction patterns of backscattered electrons after interacting with the atomic lattice of the sample. In this manner, the crystallographic orientation and grain boundary morphology can be determined. The AMOLF NanoLab Amsterdam EBSD detector is a Clarity system with a direct electron detector with very high sensitivity that allows for much lower beam current and beam voltage compared to standard EBSD. This enables damage-sensitive samples to be mapped (such as halide perovskite films).
Volume EM (cryo & room temperature)
Cells and tissues are imaged with nanometer resolution and their 3D ultrastructure reconstructed for volumes with dimensions up to several tens of micrometers. When working under cryogenic conditions, samples are fixed into a vitrified near-native state through high-pressure freezing (HPF), followed by precise milling and imaging with cryo-FIB/SEM, achieving voxel sizes down to a 5 nm. For samples at room temperature, resin-embedded samples are used with either chemical fixation or freeze-substitution methods, and imaging is performed with FIB/SEM or with scanning electron array tomography (for large volumes).
Lift-out lamella preparation for TEM (cryo & room temperature)
This is a specialized technique in FIB/SEM to extract a thin section from a specific region of a sample for high-resolution TEM imaging. It works both on room temperature resin-embedded samples and on vitrified (high pressure frozen) biological samples.
Correlative light and electron microscopy (CLEM) (cryo & room temperature)
This method correlates light microscopy data with high-resolution electron microscopy images, precisely locating predefined targets. A unique 3D cryoCLEM workflow has been developed that enables 3D correlation of cryo-fluorescence imaging with cryoFIB/SEM, capturing biological features in their near-native state. For room temperature applications, CLEM with resin-embedded samples combines fluorescence imaging with TEM or FIB/SEM for precise target localization.
Correlative EM/Raman microscopy (cryo & room temperature)
Raman microscopy enables the acquisition of spatially resolved chemical information from a sample. It can be combined with room temperature SEM to overlay chemical information with ultrastructural details of dried samples. For vitrified biological samples, cryoRaman microscopy can be correlated with cryoFIB/SEM.
○ In-situ TEM: A conventional TEM operates at room temperature under high vacuum conditions. In-situ techniques allow introducing application-relevant conditions like elevated temperatures or gas/liquid environments. This is often done via specific sample holders that incorporate electric contacts for heating and biasing or tiny chambers with gas and liquid flow.
○ Electron tomography: Conventional TEM provides 2D projection images of the sample. With electron tomography the characterization can be extended to 3D by acquiring a series of projection images under different tilt angles of the sample. Different methods exist to then reconstruct the 3D morphology from the series of 2D projection images. Electron tomography is often applied for quantification purposes and for highly anisotropic shapes.
○ Light excitation: To study photo-driven processes inside the TEM, light excitation of the sample is required. This can either be done via a dedicated sample holder or by inserting an optical window in the column itself. The latter has the advantage that the sample holder can be freely chosen and that light excitation can therefore be combined with other in-situ stimuli.
Equipment
Microscopes
- Zeiss Crossbeam 550 (cryo) FIB/SEM
- Talos F200C G2 TEM
- Zeiss Sigma 300 SEM
- WITec alpha 300R Raman microscope
- Zeiss LSM900 upright light microscope with Airyscan detector
Sample Preparation
- µ-Live CryoCapCell High pressure freezer
- Vitrobot Mark IV Vitrification Robot
- Quorum prepdek workstation with loading station for cryo-EM samples
- Cryo-Correlative Linkam CMS196 Microscopy Stage
- Leica Vibratome VT1200
- Leica Artos 3D Ultramicrotome
- Leica ACE600 sputter coater
- Leica Ultracut UCT+ EMFCS cryo-ultramicrotome
Enschede - University Twente
MESA+ Nanolab
Description
At MESA+, we believe in realising grand solutions with the extremely small. We contribute to solving current and future societal challenges. We do this by using our fascination with the extremely small. We bring societal challenges inside and use our fascination to work on innovative and sustainable solutions. We focus on societal challenges in four application areas: Health, AgriFood & Water, Security, and Energy & Sustainability. The MESA+ NanoLab is essential for ground-breaking research. This state-of-the-art NanoLab comprises a 1250 m2 cleanroom (ISO 5 / ISO 7) and an area of 1000 m2 containing specialized analysis equipment as well as dedicated research group labs.
Contact
Techniques
Analysis is restricted to materials in the solid-state. Samples supplied by our clients are analyzed on their surface and internal structure using techniques like:
- X-ray Photoelectron Spectroscopy (XPS)
- Scanning Electron Microscopy (SEM)
- Transmission Electron Microscopy (TEM)
Multiple detectors on the microscopes can probe many different properties of your samples. We use a double beam FIB (Focused Ion Beam) for rapid prototyping as well as sample preparation.
- Focused Ion Beam (FIB)
Equipment
SEM
- ZEISS Merlin: High resolution scanning electron microscope
TEM
- Thermo Scientific Spectra 300: Probe corrected S/TEM for Materials Science
FIB
- Thermo Scientific Helios 5 UX: DualBeam Focused Ion Beam
XPS
- PHI Quantes: Dual scanning x-ray photoelectron microprobe
XRD
- Bruker D8 DISCOVER: Scanning XRD with beam size of nominal 20-30 micrometers
Optical Microscopes
- Leitz metalloplan: This wide-field microscope is used to control specimens during the grinding and polishing process.
- Olympus SZ40: Optical microscope with zoom objective lens 6.7 – 40x for sample inspection purposes. A ring light Olympus highlight 3100 accompanies the microscope objective. Used to view rather large specimens.
- Leica M420: Macroscope for high-precision work in inspection and measurement, equipped with a camera.
Critical Point Dryer
- LEICA EM CPD 300: With a critical point dryer, it is possible to dry water containing specimens in a way that they shrink almost conformal.
Advanced Plasma System
- Gatan Solaris: Advanced plasma cleaning system for removal of hydrocarbon contamination on TEM and SEM samples. Cleaning small specimen for TEM or SEM use by a low energy H2 / O2 plasma.
Dimple Grinder
- Gatan: Used to decrease the thickness of thin TEM samples. A mechanical wheel grinds the thin specimen to a thickness of less than 1 um. Afterwards, the ultimate thinning of the TEM specimen takes place in the precision ion polishing system.
Saws
- Buehler Isomet: Low-speed saw. used to slice down bigger pieces of materials to quite small ones that can be used to make TEM specimens.
- Struers Labotom 3: Rough cutting saw. Saw to cut small pieces out of a big piece of material. Metals of a thickness of 1 – 2 cm can be cut into smaller pieces. If the pieces are small enough they can be pressed into an SEM.
Sample Press
- Struers Primopress: Used to slice down bigger pieces of materials to quite small ones that can be used to make TEM specimens.
Grinder Polishers
- Buehler ecomet 3: Variable speed.
- Buehler Phoemix beta: Variable speed grinder polisher.
- Struers Labopol 21: Double grinder, single-speed, 250 rpm, for manual preparation of materialographic specimens.
- Struers Tegrapol 21: Grinder-polisher for ultimate flatness and smoothness of SEM samples.
- Knuth-rotor 2: Double grinder-polisher for grinding samples with sandpaper or carbide paper.
Coaters
- BIORAD POLARON division e6: Double grinder-polisher for grinding samples with sandpaper or carbide paper.
- Gatan Pecs: Precision etching and coating system. This system is used to etch or slope cut a specimen. Just like a cut that is possible with a FIB. Only this cut will have a sample size width. After cutting or stand-alone a coating can be applied to the sample.
Ultra Sonic Bath
- Branson B200: For the cleaning of specimens or small instruments. The cleaner uses ultrasonic energy (40 kHz) in the form of sound waves to create millions of tiny microscopic bubbles in the solution that even works their way into holes and hidden cavities.
Utrecht
UMC Utrecht - Cell Microscopy Core
Description
The Department of Cell Biology is an integrated academic center for research and education in the fields of stem cells and regenerative medicine, cancer, and immunology. Expertise and equipment for state-of-the-art fluorescence and electron microscopy techniques.
Contact
Techniques
Resin-Based (Conventional) Electron Microscopy (EM)
When ultrastructural morphologic analysis is required, resin EM is the method of choice. After aldehyde fixation and post-fixation with osmium tetroxide, the biopsies, tissues, organoids, or cultured cells are embedded in epoxy resin. This allows ultrathin sectioning of 50–70 nm sections. After additional staining with uranium and lead salts, the ultrastructural morphology can be investigated with the electron microscope.
Immuno-Electron Microscopy (immuno-EM)
The cryo-immunogold technique. The most sensitive and widely used approach to detect ultrastructural localization of molecules in cells is immuno-electron microscopy. Many protein-sorting events that determine cellular processes occur in 40–60 nm, often coated, membrane subdomains, which are below the detection level of the light microscope. The Tokuyasu cryosectioning technique has been improved and perfected in the Cell Microscopy Center so that it now generally surpasses other techniques in membrane visibility and labeling sensitivity. The method requires that samples (tissues, organoids, and cells) be chemically fixed, after which they are frozen and cut into 50–100 nm cryosections. The sections are thawed and labeled with antibodies that specifically recognize the molecule of interest, followed by gold particles that are detectable in the EM.
Electron Tomography
Ultrathin sections (50–70 nm) provide an excellent way to observe the interior of a cell. However, the thickness of a section diminishes the chance that 3D relations between subcellular structures are found. Using thicker sections (200–300 nm) increases this chance. When such a section is rotated from +65 to -65º in a 200KV electron microscope and a picture is taken every degree, the 3D ultrastructure of an area of interest can be visualized using special software.
High Pressure Freezing (HPF)
HPF is the state-of-the-art chemical method for ultrastructural preservation and is, for some applications, preferred instead of chemical fixation. Fresh samples are cryo-immobilized under high pressure so that ice crystal formation is prevented. These vitreous frozen samples can then be processed in multiple ways for EM visualization:
- Freeze Substitution: Water frozen within cells is replaced by organic solvents at subzero temperatures. The natural structure and molecule distribution in the samples are maintained until the substitution process is completed, providing superiority over chemical fixation in preserving ultrastructure as well as labile tissue antigens. Freeze-substituted samples can be embedded in plastic (epoxy or acrylic) resins for structural studies.
- Vitreous samples can be viewed immediately or after cryosectioning in the cryo-electron microscope.
- Vitreous samples can be rehydrated and sectioned as in the Tokuyasu technique for immunolabeling.
Live-Cell Imaging
The possibility of studying dynamic processes in living cells makes fluorescence microscopy an exceptionally powerful and essential method in life sciences. Especially with the latest genetic editing methods, genetic markers like green fluorescent protein (GFP) can be tagged to almost any protein to reveal its intracellular transport dynamics at endogenous levels in living cells. Besides, real-time kinetics of cellular processes can be studied using functional live-cell reporters.
Live-Cell Correlative Light & Electron Microscopy (CLEM)
Live-cell imaging reveals the dynamics of protein and organelle movements, yet lacks the structural resolution against which the fluorescent signal can be interpreted. Immuno-electron microscopy is unique in its capacity to localize molecules to their functional intracellular locations but is limited in its interpretation of dynamic processes. To fill this gap between live-cell imaging and EM, we have recently developed correlative-microscopy methods by which a fluorescently marked structure followed by live-cell imaging can be fixed at any time during its itinerary and be processed for visualization by electron microscopy. These approaches uniquely link intracellular dynamics of proteins and/or subcellular structures (e.g., organelle dynamics) to the underlying ultrastructure.
On-Section CLEM
Rare cellular events or regions of interest (ROI), e.g., aberrant cells in a pathologic tissue, can be hard to find with the high-resolution, however narrow, field of view of the EM. In the light microscope, the field of view is much larger, which allows rapid identification of the ROI. When an ultrathin section is processed for (immuno-)electron microscopy, it is possible to first screen the section on the grid in a sensitive light microscope and locate the ROI. Next, the grid can be investigated in the electron microscope for ultrastructural context information. The cell of interest is located quickly using the grid's location markers. In addition, this method presents a valuable tool for ultrastructural localization of scarce antigens by bridging fluorescence microscopy with EM data.
Volume Electron Microscopy (vEM)
Volume Electron Microscopy (vEM) is a group of techniques that reveal the 3D ultrastructure of cells and tissues through continuous depths at nanometer resolution. Among these, FIB-SEM is the method of choice to visualize 3D structural information of intracellular structures with high isotropic resolution (<5nm x, y, and z). Samples are fixed chemically or HPF, stained for EM, and embedded in resin before imaging in FIB-SEM. vEM can be combined with correlative methodologies, especially live-cell CLEM. Other vEM methods (e.g., Array Tomography) are being developed and optimized for various sample types (cells, organoids, and tissues) in our facility.
Equipment
Equipment for (Immuno)-Electron Microscopy
- 1 FEI Tecnai 20 electron microscope
- 1 FEI Tecnai 12 electron microscope
- 1 JEOL 1010 electron microscope
- 3 Leica ultra microtomes
- 5 Leica ultra-cryomicrotomes
- 1 Leica EM ICE high-pressure freezer
- 1 Balzers critical point dryer
- 1 Leica AFS 2 freeze substitution machine with EM FSP
- 1 Leica AC20 automated gridstainer
- 1 FEI SCIOS FIB SEM scanning electron microscope
- 1 Phenom Pro tabletop SEM
- 1 Sputter coater
- 1 Edwards Auto 306 Carbon Coater
Equipment for Light Microscopy
- 1 Leica Thunder with Tirf and infinity scanner
- 1 Zeiss LSM700
- 1 ECHO Revolve, color camera and fluorescent microscope
- 1 Deltavision RT Core system
- 1 Cell Insight next high throughput microscope
Utrecht University - Electron Microscopy Centre
Description
Covers the entire range of specimen preparation, electron microscopy data collection and analysis, spectroscopic methods, and 3D reconstruction techniques. The Electron Microscopy Centre at Utrecht University (UU) is devoted to the development and application of electron microscopy methodologies for life sciences and materials science research. The infrastructure includes several advanced Transmission Electron Microscopes (TEM) and Scanning Electron Microscopes (SEM), with a full range of imaging modes and analytical tools.
Contact
Techniques
Life Sciences
- Equipment for the preparation of biological specimens with preservation of molecular structures (including plunge freezing and high-pressure freezing)
- Single-particle Cryo-EM to obtain atomic structures from biochemically purified samples
- High-resolution Cryogenic Electron Tomography (Cryo-ET) to study three dimensional structure of (near) native samples such as cells and organelles
- Cryo-focused Ion Beam (FIB) milling to prepare lamellae for Cryo-ET
- Cryo-light fluorescence light microscopes for Correlated Light and Electron Microscopy (CLEM)
Materials Science
The facility offers a wide range of imaging and spectrometric modalities, such as:
- Bright-field and Dark-field Scanning Transmission Electron Microscopy (STEM)
- Electron Diffraction (ED)
- Chemical mapping using Energy Dispersive X-ray Spectrometry (EDX) and Electron Energy Loss spectrometry (EELS)
- For performing experiments inside the electron microscope, dedicated specimen holders are available including cryo-, heating, liquid-, and gas-cell holders.
Equipment
TEM
- TFS Spectra300 (materials science): 30-300 kV (S)TEM. Double aberration corrected microscope with a variable acceleration voltage (30, 80 and 300 kV), enabling high-resolution imaging up to 50 pm both in TEM and STEM imaging mode. Equipped with energy dispersive X-ray spectrometry (EDX) for chemical mapping, and ultra-high-resolution electron energy loss spectrometry (UHR-EELS) enabled by its double monochromator and Gatan Continuum filter. It also has a direct-direction Gatan K3 IS camera allowing imaging of soft and beam-sensitive materials.
- TFS Talos Arctica (life sciences): 200 kV cryo-TEM equipped with a Gatan K2 direct-detection camera. This microscope is dedicated to high-resolution imaging and electron tomography under cryo conditions, for 3D reconstructions of cells and protein complexes.
- TFS Talos F200X (materials science): 200 kV (S)TEM for near-atomic imaging and characterization of materials science samples. High-brightness X-FEG electron gun, high-resolution imaging up tot 1.1 Å, electron diffraction, electron tomography, and high-sensitivity EDX chemical mapping.
- TFS Talos L120C (life sciences and materials science): 120 kV (S)TEM for imaging of both life sciences and materials science specimens. Equipped with a cryo-box enabling prolonged cryo-EM inspections.
- TFS Tecnai 20: Basic TEM for training purposes and screening of samples.
FIB-SEM
- TFS Helios Nanolab G3: 5-30 kV FIB-SEM for high-resolution imaging of surfaces, compositional and structural analysis, and slice-and-view 3D reconstructions. Equipped with EBSD, CL, and EDX mapping capabilities, and a cryo specimen stage. The focussed ion beam (FIB) allows removing material so that cross-sectional imaging perpendicular to the surface is possible, as well as extracting FIB-made lamellae that can be subsequently inspected in a TEM microscope.
SEM
- Zeiss Gemini 450: Variable pressure SEM allowing high-resolution imaging of sample topology including large area samples. Equipped with EDX, EBSD, cryo-stage, panchromatic and wavelength-filtered CL
- Zeiss Evo 15: Environmental SEM dedicated to imaging under environmental conditions such as humidity and low gas pressures. Equipped with Peltier cooling stage and EDX.
- TFS Aquilos: cryogenic FIB / SEM equipped with integrated Delmic Meteor fluorescence light microscope and CERES cryo shield to prepare targeted lamellae for cryo-ET.
- Phenom Pro: Table-top screening SEM allowing fast insertion and inspection of samples.
Wageningen - Wageningen University
Wageningen Electron Microscopy Center
Description
The Wageningen Electron Microscopy Centre provides microscopy and specimen preparation facilities for biological and materials science research. In addition, the centre offers necessary training and access to all microscopes to faculty, staff, and students of Wageningen University & Research as well as external users.
Contact
Techniques
Cryo-Scanning Electron Microscopy (CRYO-SEM)
The FEI Magellan 400 is equipped with a Leica cold stage for cryo-microscopy. Low-temperature SEM can be performed on frozen material.
Energy Dispersive X-ray Spectroscopy (EDS-SEM)
During SEM imaging, X-rays are emitted from the sample. Interaction of the electron beam with atoms in the sample causes shell transitions, which result in the emission of X-rays. An emitted X-ray beam has an energy which is characteristic of the parent element. Determining the emitted X-ray energies can be used for the quantitative elemental analysis of the sample. Energy-dispersive X-ray spectroscopy (EDS) can also be used to form maps or line profiles, showing the elemental distribution in a sample surface (sampling depth 1-2 microns).
Transmission Electron Microscopy (TEM)
WEMC has two Transmission Electron Microscopes which offer the following features:
- Standard TEM
- High-resolution TEM
- Tomography/Three dimensional imaging
- Cryo-TEM
- Negative staining electron microscopy
- Immuno electron microscopy
Equipment
Microscopes
- JEOL JEM-1400Plus:
- The JEM-1400Plus features high resolution/high contrast imaging, outstanding TEM analytical performance, cryomicroscopy, 3D tomography, and montaging. This compact, easy-to-use TEM is suitable for biological, polymer, and materials science applications. JEOL JEM-1400Plus has an acceleration voltage up to 120kV. The machine accommodates measurements under cryogenic temperatures, using the available cryo-holder and sample preparation equipment for imaging thin biological and other aqueous samples.
- FIB-SEM Zeiss Auriga (Crossbeam):
- The Zeiss Auriga is a high resolution Focused Ion Beam Scanning Electron microscope. The Schottky field emitter allows a resolution downto 1 nm of the full 30 to 1 kilovolt range. The microscope has Inlens, Everhart-Thornley and backscatter detectors. Furthermore the microscope is equipped with a Gatan Alto 2500 cryo-stage, cryo-transfer and coating system. The EDS system is from Oxford Instruments for Energy Dispersive X-ray Spectroscopy. The Focused Ion Beam can directly modify or “mill” a sample surface with nanometer precision. The focused ion beam is used to etch the sample, thereby exposing a new surface which van be imaged by SEM. Repeating this process can reveal the full 3D representation of the internal structure.
- FEI Magellan 400 FESEM:
- The Magellan 400 is a fully digital FESEM with Schottkey field emitter source providing subnanometer resolution over the full 1 kV to 30 kV electron energy range. The microscope has two detectors a Everhart-Thornley SE detector for SE detection, and NG in-lens detector (TLD) designed for high-resolution imaging even at low kV’s. The Magellan is equipped with a new generation energy dispersive spectroscopy (EDS) system from Oxford Instruments. Furthermore the Magellan is equipped with a cryostage and cryotransfer system.
Critical Point Drying
- Leica CPD-030: The critical point dryer CPD-030 is used for drying of samples. It prevents major drying artifacts caused by capillary forces.
High-Pressure Freezing
- Balzers HPM-010: Rapidly freezing samples at high pressure drastically reduces the nucleation and growth of ice crystals and therefore results in less structural damage.
Ultra (Cryo-)Microtomy
- Leica FCS: Ultramicrotomes are used to prepare ultra-thin sections (<100nm) of resin embedded or frozen material for transmission electron microscopy. This can be done at room temperature or at low temperatures (down to -150°C), using an ultracryotome.
Freeze Substitution
- Leica AFS and FreezySub: Freeze-substitution is used to dehydrate a sample while preserving the original structure. At -90°C, samples are put in an organic solvent and the ice will be replaced by the organic solvent resulting in a dehydrated sample.
Sputter Coating
- Leica and Jeol: Sputter coating is used to produce thin (0.5- 20nm) conducting layers on non-conducting samples. Available at WEMC are gold, tungsten, platinum and iridium.
Carbon Coating
- Carbon coating is used in scanning electron microscopy to make specimens conductive and in transmission electron microscopy (TEM), it is used as specimen support films on TEM grids.
Vitrification using the Vitrobot
- The FEI Vitrobot is an automated, climatecontrolled plunge freezing device. The Vitrobot freezes the sample so quickly that water molecules do not have time to crystallize. Instead the water molecules form an amorphous ice that does no damage to the structure. Cryo-observation of vitrified samples allows the ultrastructural study of macromolecules, molecular assemblies and cells in their natural (= hydrated) environment.
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