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Nodes

The NEMI infrastructure is distributed over 10 regions in the Netherlands, divided into Regional Nodes (offering mid-level EM infrastructure and pilot testing) and a selection of Flagship Nodes (concentrating highly advanced or specialized EM techniques to restricted sites only).

Amsterdam

Description

The 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 sample in fluorescence microscopy and then image the same sample using electron microscopy to combine the images and localize fluorescence in TEM.

Equipment

  • 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
  • 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,

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:
    • Dr. Wiebke Albrecht (W.Albrecht@amolf.nl).
    • Prof. dr. Erik Garnett (E.Garnett@amolf.nl)
  • AMOLF NanoLab Amsterdam:
    • Hans Zeijlemaker (H.Zeijlemaker@amolf.nl),
    • Prof. Dr. Ewold Verhagen (E.Verhagen@amolf.nl)

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

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Delft

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

  • Arjen Jakobi (a.jakobi@tudelft.nl)

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

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Eindhoven

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Groningen

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Leiden

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Maastricht

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Nijmegen

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Enschede

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Utrecht

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Wageningen

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