MerlinEM
The Direct Electron Detector (DED) pushing the boundaries of capability in TEMs.

In this note, we will show examples of using a MerlinEM detector to generate established signals in STEM. We will use LiberTEM2software to reconstruct the data and specifically its GUI web interface. We will show examples of virtual STEM images and convergent beam electron diffraction (CBED) from a few different samples
MerlinEM Installation Sites
Title | Address | Description |
---|---|---|
University of Glasgow | Glasgow G12 8QQ, UK | |
University of Oxford | Diamond House, Harwell Science and Innovation Campus, Fermi Ave, Didcot OX11 0DE, UK | |
NIST | 100 Bureau Dr, Gaithersburg, MD 20899, USA | |
University of Victoria | Victoria, BC V8P 5C2, Canada | |
EMAT University of Antwerp | Prinsstraat 13, 2000 Antwerpen, Belgium | |
MPI Stuttgart | Heisenbergstraße 3, 70569 Stuttgart, Germany | |
Ernst Ruska Centre | 52428 Jülich, Germany | |
Brookhaven National Laboratory | 98 Rochester St, Upton, NY 11973, USA | |
RIKEN | Japan, 〒351-0105 Saitama, Wako, Nishiyamatodanchi, 2−1 2-1 | |
The Univeristy of Queensland | St Lucia QLD 4072, Australia | |
TU Darmstadt | Karolinenpl. 5, 64289 Darmstadt, Germany | |
University Paris Sud | 15 Rue Georges Clemenceau, 91400 Orsay, France | |
National University of Singapore | 21 Lower Kent Ridge Rd, Singapore 119077 | |
Fraunhofer Institute for Microstructure of Materials and Systems IMWS | Walter-Hülse-Straße 1, 06120 Halle (Saale), Germany | |
Wuhan University | Wuchang District, Wuhan, Hubei, China, 430072 | |
TU Berlin | Straße des 17. Juni 135, 10623 Berlin, Germany | |
Shanghai Tech University | 393 Huaxia Middle Rd, Pudong Xinqu, China, 201210 | |
Norwegian University of Science and Technology (NTNU) | Høgskoleringen 1, 7491 Trondheim, Norway | |
The University of Cambridge | The Old Schools, Trinity Ln, Cambridge CB2 1TN, UK | |
University of Texas in Austin | Austin, TX 78712, USA | |
University of Manchester | Oxford Rd, Manchester M13 9PL, UK | |
CNRS - Institut Néel | 25 Avenue des Martyrs, 38042 Grenoble, France | |
University of York | Heslington, York YO10 5DD, UK | |
University Paris Sud- Orsay | 15 Rue Georges Clemenceau, 91400 Orsay, France |

MerlinEM
The MerlinEM Direct Electron Detector (DED) is an advanced detector development in the field of Electron Microscopy, combining direct detection of electrons and rapid readout in a pixelated format ideal for applications such as 4D STEM and TEM dynamic imaging. Each sensor pixel is individually bump-bonded to an intelligent chip which uses threshold discriminators to distinguish electrons from the background, effectively eliminating all readout noise. This allows for integral mode imaging where multiple short exposure images are acquired and summed together. Uniquely, neighbouring pixels can communicate to mitigate charge-sharing effects, and this, combined with the direct detection of electrons, yields enhanced performance. As beam energies decrease toward 60 keV, the Merlin for EM has been shown to provide near-ideal DQE and MTF detector response.
Specifications
Rapid readout
Kilohertz frame rates in continuous mode with zero deadtime offers more experimental flexibility than ever before, minimising effects such as sample drift, and enabling single shot and “pump and probe” dynamic experiments.
Direct detection
Noiseless detection of single electron events.
Effectively noise free
Two threshold discriminators in each pixel means zero read noise and dark current.
Dynamic range
Up to 24-bit counting depth enabling 1:16.7 million intensity range in a single image, ideal for recording diffraction patterns.
Charge Summing Mode (CSM)
Communication between pixels designed to mitigate charge sharing effects for maximising both DQE and MTF.
Wide energy range and radiation tolerance
Minimum 30 keV threshold making low energy EM imaging possible, and radiation tolerant design to 300 keV.
No beamstop requirements
Radiation tolerant design means no need for a beamstop in diffraction experiments.
Mount
Static and retractable mounts available to fit many electron microscopes.
Software
The various acquisition modes, as well as many other input parameters for the optimisation of the MERLIN system, are easily chosen by a user friendly Graphical Interface as well as remotely controlled via TCP/IP protocol, and Digital Micrograph. Merlin data can be used with many other software tools, including: – HyperSpy: https://hyperspy.org/ – pixStem: https://pixstem.org/ – pyXem: for working with scanning (precession) electron diffraction (S(P)ED) data, https://pyxem.github.io/pyxem/ -more tools can be found here https://www.gla.ac.uk/schools/physics/research/groups/mcmp/researchareas/pixstem/ Tools for handling data from fast pixelated detectors such as Merlin are a dynamic and very active field of research, so please let us know if you are working on any and would like us to link to your libraries. Collaboration fuels progress!
Hybrid Pixel Technology
Merlin is a new type of technology in the field of electron microscopy. It is a detector based on a hybrid pixel architecture. The detector assembly consists of a thick, highly resistive semiconductor sensor coupled to a Medipix3 chip. Incoming radiation generates charge in the sensor which diffuses under an applied bias to the CMOS circuitry of the individual pixels (via an array of micro-bump bonds). Each pixel contains >1100 transistors (within the 55 micrometer pitch), enabling on-chip counting of incident electrons and enhanced operation modes such as Charge Summing Mode (more about this later). The counting process consists of analogue comparison of the collected charge to a user selected energy threshold, and subsequent digital counting at 1 MHz if the threshold is exceeded. Thus, since the data readout relating the number of electrons counted by each pixel is digital, the Merlin detector operates free of readout noise. This is a feature unique to hybrid pixel technology and strongly differentiates it from analogue integrating detectors, such as CCD technology. Counting detectors are known to offer highest imaging performance in terms of modulation transfer function (MTF) and detective quantum efficiency (DQE). The Merlin detector has been shown combine ideal TEM performance at the low energies needed to study 2D materials such as graphene for 60keV electrons 1 with 1000’s per second frame rates.
Data Binning in Merlin
MERLIN provides high versatility with a variety of intrinsically fast (due to highly parallelized digital readout) large dynamic range acquisition options, namely: 14,400 fps@1 bit depth, 2,400 fps @ 6 bit depth, 1,200fps @12 bit and 600fps@24 bit depth. These readout modes (unlike the speed-up strategies employed with CCD technology) are unbinned and therefore imply no reduction of pixel resolution or field of view. Moreover, due to the electron counting approach of the detection system as well as the fully digital readout, MERLIN adds zero noise allowing a Signal to Noise Ratio (SNR) as high as a 16.7 million:1.
Dead Time in Merlin
There is no dead time in data collection! The advanced pixel architecture implements two readout counters per pixel and provides a continuous read/write acquisition mode with zero detector dead time (CCD technologies rely on non active detector frame store areas to reduce detector dead time). The various acquisition modes, as well as many other input parameters for the optimisation of the MERLIN system, are easily chosen by a user friendly Graphical Interface as well as remotely controlled via TCP/IP protocol.
Installation of Merlin
The MERLIN system is really “Plug and Play”, with the detector simply connected by one or two cables, depending on the type of installation (static or retractable). The Medipix3 chip has a very low (<1 Watt) power consumption, requiring minimal cooling and no need for connection to microscope water supplies or to pneumatics. The readout electronics are connected to the detector head via a 10 meter cable, thus giving ultimate flexibility. Therefore, MERLIN installation is rapid and designed not to impact on other microscope services.
Publications
4D-STEM
2019
- Synthesis and Properties of a Compositional Series of MIL-53(Al) Metal–Organic Framework Crystal-Glass Composites
American Chemical Society. p. 15641–15648. 2019
- Electron Ptychography Using Fast Binary 4D STEM Data
p. 1662–1663. 2019
- Three-dimensional subnanoscale imaging of unit cell doubling due to octahedral tilting and cation modulation in strained perovskite thin films
American Physical Society. p. 1–7. 2019
- Comparison of first moment STEM with conventional differential phase contrast and the dependence on electron dose
Elsevier B.V.. p. 95–104. 2019
- Electrical Polarization in AlN/GaN Nanodisks Measured by Momentum-Resolved 4D Scanning Transmission Electron Microscopy
American Physical Society. p. 106102. 2019
- Metal-organic framework crystal-glass composites
p. 1–28. 2019 - Strain Anisotropy and Magnetic Domains in Embedded Nanomagnets
Nord, M., , , , , , , , , , , , , , Small 2019, 15, 1904738.
2018- Imaging Structure and Magnetisation in New Ways Using 4D STEM
p. 180–181. 2018
2016- Pixelated detectors and improved efficiency for magnetic imaging in STEM differential phase contrast
Elsevier. p. 42–50. 2016
- Synthesis and Properties of a Compositional Series of MIL-53(Al) Metal–Organic Framework Crystal-Glass Composites
Low dose imaging
- Electron Ptychography Using Fast Binary 4D STEM Data
p. 1662–1663. 2019
- Metal-organic framework crystal-glass composites
p. 1–28. 2019
- Synthesis and Properties of a Compositional Series of MIL-53(Al) Metal–Organic Framework Crystal-Glass Composites
American Chemical Society. p. 15641–15648. 2019
Electromagnetic fields
- Electrical Polarization in AlN/GaN Nanodisks Measured by Momentum-Resolved 4D Scanning Transmission Electron Microscopy
American Physical Society. p. 106102. 2019
- Imaging Structure and Magnetisation in New Ways Using 4D STEM
p. 180–181. 2018
- Pixelated detectors and improved efficiency for magnetic imaging in STEM differential phase contrast
Elsevier. p. 42–50. 2016
- Internal structure of hexagonal skyrmion lattices in cubic helimagnets
IOP Publishing. p. 095004. 2016
Time resolved imaging
Atomic resolution electric fields
2019
- Comparison of first moment STEM with conventional differential phase contrast and the dependence on electron dose
Elsevier B.V.. p. 95–104. 2019
- Electrical Polarization in AlN/GaN Nanodisks Measured by Momentum-Resolved 4D Scanning Transmission Electron Microscopy
American Physical Society. p. 106102 2019
2D-materials
2019
- Electron Ptychography Using Fast Binary 4D STEM Data
p. 1662–1663. 2019
- Hollow Electron Ptychographic Diffractive Imaging
American Physical Society. p. 146101. 2018
3D imaging
- Three-dimensional subnanoscale imaging of unit cell doubling due to octahedral tilting and cation modulation in strained perovskite thin films
American Physical Society. p. 1–7. 2019
- Imaging Structure and Magnetisation in New Ways Using 4D STEM
p. 180–181. 2018
Ptychography
- Electron Ptychography Using Fast Binary 4D STEM Data
p. 1662–1663. 2019
- Hollow Electron Ptychographic Diffractive Imaging
American Physical Society. p. 146101. 2018
Pharmaceuticals
TEM imaging
- Characterisation of the Medipix3 detector for 60 and 80 keV electrons
Elsevier B.V.. p. 44–53. 2017
Diffraction imaging
- 2019
- Synthesis and Properties of a Compositional Series of MIL-53(Al) Metal–Organic Framework Crystal-Glass Composites
American Chemical Society. p. 15641–15648. 2019
- Metal-organic framework crystal-glass composites
p. 1–28. 2019
20182019- Three-dimensional subnanoscale imaging of unit cell doubling due to octahedral tilting and cation modulation in strained perovskite thin films
American Physical Society. p. 1–7. 2019
2017 - Synthesis and Properties of a Compositional Series of MIL-53(Al) Metal–Organic Framework Crystal-Glass Composites
Detector characterisation
- 20192017
- Characterisation of the Medipix3 detector for 60 and 80 keV electrons
Elsevier B.V.. p. 44–53. 2017 Amorphous materials
- 2019
- Metal-organic framework crystal-glass composites
p. 1–28. 2019
- Synthesis and Properties of a Compositional Series of MIL-53(Al) Metal–Organic Framework Crystal-Glass Composites
American Chemical Society. p. 15641–15648. 2019
2017 - Metal-organic framework crystal-glass composites
- Characterisation of the Medipix3 detector for 60 and 80 keV electrons