On the Merlin for EM product page we have collected all the information we have available on the product. Access resources, articles and application notes or read through the extensive collection of knowledge presented in an easy to read format directly on the web!

What is it? How does it work?

The Merlin for EM Hybrid Pixel Detector (HPD) 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.



Electron diffraction






Pump and probe experiments


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 20 keV threshold making low energy EM imaging possible, and radiation tolerant design to 300 keV.


Static and retractable mounts available to fit many eletron microscopes.

No beamstop requirements

Radiation tolerant design means no need for a beamstop in diffraction experiments.


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: – pixStem: – pyXem: for working with scanning (precession) electron diffraction (S(P)ED) data, -more tools can be found here 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!

Olivia Sleator

Olivia Sleator

Sales Manager

Application notes



Q. How can Merlin be calibrated?
A. Your Merlin system comes pre-calibrated.  Should you wish to add more calibration points to a particular energy, this can be done through the LabView GUI and editing of a calibration text file.  Details on how to do this are in the Manual.

Q. Does Charge Summing Mode increase dead time?
A. Yes, very slightly since there is additional logic here.

Q. How long is the cable from the PC to the detector head?
A. Up to 10 meters.

Q. Is it possible to access the FPGA memory directly?
A. No, the system writes to local disk and/or TCP/IP link


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.


Charge Summing Mode (CSM)

When an electron strikes near the edge of a pixel (illustrated left), the resulting charge may leak into neighbouring pixels, thus reducing the MTF.  MERLIN has a unique capability where information is shared between adjoining clusters of four pixels, in what is known at the Charge Summing Mode. When charge spread occurs over the four adjoining pixels, MERLIN recognizes that this information belongs to one event on one pixel rather than up to 4 weaker events on 4 pixels.  By reconstructing the event using the diffused charge data, MERLIN increases the resolution and ensures an accurate reading of the event giving improved results quality.


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.


    • Nature Communications volume 10, Article number: 1127 (2019) “Atomic electrostatic maps of 1D channels in 2D semiconductors using 4D scanning transmission electron microscopy” Shiang Fang, Yi Wen, Christopher S. Allen, Colin Ophus, Grace G. D. Han, Angus I. Kirkland, Efthimios Kaxiras & Jamie H. Warner 
    • Scientific Reports volume 9, Article number: 3919 (2019) “Atomic Resolution Defocused Electron Ptychography at Low Dose with a Fast, Direct Electron Detector” Jiamei Song, Christopher S. Allen, Si Gao, Chen Huang, Hidetaka Sawada, Xiaoqing Pan, Jamie Warner, Peng Wang & Angus I. Kirkland 
    • Ultramicroscopy 182 (2017) 44–53: “Characterisation of the Medipix3 detector for 60 and 80 keV electrons” J.A. Mir a , R. Clough a , R. MacInnes c , C. Gough c , R. Plackett b , I. Shipsey b , H. Sawada a , e , f , I. MacLaren c , R. Ballabriga d , D. Maneuski c , V. O’Shea c , D. McGrouther c , ∗, A.I. Kirkland, e a University of Oxford, Department of Materials, Parks Road, Oxford OX1 3PH, United Kingdom b University of Oxford, Department of Physics, Parks Road, Oxford OX1 3PH, United Kingdom c University of Glasgow, School of Physics and Astronomy, Glasgow G12 8QQ, United Kingdom d CERN, 1211 Geneva 23, Geneva, Switzerland e Electron Physical Sciences Imaging Centre, Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom f JEOL UK Ltd. JEOL House, Silvercourt, Watchmead, Welwyn garden City, Herts AL71LT, United Kingdom. URL:
    • Ultramicroscopy:165(2016)42–50 “Pixelated detectors and improved efficiency for magnetic imaging in STEM differential phase contrast” Matus Krajnak, Damien McGrouther, Dzmitry Maneuski, Val O’ Shea, Stephen McVitie Scottish Universities Physics Alliance, School of Physics and Astronomy, University of Glasgow, Glasgow G128QQ, United Kingdom. URL:
    • Nuclear Inst. and Methods in Physics Research, A: “Direct imaging detectors for electron microscopy” A.R. Faruqi *, G. McMullan MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK. URL:
    • Phys. Rev. Materials 2, 104406 – Published 17 October 2018 “Antiferromagnetic-ferromagnetic phase domain development in nanopatterned FeRh islands” R. C. Temple, T. P. Almeida, J. R. Massey, K. Fallon, R. Lamb, S. A. Morley, F. Maccherozzi, S. S. Dhesi, D. McGrouther, S. McVitie, T. A. Moore, and C. H. Marrows 
    • Metal-Organic Framework Crystal-Glass Composites Preprint submitted on 17.09.2018, 13:54 and posted on 18.09.2018, 16:32 by Jingwei Hou Christopher W. Ashling Sean M. Collins Andraž Krajnc Chao Zhou Louis Longley Duncan Johnstone Philip A. Chater Shichun Li François-Xavier Coudert David A. Keen Paul A. Midgley Gregor Mali Vicki Chen Thomas Bennett
    • Hollow Electron Ptychographic Diffractive Imaging Biying Song, Zhiyuan Ding, Christopher S. Allen, Hidetaka Sawada, Fucai Zhang, Xiaoqing Pan, Jamie Warner, Angus I. Kirkland, and Peng Wang Phys. Rev. Lett. 121, 146101 – Published 1 October 2018
    • Kirsty Annanda,⁎, Magnus Norda, Ian MacLarena, Mhairi Gass, The corrosion of Zr(Fe, Cr)2and Zr2Fe secondary phase particles in Zircaloy-4 under 350 °C pressurised water conditions Science Volume 128, November 2017, Pages 213-223
    • Characterisation of amorphous molybdenum silicide (MoSi) superconducting thin films and nanowires Archan Banerjee1, Luke J Baker1, Alastair Doye2, Magnus Nord2, Robert M Heath1, Kleanthis Erotokritou1, David Bosworth3, Zoe H Barber3, Ian MacLaren2 and Robert H Hadfield1


Conference Proceedings

  • Song, Jiamei; Song, Biying; Zou, Liqi; Allen, Christopher; Sawada, Hidetaka; Zhang, Fucai; Pan, Xiaoqing; Kirkland, Angus I; Wang, Peng;,Fast and Low-dose Electron Ptychography,Microscopy and Microanalysis,24,S1,224-225,2018,Cambridge University Press
  • Allen, Christopher S; Song, Jiamei; Danaie, Mohsen; Wang, Peng; Kirkland, Angus I; ,Low Dose Defocused Probe Electron Ptychography Using a Fast Direct Electron Detector,Microscopy and Microanalysis,24,S1,186-187,2018,Cambridge University Press
  • MacLaren, Ian; Nord, Magnus; Conner, Suzanne; McGrouther, Damien; Allen, Christopher S; Danaie, Mohsen; Kirkland, Angus I; Bali, Rantej; Hlawacek, Gregor; Lindner, Jürgen; ,Imaging Structure and Magnetisation in New Ways Using 4D STEM,Microscopy and Microanalysis,24,S1,180-181,2018,Cambridge University Press
  • Nord, M., Ross, A., Hallsteinsen, I., Tybell, T., & MacLaren, I. (2016). Towards Mapping Perovskite Oxide 3-D Structure Using Two-Dimensional Pixelated STEM Detector. Microscopy and Microanalysis, 22(S3), 476-477. doi:10.1017/S1431927616003238
  • Pixelated STEM detectors: opportunities and challenges Ian MacLaren Magnus Nord Andrew Ross Matus Krajnak Martin Hart Alastair Doye Damien McGrouther Rantej Bali Archan Banerjee Robert Hadfield First published: 20 December 2016
  • Nord, M., Krajnak, M., Bali, R., Hlawacek, G., Liersch, V., Fassbender, J., . . . McGrouther, D. (2016). Developing Rapid and Advanced Visualisation of Magnetic Structures Using 2-D Pixelated STEM Detectors. Microscopy and Microanalysis, 22(S3), 530-531. doi:10.1017/S1431927616003500
  • MacLaren, I., Nord, M., Conner, S., McGrouther, D., Allen, C., Danaie, M., . . . Faßbender, J. (2018). Imaging Structure and Magnetisation in New Ways Using 4D STEM. Microscopy and Microanalysis, 24(S1), 180-181. doi:10.1017/S1431927618001393