What is it? How does it work?
The Merlin photon counting detector system with Medipix3 ASIC packs a lot in for its size. With a vast range of applications, Merlin is a high performance X-Ray imaging detector that requires no additional cooling system and, being around the size of a mobile phone, is easily installed into small spaces. The system is supplied with a LabView GUI to get you up and running quickly while TANGO and EPICS drivers have been written to allow you to integrate it into your system.
Key Features & Benefits
- Photon Counting Eliminating Dark Noise
- Zero Dead Time Between Franmes
- Spectroscopic Imaging
- No External Cooling System
- Compact Size
- 55 μm
- 1200 Frames Per Second
- 1 μs Exposure Time
- 5 – 17 keV Range
- 12 and 24 Bit Counter Modes
The video shows a Quad Merlin (512 x 512 pixels, 28.2 x 28.2mm) recording a rotating chopper at a frame rate of 1KHz with no deadtime
Merlin is capable of taking 1200 frames per second in burst mode and 100 frames per second in continuous mode. Allocated to each of its 55µm pixels are 2 x 12 bit counters which allows continuous read/write with no dead time between frames. With 2 threshold levels per pixel, up to 8 thresholds can be set by creating a super-pixel (combining 4 pixels together). Stepping through the resulting threshold images allows easy interpretation of the intensity of X-Ray absorption at user defined energy levels. Merlin is available with either a Single medipix3 chip (256×256) or Quad (512×512) system and has excellent sensitivity in the 5-17 KeV range. The detector is already installed on 5 beamlines at Diamond Light Source and has had successful trials at other synchrotrons.
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.
Up to 24-bit counting depth enabling 1:16.7 million intensity range in a single image, ideal for recording diffraction patterns.
Communication between pixels designed to mitigate charge sharing effects for maximising both DQE and MTF.
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.
- Coherent X-ray Diffraction
- Bunch Synchronised Experiments
- Surface Diffraction
- Phase Contrast Imaging
- Pump and probe experiments
- Powder diffraction
- Multi energy imaging
- High speed real time imaging
- Scanning Transmission Electron Microscope
The Merlin readout electronics are based on a National Instruments PXI FPGA system with some additional custom control electronics. This is a robust, extensible and well supported platform with a long product lifetime. It integrates an embedded high performance industrial grade PC and FPGA card with 512GB dedicated RAM. The detector head is connected by a high density cable link that can be up to 10m long allowing a significant degree of flexibility in the mounting of the system.
As the Merlin contains an integrated PC, it requires no external input other than mains power to run. In addition to its own intuitive graphical interface, the system also implements a TCP/IP based remote control function that allows easy integration with a users control systems.
Medipix3 was developed by an international consortium including CERN, DESY, ESRF and Diamond and provides a range of features that are unavailable in other hybrid pixel detectors, including continuous read-write, colour mode, 12 or 24 bit mode selection and all in 55µm pixels. See the datasheet below or the paper for more details.
Figure. Reconstructed phase image using the Medipix3 detector MerlinX at Brookhaven National Laboratory’s NSLS-II. of a Au nanoparticle array. Particle size is 50 nm and field of view 1 x 1 um^2.
Brookhaven National Laboratory NSLS-II
A research group lead by Hanfei Yan at Brookhaven National Laboratory’s National Synchrotron Light Source II have achieved spatial resolutions approaching 10 nm implementing the Medipix3 detector MerlinX for ptychography with multimodal scanning hard x-ray imaging. The multimodal imaging is realised by utilising simultaneously absorption-, phase-, and fluorescence-contrast mechanisms.
Their work is an important milestone in hard x-ray scanning microscopy, effectively eliminating the gap between demonstration of optical resolution under ideal experimental conditions and actual imaging resolution for routine scientific measurements.
A 512×512 MerlinX Medipix3 detector with a 55 micrometer pixel size was placed 0.5 metres downstream of the target and used to capture the absorption and phase images. At the same time a Vortex three-element silicon drift detector was used to capture the fluorescence image. By simultaneously utilising absorption-, phase- and fluorescence contrast mechanisms sufficient resolution was acquired to investigate an ionic-electronic conducting ceramic-based membrane material employed in solid oxide fuel cells, as well as membrane separations, revealing the existence of an emergent material phase and quantified the chemical complexity at the nanoscale.
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.
- 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 a , 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
- 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
- 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