1676 IEEE TRANSACTIONS ON NUCLEAR SCIENCE, VOL. 53, NO. 3, JUNE 2006

3DX: An X-Ray Pixel Array DetectorWith Active Edges

Sherwood I. Parker, Christopher J. Kenney, Dario Gnani, Albert C. Thompson, Emanuele Mandelli,Gerrit Meddeler, Jasmine Hasi, John Morse, and Edwin M. Westbrook

Abstract—We are developing a prototype X-ray detectionsystem that should be ideal for many types of synchrotronscience. X-rays are captured directly in thick, high-resistivity,single-crystal, silicon pixel sensors. Unlike other X-ray detectors,which have a substantial dead area around their borders, thesehave “active edges”—edges formed from electrodes in the thirddimension, perpendicular to the top and bottom surfaces, withfull sensitivity to within a micron of the physical border. Eachsensor is 0.96 mm 0.96 mm, having a 64 64 two-dimensionalarray of 150 m pixels. Behind each sensor, a custom CMOSreadout chip is bump-bonded to the sensor. It provides high-speed(64 s/full-array) readout of each pixel, with a dead time for eachrow, during pixel reset, of 1 s. On three edges, it lies completelyhidden behind the sensor. A 3 mm wide region on the remainingedge of each CMOS chip contains readout circuits and connec-tions. Here it protrudes beyond the sensor edge, but is covered bythe active region of a neighboring sensor module in an array sim-ilar to that of shingles on a roof. Sensor units can be easily arrayedto cover large areas. The readout chip has 128 ADCs and, for eachpixel, a charge amplifier. To save fabrication costs, the prototypereadout has just 8 64 pixels. Using pulse heights, we shouldbe able to combine signals when X-rays share charge betweenadjacent pixels. We have already made accurate quantum-countsof 0 to 7 X-ray events/pixel during each 64 s readout cycle.

Index Terms—Active edges, detectors, guard rings, insensitiveedge regions, protein crystallography, semiconductor sensors, sil-icon sensors, structural molecular biology, three-dimensional (3D)electrodes, 3D sensors, X-ray detectors.

I. INTRODUCTION

X-RAY crystallography is a critical technique for under-standing the structures of biological macromolecules such

as proteins and nucleic acids. The human genome project has

Manuscript received May 26, 2005; revised March 9, 2006. This work wassupported in part by the U.S. National Institutes of Health, Center for ResearchResources, under Grant R01 RR16230, in part by the U.S. Department of Energyunder Grant DEFG0204ER41291, in part by the Director, Office of Science,Office of Basic Energy Sciences, U.S. Department of Energy, under ContractDE-AC02-05CH11231, and in part by the U.K. Particle Physics and AstronomyResearch Council.

S. I. Parker is with the University of Hawaii, Honolulu, HI 96822 USA(e-mail: sher@slac.stanford.edu).

C. J. Kenney, A. C. Thompson, and E. M. Westbrook are with the MolecularBiology Consortium, Chicago, IL 60612 USA.

D. Gnani was with the Molecular Biology Consortium, Chicago, IL 60612USA. He is now with the Lawrence Berkeley Laboratory, Berkeley, CA 94720USA.

E. Mandelli and G. Meddeler were with the Lawrence Berkeley Laboratory,Berkeley, CA 94720 USA. They are now with AltaSens, Thousand Oaks, CA91360 USA.

J. Hasi is with Brunel University, Uxbridge, Middlesex UB8 3PH, U.K.J. Morse was with the Molecular Biology Consortium, Chicago, IL 60612

USA. He is now with the European Synchrotron Radiation Facility, 38043Grenoble, CEDEX 9, France.

Digital Object Identifier 10.1109/TNS.2006.873713

given us the sequence of nucleotides, but not the three-dimen-sional shapes of the resultant proteins which are necessary foran understanding of their biological activity. They are far toosmall to be seen in an optical microscope, have too much in-ternal detail for scanning tunneling microscopes, and are toodelicate for the vacuum and electrical conditions of an electronmicroscope. Although NMR spectroscopy can determine struc-tures of small proteins, it is not as cost-effective, nor as general,as single-crystal X-ray diffraction.

Protein molecular structure is best determined by the well-developed discipline of crystallography [1], [2]. For this work,X-ray wavelengths must be comparable to the inter-atomic dis-tances in the protein, about 0.1 nm, corresponding to X-rayenergies of about 12 keV. The most intense monochromatic,well-collimated X-ray beams available today for this purposeare provided by electron storage rings equipped with special-ized X-ray optical equipment. There are six in use today withinthe United States, and dozens more world wide. About 30 ex-perimental stations at these USA facilities have been built thatconduct protein crystallographic studies, and another 100 areactive overseas.

At these energies, X-rays have small interaction probabilitieswith matter. For example, 12 keV photons have an absorptionlength in water of about 2 mm, i.e., several million times thetypical separation distances of neighboring molecules. The co-herent scattering probability is less than 5% of that total crosssection (which comes mostly from the photoelectric ejection ofan electron). So, to get enough counts in the experiment, manymolecules must be used. To keep their scattering patterns co-herent, they must be aligned in a crystalline form. Each X-raystructure factor gives information from a different view of themolecule, and represents the Fourier transform of the structure,from that vantage point. To define the structure of a protein, it isnecessary to record the amplitudes of many thousands of struc-ture factors. Typically, the measurements of structure factor am-plitudes must be accurate to a few percent to determine the struc-ture of a large protein.

Since 1990, many technical developments—3rd generationelectron storage rings, modern X-ray optics, improved crystal-lization techniques, molecular biological methods to make andpurify experimental samples, cold-temperature preservation ofprotein crystals—have brought about a revolution in structuralbiology. Today we can solve the crystal structure of a proteinwith single crystals that may be less than 50 m on each side,and it can be solved in an afternoon.

The development of large area CCD X-ray detectors in the1990s [3] was also one of the critical steps in bringing aboutthe structural biology revolution. However, today synchrotron

0018-9499/$20.00 © 2006 IEEE

PARKER et al.: 3DX: AN X-RAY PIXEL ARRAY DETECTOR 1677

sources and their associated beam lines are capable of deliv-ering many more photons than CCD detectors can handle. Inparticular, experiments that are aimed at studying biologicalfunction with a time series of crystallography images are seri-ously limited by the readout speed and dynamic range of currentdetectors.

Active pixel arrays can overcome the present limitations ofCCD sensor systems in crystallographic detectors. In an activepixel array detector, each pixel is read out individually, ratherthan in series, as is the manner of CCDs [4]. Consequently,pixel array detectors can handle all the flux available at asynchrotron beam line, yet count each photon as an individualevent. Pixel array detectors can be very efficient (exceeding80%) at capturing X-ray photons, and their efficiency will notdeteriorate for weak Bragg diffraction spots, as is the casefor CCD detectors. Because they are counting detectors, tothe extent they count accurately, pixel arrays do not exhibitnoise. Because they are fast, pixel arrays will permit crystaldiffraction images to be acquired frequently as the crystalsample rotates, thus providing very accurate angular resolutionof the three-dimensional diffraction pattern. We are currentlydeveloping a prototype pixel array detector system for proteincrystallography. So far, its performance characteristics are verypromising. Once we build a full-sized array detector with oursystem, we expect its outstanding performance will dramati-cally improve crystallographic data measurements.

II. SCATTERING FROM CRYSTALS

Proteins can crystallize in many, although not all possible,forms of crystals. The physics of protein crystal diffraction iscovered in standard books on crystallography and protein crys-tallography [1], [2]. The Fourier analysis of Bragg diffractionfrom crystals plays a crucial role in the determination of proteinstructure. Coherent scattering from a crystal plane occurs whenthe incident and reflected angles are equal. For specific anglesthat also produce coherence between adjacent planes, Bragg re-flections are generated. The intensity of the individual spots willdepend, in addition, on the detailed structure of the crystallizedmolecules. The central experimental process in protein crystal-lography is to measure those spot intensities as accurately aspossible [2].

Unlike small-molecule crystals, macromolecular crystalsamples also produce non-Bragg scattering, since only abouthalf of the sample mass of a biological macromolecular crystalobeys crystal symmetry; the remainder is water or vitreousice. Scatter noise can be reduced relative to Bragg signals bymoving the detector back. Scatter noise decreases as ,while Bragg diffraction intensities, decreasing mainly fromcrystal imperfections and the angular spread of the incomingbeam, do not decrease so rapidly. This is one reason to makedetectors larger.

Once grown, protein crystals are frozen to reduce chemicaldamage from free radicals and other chemical by-productsgenerated by X-ray interaction with the experimental sample.Nevertheless, frozen crystal samples do deteriorate in the with-ering X-ray field used at modern synchrotron sources lastingfor about X-rays (about 100 seconds) over a typical area of0.1 mm 0.1mm. It is necessary, in order to solve a structure,

to record complete three-dimensional diffraction data from acrystal sample at 3–4 X-ray energies, thus increasing by 3–4fold, the radiation damage of the sample. Modern softwaredevelopment is underway to solve structures with data fromonly one or two energies, in order to minimize X-ray exposureto the experimental sample crystals. Equally important, areon-going efforts to improve detector efficiency, sensitivity, andspeed.

Since the position of the incoming beam is fixed, the crystalmust be rotated during data taking, to stimulate the diffractionof all possible Bragg spots. Crystal symmetry and the crystalorientation with respect to the X-ray beam, define the total an-gular range that must be acquired to record all Bragg spots. Typ-ically, a crystal must be rotated 90 or 180 to record a fulldata set. Data are organized as two-dimensional files, each rep-resenting a rotation width, typically, of 1.0 . With the near-con-tinuous readout of the proposed detector and with a full readoutevery 64 s, we anticipate that these new detectors will permitdata collection with much finer angular resolution, 0.01 –0.10 .This will significantly increase both the quality of data, and theefficiency with which data are collected from macromolecularcrystals.

III. PRESENT X-RAY DETECTION SYSTEMS

In the most advanced detector systems today, X-ray photonsare converted to visible light in a phosphor film. The light istransmitted by arrays of tapered fiber optics to a set of CCDs,one for each taper. Each CCD converts light to an electroniccharge that is subsequently digitized. Compared with earliersystems, CCD detectors are fast, with an inactive time duringread out of as little as 1 second [5]. Their efficiency can exceed50%, but efficiency decreases at low signal strength, since theyare analog systems and exhibit noise.

The dynamic range of CCDs is limited by the electronic ca-pacity of its pixels and their response is not perfectly linear,since the work required to store additional electrons increasesas the number already stored increases. Typically, for commer-cially available scientific grade CCDs, the signal response de-viates significantly (greater than 1%) from linear when a pixelis about 80% saturated, somewhere between 200 000–400 000electrons, while the readout noise is typically 9–10 electrons. Itis standard to sample this response range with a 16-bit analog-to-digital conversion (65 535 digital units), a bit more than thetrue dynamic range of about 300 000/30 or 13–14 bits, assumingthe smallest signal must be several times the noise. The signallevel from each X-ray photon is intentionally kept small (3–10electrons/X-ray photon), so that each pixel can record thousandsof photons within the limited pixel storage capacity.

Noise in CCD detector systems comes both from leakagecurrent and from readout noise. Readout noise can be reducedby slowing the readout speed, but the readout time is alreadya significant part of the total time of an experimental mea-surement. Current CCD design permits readout noise to re-main low (5–10 /pixel) up to 1 MHz readout speed, so 1second readout is possible with modern CCD detectors. But ata 3rd generation synchrotron, a good image can be had from awell-diffracting crystal in substantially less than one second. Inaddition, time-resolved studies could use much faster imaging.

1678 IEEE TRANSACTIONS ON NUCLEAR SCIENCE, VOL. 53, NO. 3, JUNE 2006

Muscle diffraction studies as the muscle is electrically stim-ulated to contract could use sub-millisecond time slicing, ascould the observation of small-angle scattering changes duringprotein aggregation or enzyme catalysis, in solution. This fasttime resolution will also permit the recording of diffractionpatterns with very fine angular resolution as the crystal samplerotates, continuously.

Noise associated with leakage current has been reduced byadopting MPP (multi-pinned phased) mode and by cooling theCCD [4]. But MPP mode reduces the well depth, while ex-cessive cooling leads to its own engineering problems, suchas water condensation. These well depth and low-noise limitscombine to limit the achievable dynamic range of any CCDinstrument.

Large CCD array systems are very expensive, because thecomponents needed to make big arrays are inherently expensive.Money alone limits the size of CCD arrays which beam lines (sofar) have been willing to buy.

Modular CCD systems exhibit gaps between imaging seg-ments. It is usually prudent to throw away Bragg spots strad-dling these gaps, resulting in 1–2% rejection rates.

Detectors that image a phosphor film, exhibit a point responsethat has wide tails, extending out over many pixels. These tailsare caused by light scatter in the phosphor itself, in the fiberoptic tapers, and at the junction between taper and CCD. Widepoint responses limit our ability to resolve neighboring Braggspots, and therefore limit the density of information that can begathered by a CCD detector.

IV. DETECTORS BASED ON DIRECT CONVERSION IN SILICON

Direct photoelectric conversion of X-rays to charge in a pho-toconductor addresses many of the problems of CCD detectorsystems. The signals are quite large. In silicon, photoelectricconversion produces one electron-hole pair on average for every3.62 eV of X-ray energy—about 3 500 e- for each 12.66 keVX-ray photon. This helps to produce a large signal/noise ratio.High-purity single crystal silicon is a commodity manufacturedcheaply in large quantities, and the electronic chips required forthe readout of the sensors once designed and debugged, are rel-atively inexpensive. Some CCD problems, such as Cerenkovlight in the light pipes from radioactivity, do not exist for silicon,and some that do such as cosmic rays, can be distinguished dueto the small sensitive pixel volumes and sensitive times. Manyothers can be designed away. For example, the detector sys-tems can be very fast, since the time required to sample a pixel,with modern, low noise, electronic circuits, is about 1 s, andthe readout of a silicon pixel array can be highly-parallel. Thepoint response of these detectors should be confined entirelyto within one pixel, except for X-rays landing close to pixelboundaries. Sharp point response not only will give these detec-tors significantly better resolving power than CCD systems, butits ability—described in Section 9—to count individual X-rayquanta, will allow for easier calibration and better linearity.

X-ray Capture in Silicon: Silicon ( g/cm )is highly effective as an absorber of X-rays in the energy range(3.5–20 keV) most useful for macromolecular crystal diffrac-tion. At the low X-ray energies used for crystallography, ra-diation is absorbed predominantly by photoelectric capture in

bulk silicon. At 12.66 keV (the absorption edge of selenium), a0.3 mm silicon wafer absorbs 68% of normally incident radia-tion, a 0.5 mm wafer absorbs 87%, and a 1.0 mm wafer absorbs98%. (Compton scattering produces only a small background,and electron / positron pair production does not occur.)

Silicon Pixel Array Detector Architecture: Silicon PINdiodes have been widely used as radiation sensors, partic-ularly since planar technology, invented by Jean A. Hoerniof Fairchild Semiconductor in 1958 [6], [7], was applied tosensor fabrication two years later [8]–[11]. The developmentof high-channel count, custom VLSI readout chips [12] mademicro-strip and small pixel systems practical for large area sys-tems. With this technology, all fabricated elements are locatedon or very close to the wafer surfaces, and oxide passivationlayers tie up otherwise loosely bound surface charges.

Development of silicon sensors for the detection of these scat-tered X-rays has started. Three projects are described below.

V. STRUCTURAL BIOLOGY PIXEL ARRAY PROJECTS

CURRENTLY IN PROGRESS

One example of a planar-architecture detector is thePrinceton/Cornell pixel array detector system [13]–[15]. Itis an interesting approach to a specific application, designed forhigh-speed time-resolved studies. It is not a general solution tostandard crystallographic diffraction measurement.

LAD1, underway in Britain at Rutherford Appleton Labs [16],is a modular system of planar-architecture, 0.5 mm thick, sil-icon sensor arrays. Each module is 9.6 mm 67.2 mm (array of64 448 pixels, each 150 m 150 m square) and has a deadregion about its edge between 300 and 600 m wide. Althoughevery effort is made to minimize dead areas in the imaging regionby overlapping the modules, this detector does have dead stripesapproximately 0.5 mm wide, repeating each cm. Data accumu-lation ceases during the 384 s readout of the array, so there isalso a dead time, similar to that of a CCD detector.

Another active project in progress is PILATUS, being devel-oped at the Swiss Light Source [17]–[19]. This project has fab-ricated a 24.3 cm 21.0 cm active area detector of 1 120 967pixels. As in the LAD1 system, PILATUS has a periodic arrayof dead stripes, and a readout dead time similar to that of LAD1.Approximately 15% of the PILATUS surface area is inactive.

A third planar-architecture detector project is the Medipix2VLSI readout chip, which was developed by a consortium, cen-tered at CERN, of European Universities and Research Insti-tutes. The chips can be attached to a variety of semiconductorsensors, and they read pulses from the direct detection of in-dividual photons [20]. It is a general approach for reading outplanar-architecture sensor arrays. It also is designed to be mod-ular, and shares many of the features of the LAD1 and PILATUSapproaches.

A basic problem with all of these planar systems is their pat-tern of periodic dead stripes. No matter how narrow the deadstripe may be, the area in which Bragg spots are lost will bealmost 2 mm wider than the stripe, because at least 1 mm ofsurface area must be free of blemishes to process each Braggspot. Perhaps careful attention to 3D profile fitting [21] may sal-vage some Bragg spots at the edges, but there are dangers to thisapproach.

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Fig. 1. Schematic cross-section view of a standard sensor edge, showing some reasons for the insensitive region there: (a) space may be needed for guard andvoltage-dropping rings, (b) the saw-cut edges are conducting, and (c) often contain chips or small cracks, all of which must remain clear of (d), the bulge of theedge of the electric field in the depleted region.

VI. 3DX SENSORS

3DX technology addresses several basic problems, both ofCCDs and of planar-architecture detector systems, includingdead spaces, dead times, and charge-sharing [22]–[30] (whichwill be covered in Section 10.).

The sensors for this project use the same surface oxide passi-vation of planar technology, but in addition they feature activeedges [23], [26], [31]. 3DX sensor edges are implanted, oxi-dized and etched, rather than being sawed with no special treat-ment, as has been standard up to now.

Insensitive Edges: Conventional planar sensors have an in-sensitive region about their edges, for at least three reasons:

• The sensors are fabricated on uncut, large silicon wafers,and then cut into individual units. The saw cuts that definetheir edges are conducting because they contain danglingsilicon bonds, and so must be kept away from the collectionvolume of the signal charges. Manufacturers must keep asafety margin between these edges and the boundary of thesensor active area to avoid shorting out its electric field.This field can extend out from the edge electrodes towardsthe edges, to distances about equal to the chip thickness.

• There are often chipped and cracked regions along the sawcuts, further increasing the needed margin.

• Guard rings must be fabricated to surround the active re-gion, to prevent surface leakage current from reaching thesignal electrodes, and to drop the front-to-back voltage dif-ference in a controlled fashion. Thicker sensors have higherdepletion voltages, and normally require wider guard ringstructures.

Given the short ionization tracks produced by X-rays, insen-sitive regions facing the X-ray beam reduce the fill factor of thedetector. Since ALL edges of conventional planar sensors areinsensitive, it is impossible to tile or shingle these sensors inany way that eliminates these non-imaging regions.

Fig. 1 illustrates this problem. Fig. 2 of [26] shows a pho-tograph of cracks on a sawed edge. An insensitive region ofthat size may be adequate for some applications, but accuraterecording of Bragg diffraction patterns is not one of them.

Active edge sensors are made using fabrication steps thatallow regions with collection fields to extend to within a micronof the physical edge [31], and so allow large area sensors to beformed from smaller, shingle subunits with no significant lossof information from near-border X-rays that are not detected.Fig. 2 gives a schematic view of their fabrication. The fabrica-tion steps are outlined in somewhat more detail in [31].

Fig. 2. Corners of two active edge sensors during their fabrication. (a) Sensorsafter oxide-bonding to support wafer, fabrication of p signal electrodes, etchingof active edge trenches, doping and oxidizing of trench faces, and filling withpolycrystalline silicon, (b) after dicing etch, which goes to the oxide etch-stops.

Fig. 3. Schematic diagram of an X-ray sensor.

Fig. 3 shows a schematic diagram of the fabricated sensor.The diode junction is on the large-area entrance and side sur-faces. The ohmic contacts are under each output contact. Thisreduces the bias voltage needed to deplete the far corners, andreduces the peak fields at the small pixel contacts since the geo-metric field intensification there is not combined with the highfields associated with the diode junction. Experimental results,including near-edge sensitivity, are described in [31].

1680 IEEE TRANSACTIONS ON NUCLEAR SCIENCE, VOL. 53, NO. 3, JUNE 2006

Small Module Size is a Virtue: Since our detector moduleshave active edges, each module can be made small, yet large sur-face areas can be covered by arranging the modules in a shinglearray. Making a given size device from small units may increaseassembly costs somewhat, but smaller devices can be made witha higher yield of good units, because the probability of a defectoccurring per unit area increases with size. Consider a modelsystem, with bump-bonded electrodes in 150 m square raster.A 1 cm 1 cm square array has bonds, a2 cm 2 cm square array has 16 384 bonds, and a 3 cm 3 cmsquare array has 36 864 bonds. If there is a 99.99% chance thateach bond is good, then the probability that the 1 cm deviceis perfect would be 66%, whereas only 19% of the 2-cm chipsand only 2.5% of the 3 cm chips will be perfect. The numberswill differ for systematic flaws, but their probability generallyincreases with size. If chips without imperfections are required,it is clearly much better to build a detector with smaller subunits.Similar considerations will apply to other stages of the assemblyprocess.

It requires about 2 kg of force to bond our current 3DXmodule, which has 512 bonds (8 64) so it will take about16 kg to press together the complete 64 64 module. Onceagain, small size is an advantage in this process. Another re-quirement for bonding is device flatness. Our indium bumps areonly about 5 m high, and they are compressed substantiallyduring bonding. The bigger the chip, the more likely it is to beslightly warped or bent. Even a 5 m warp will significantlydecrease bonding success rates. About 70% of our 64 64pixel sandwiches are free of any defect—consistent with theabove model failure frequency of about 0.01% for bump bonds.

In addition to these two considerations, others lead one to theuse of small sizes:

1 Readout chips are currently limited to about 2 cm 2 cmby the precision optics and masks used to expose the pho-toresist in mask aligners.

2 If the assembled units are not too large, there is little in-vested in each one, so little is lost by rejecting a bad one.But if they are big, one defect—that is much more likelyto occur in big units—ruins a large (and more expensive)device.

3 A larger fraction of the circular wafer can be used if the(normally rectangular) sensors are small.

4 Using small modules allows the designer to adjust eachmodule orientation to be more perpendicular to diffractedX-rays from the experimental sample, thus reducingparallax.

5 While small modules require small readout units, this is nota disadvantage since a large image can be read out morerapidly using simultaneous parallel readout of all chips.

VII. DESIGN OF THE PIXEL READOUT CHIP

We are developing a custom integrated circuit, designed andfabricated with 0.25 m technology, as our readout chip. It hasa 64 64 pixel raster. It cyclically reads out our sensor every64 s. Electronic noise in the first-stage amplifier is the domi-nant source of signal uncertainty. Thus, within the linear rangeof the electronics, the signal to noise ratio for n X-rays improves

Fig. 4. Use of metal conductors of varying length to join electrodes and bumppads (on a different pitch) to readout chip.

by a factor of n. Fano fluctuations (which come from statis-tical variation in the division of deposited energy in the sensorbetween ionization and excitation) [32], [33] do increase withn, but are much smaller than electronic noise. Distinguishing nX-rays from is no more difficult than 1 from 0 so long asthe amplifier is not saturated. We have demonstrated already thatwe can distinguish up to seven 12 keV X-ray photons strikingeach pixel during each cycle. For a chip running with a 64 scycle time, this would correspond to an instantaneous countingrate of over 100 000/s. Further increases in this rate, as elec-tronics improves, could come from a number of sources, for ex-ample, reduced noise in this chip, allowing for a reduced gain,which in turn allows for more photon hits before the amplifiersaturates, and/or from smaller pixels.

In addition to high counting rates, implementing fast cyclicreadout of our detector can also provide benefits such as men-tioned in Section III.

The readout ASIC incorporates these features:• A low-noise integrating amplifier, with calibration, adjust-

ment, control, reset, and readout electronics, all designedto fit into a small space within each pixel. It is also designedto consume a minimum of power.

• To keep the readout chip completely behind the sensor, itspixel raster is 144 m, smaller than the 150 m raster ofthe sensor. Aluminum traces, of lengths that increase fromthe center of the module to its edge, connect each sensorpixel output pad to its readout circuit. Fig. 4 (left) showsa mask layout and Fig. 4 (right), a photograph of part of asensor with such a changing offset.

• The digital signals must pass close to, under, and over ac-tive analog lines, but they do not disturb the much smalleranalog voltages on them.

• The analog voltages are digitized at a very high rate, toavoid complex analysis of analog signals that have contri-butions from partial X-ray signals, leakage currents, andamplifier noise. Signal analysis and processing is digitalwherever possible.

• Digital signal analysis includes corrections for base line(pedestal) shifts, subtraction of leakage charges, suppres-sion of zero signals, and combination of signals from singleX-ray hits that spread to adjacent pixels.

Many of the digital blocks used in the design of the 3DXreadout chip have been adapted from chips previously designedat the Lawrence Berkeley National Laboratory. However,enough is new, particularly in the analog sections, that severaltest fabrication runs have been needed to find and eliminatedesign and fabrication errors. We are using MOSIS, a uni-versity run, shared-wafer service, to reduce the costs of these

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Fig. 5 Preliminarytest readout chip.

prototyping fabrication test runs. Another cost-minimizingtactic we have been using is to fabricate test chips with only 8rows, but with all 64 columns of pixels. One column containsall 64 pixels (folded 90 to lie parallel to the rows), to allow usto test most features of a full-sized chip. Fig. 5 is a photographof this device. Since this design will only be used for a limitedtime, we will now describe the planned final 64 64-pixelchip. Fig. 6 is a schematic diagram of the planned chip. Thechip uses closed-geometry, radiation-hard, 0.25 m electronicswith 2.5 V digital and analog supplies. The first stage amplifierintegrates the calibration or input signals on capacitor C1 whenthe switch S1 is open.

When S1 and S2 are closed (conducting) the capacitors C1and C3 are reset. S2 remains closed while S1 is opened. Thevalue of the noise voltage (KTC noise) due to the channelresistance of S1 at turn-off remains impressed on C1, butsince S2 is still closed, the input of the second amplifier actsas a virtual ground, and a canceling charge is placed on thecoupling capacitor C2. S2 is then opened and the cell is ready tointegrate. (The noise of S2 is not canceled, but is less importantsince the signal, at that stage, has been amplified.) The secondstage has a differential input, and a pedestal voltage can besubtracted using the DAC generating the input. Valuesfor this subtraction were loaded in to a set of registers setduring the calibration process.

All digital signals are differential, providing further protec-tion to analog signals. The analog buses to the line receivers areshielded by metal layers above and below and by connectingmetal vias on either side. Five bits, stored in registers in eachpixel, control the DAC to set Vped. Three additional lines canadjust the stage-1 gain (S-amp adds C1’ in parallel with C1),provide a test pulse (S-cal), and can turn off the pixel (S-off).There are 128 line receivers, ADCs, and RAM sets, so two rowsare read out together.

The output signal is stored on , and is preserved duringthe pixel reset by the opening of S3. When S4 is closed, thecharge, q, is transferred to , the feedback capacitor of theline receiver. The effective input capacitance is

pF (where A is the line receiver open loop gain), typicallyabout 200 times the capacitance of the bus . Given thislarge ratio, the output voltage, appears almost entirelyat the output, with almost no shift of the bus voltage. Thelow input impedance provides yet another form of protection

from the coupling of digital signals through the small (and sohigh-impedance) parasitic capacitors where digital signal linescross. One DAC generates a reference voltage to set the DClevel of the bus, and another adjusts the line receiver open-loopgain.

The 66 MHz clock, the counter, Cped, its bus, and the rampgenerator, are common to all channels. An initial voltage step,opposite to the ramp in direction, will ensure that the rampvoltage crosses all line-receiver output voltages. A readout con-troller starts the clock and the ramp to the Wilkinson ADCs,which will latch the counter value in a RAM location when themagnitude of ramp voltage exceeds its line receiver output. Thelatch injects a fixed step through Clatch ( fF) to a sum-ming bus and then into Cped ( pF). When the voltage onCped exceeds Vth, the reset is turned off, and the counter startscounting. This will normally be near the start of the ramp, whenthe ramp exceeds the levels on the many non-hit pixels, and all ofthem place their steps on Cped. However, environmental noise(pickup) is often found that shifts all values of the row, changingthem together, with each readout cycle. The amplitude of thesefluctuations is often large enough to interfere with the zero sup-pression readout. For the relatively low counting rates expectedhere, with most of the channels not having X-ray hits, and withan appropriate setting of Vth, this pedestal shift delays the latchoutput to Clatch from all of these channels, and correspondinglydelays the start of the ADC counter, preventing the shift fromchanging the ADC values.

The two rows to be read out are automatically selected by a5-bit row-select bus (not included in Fig. 6). At time zero for anyrow readout, the signals from two rows are isolated on the Cmemcapacitors in each pixel with the opening of the S3 switches, andplaced on the capacitors Cr with the closing of S4. By 0.5 s,the clock and ADC ramp have started. The pixel reset (using S1and S2) is complete and signal integration is resumed by 1 s.By 2 s:

• digitization is complete;• the results have been transferred to either the output bus

RAM-a or RAM-b;• the S5 and S6 switches, controlled by a common signal,

have reset the line receivers (in about 500 ns);• the V-ref. comp. voltage has reset the ramp bus;• the summing bus has been reset;• and readout of the next two rows starts.Readout of the set of RAMs for the preceding two rows goes

on simultaneously, so each row collects data for 63 of every 64s, and the entire pixel array is read out every 64 s.

VIII. READ NOISE AND HEAT

The pixel amplifier, with electronic noise equivalent to thesignal from a 1.5 keV X-ray photon, dissipates about 0.2 mWper analog channel plus a fixed 200 mW for the digital bottom(digital power does not scale with the number of channels). Ex-trapolation to 64 64 and adding other functions, gives between1 and 2 watts per module. The circuit boards will be mountedon copper bars in thermal contact with vertical support bars con-taining flowing water. The modules will be in air so we can usefans to remove some heat.

1682 IEEE TRANSACTIONS ON NUCLEAR SCIENCE, VOL. 53, NO. 3, JUNE 2006

Fig. 6. Block diagram of VLSI readout circuit. Capacitor values (fF): C1 = 37;C1 = 25; C2 = 75;C3 = 25;C�mem = 900; C�receiver =

450;C� cal = 16;C� latch � 10;C�ped � 1000;C�column bus�3000.

IX. COUNTING INDIVIDUAL X-RAY PHOTONS

IN THE COMPUTER

The stored pixel charge sum can be converted (in software)into an X-ray quantum count for each Bragg spot, because:

• Only mono-energetic X-rays are used.• The readout is rapid enough, that only a few X-ray photons

hit the busiest pixels between readout cycles. Indeed, by farthe most common X-ray count during a 64 s time intervalwill be zero. It is a feature of protein crystal diffraction,that truly bright spots are very rare.

• The detector has sufficient energy resolution to clearly dis-tinguish X-ray pulses from noise.

• The energy resolution is also sufficient to distinguish be-tween the charge signal from n and X-ray photons,where n is the maximum number expected in any spotduring a readout cycle. The fluctuations from Fano factoreffects are small compared with electronic noise, and elec-tronic noise does not increase with n.

• Normally, data will consist of a few localized intense spots,against a background of pixels most of which will not be

hit by any X-ray photon. With our 150 m pixel raster,it will be rare that an X-ray photon, striking at or near apixel boundary, will generate charge shared by neighboringpixels. When it does occur, post-processing these eventswill be accomplished by recognizing that partial signals oc-cupy neighboring pixels, and combining them as one event.

128 parallel ADCs digitize the charge signals in all pixels ofeach sensor and output the counts. Calibration data is used tocorrect the values, and the data is stored in buffers. When in-formation from adjacent pixels is available, signals that havespread across borders can be recombined, and a quantum countfound. Detector areas with average total counts (20 000 X-raysper mm ), with an exposure time of 1 second, will have an av-erage pixel count per readout cycle (64 s) of 0.0288 X-raycounts. Thus, most of the time, the software has only to distin-guish between 0 and 1. The busiest pixel in a bright Bragg spotwill see about X-rays per second, about 6.4 counts per 64

s readout cycle on average.Fig. 10, later in this paper, will show clear separations be-

tween 5, 6, and 7 X-ray counts in a single pixel. This separation

PARKER et al.: 3DX: AN X-RAY PIXEL ARRAY DETECTOR 1683

will decrease above 8 or 9 hits, when the pixel output starts tosaturate. Even at , and with the current electronics, between80% and 90% of the readout events will not be saturated. Sinceall counts are sent to the computer or a front-end gate-array, areasonably accurate count still can be found in this case by fit-ting a Poisson distribution to the below-saturation part of thedistribution together with the fraction of events with saturatedpulse heights. Thus accuracy will decrease only gradually, ratherthan dropping abruptly at some limiting rate.

It is possible for charge to be incompletely recorded at thestart or end of the data collection period. Collection times willdepend on the conversion point and the pixel voltage, but shouldbe about 25 ns. The fraction of events with such partial signalswill be about 25 ns at the start of integration plus 25 ns foldedinto the 400 ns rise time of the amplifier at the end. This fractionis about of one percent, and could be further reduced, if itwere ever necessary, by adding a fast input-cutoff gate to thereadout pixel.

Another possible source of error could be incomplete chargecollection. In silicon, however, typical capture times are morethan 10 000 times as long as the collection times. The 3D activeedges have built in collection fields, and the interior planar elec-trodes should have insensitive volumes that are less than 0.1%of the total sensitive pixel volume. Thus, this too appears to rep-resent a highly unlikely source of error.

X. COMPARISON WITH ARRAYS HAVING COMPARATORS

AND COUNTERS IN EACH PIXEL

Other groups around the world, who are trying to developsilicon pixel technology for structural biology, place a fixed-threshold comparator and counter in each pixel. Why don’t wefollow this paradigm?

First, measuring the amount of charge deposited in each pixelduring a given time (frame), allows corrections of the detectordata for synchronous baseline fluctuations.

A more serious problem, for which we see no easy solution,is the systematic errors that come from missed counts or doublecounts at the pixel borders and corners. As ionization chargedrifts towards the collection electrodes, it will diffuse manymicrons laterally [34], [35]. (In a typical field, the Gaussianlateral diffusion length will be about 12 m for a drift lengthof 300 m [36]). If this event occurs near a pixel border, muchof the charge cloud will diffuse across to the neighboring pixel[30]. The readout chip (and thus every collection electrode) isbehind the sensor, while 12 keV X-rays will most frequentlyconvert close to the sensor front surface. So, this will be acommon problem for the 10%–20% of X-rays that strike withina diffusion-length or two of the pixel borders, for sensors thickenough to detect efficiently such events.

When the charge split between two pixels is approximatelyequal, most discriminator settings will result in either doublecounts or no counts at all. If somehow, the double and missedcounts in one Bragg spot could be made to cancel each other,they will not, in general, do so for other spots that have pro-portionally more or less of their area near the pixel edges andcorners, where charge may be shared with 2–4 pixels. Further-more, the errors depend on the details of the counting efficiencyof each pixel discriminator as a function of pulse height, as well

as on the event-by-event charge distributions, and so cannot becorrected by flood-field calibration. In addition, it is not clearhow one can reliably measure the accuracy of the cancellationfor any specific spot.

This problem can never be truly solved in a discriminator-per-pixel system. For example, Fig. 9 of reference [34] shows gooduniformity on the border between two pixels, but a 15% dip incounting rate at the corners of 4 pixels. Local counting errors ofthe order of several percent will always exist.

XI. MECHANICAL DESIGN

The shingled assembly arrangement shown in Fig. 7 allowsthe entire area facing the experimental sample to be sensitive:there will be no dead areas and the detector will have a 100%fill factor. The support bars under each module will lock into,and position, the modules and will in turn, lock into and be po-sitioned by two sets of alignment blocks. This design has es-sentially cylindrical symmetry, but provides near-perpendicularincidence of the X-rays without the complexity that would re-sult from attempting a spherical arrangement. All support bars,except the center ones, are identical for any radius, and will bemade with a numerically controlled milling machine. They willalso provide cooling to the modules. With the bars standing up-right, Fig. 7(a) is a top view looking down, Fig. 7(b) a front view,looking at the detector from the sample position, and Fig. 7(c)is a side view of one bar and its sensors. Fig. 7(d) is a side viewof the central column divided in two parts to provide a centralhole, if desired. The size of such a central hole can be set by thesize and location of the alignment blocks supporting the cen-tral support bars. The flexible printed circuit is shown only inFig. 7(a). The alignment blocks will be staggered alternately upand down for easy attachment to the support bars. Note only asmall number of modules are shown and the figure is simplified.But it is not difficult to understand that this assembly scheme isquite practical. It is also flexible and can be adapted to a widerange of experimental conditions. With normal incidence overthe entire sensor array at the design location, it can be movedfurther, for any given maximum angular deviation, than a flatarray, which starts out with non-optimum angles of incidence.

Each column of modules, as illustrated in Fig. 7(c), will bepreassembled, wired, and tested. Then a number of these pre-assembled columns will be attached together with the alignmentblocks to form the cylindrical detector. Removing one set ofblocks will split the detector into two parts. Removing two adja-cent sets will free the bar between for easy access to the detectormodules for repair or replacement. Virtually any arrangement ofmodules can be realized in this assembly method.

XII. TEST UNIT: SENSOR, READOUT CHIP,INPUT DRIVER, OUTPUT

Testing the initial unit was done using standard components,rather than with the specially designed equipment planned forthe complete system. An 8 64-pixel sensor was bump-bondedto one of our prototype readout chips. This hybrid module wasthen mounted within a chip carrier, placed on a circuit board, andcontrolled with a National Instruments PCI card. Fig. 8 showsthe circuit board mounted on a probe station under electrical test

1684 IEEE TRANSACTIONS ON NUCLEAR SCIENCE, VOL. 53, NO. 3, JUNE 2006

Fig. 7 Simplified,schematic views of detector modules and mechanical assembly method. (a) Top view of 3 modules (in central plane, so the sensors are normalto the page). (b) Front (X-ray) view of part of 1 column. (c) Side view of each side column (support bars held by 4 alignment blocks) (the center of each sensor isset to be normal to the diffracted X-rays). (d) Side view of central column (each support bar held by 4 alignment blocks).

(a) and under increased magnification (b). The cylindrical objectin Fig. 8(a) is the probe station microscope objective.

In August 2004, we tested the newly assembled prototypeapparatus, shown in Fig. 8, on beam line 4.2.2 of the AdvancedLight Source at the Lawrence Berkeley Laboratory using12 keV X-rays. The beam was collimated to approximately50 m 50 m cross section and was approximately centeredon a 150 m 150 m pixel. The beam intensity was decreasedby detuning the second crystal of the monochromator. A Bicronphotomultiplier tube was used to count the X-ray photons.

The sensor had an n-type bulk, an n-type implant on the en-trance face and sides, p implants on the readout-face, and was0.25 mm thick, and so had a detection efficiency for 12 keVX-rays of about 69%. Limitations of our National Instrumentsinterface card slowed our system to a cycle time of 211 s, ratherthan the 64 s capability of the readout chip. The detector biaswas 60 V, the clock period was 50 ns and the delay between in-tegration periods was 3.7 s. We collected 29 250 observationsfor this experiment. The full response of the system was 180analog to digital units, with an offset reducing that to an effec-

Fig. 8. Sensor—readout chip—chip carrier mounted on a circuit board andplaced on a probe station (a), and at larger magnification (b). The wire bonds tothe chip carrier are visible in the right view.

PARKER et al.: 3DX: AN X-RAY PIXEL ARRAY DETECTOR 1685

tive range of 150 units. To reduce leakage current in the sensorand remove amplifier heat ( W), it was cooled to about Cusing an Oxford Cryostream sample cooler.

XIII. TEST UNIT: RESULTS

Our preliminary results are described here briefly. Thewriting, modification, and testing of data acquisition software,testing of all readout circuit functions, optimization of thecircuit internal settings, circuit board design, board componentvalues, and of the system as a whole, as well as the diagnosis ofthe observed problems is now at an early phase. In the course ofthis work and in taking calibration and X-ray data, a number ofdesign errors have been discovered in this first working VLSIreadout chip (see Fig. 6). These included:

• The automatic baseline-shift compensation circuit does notwork. All related signals that can be tested by probe padsgive no sign of malfunctioning. An alternate software com-pensation scheme, using background events, has been de-vised that requires extra acquisition time and data storage.

• The current from the V-ref DAC, via S5, to the columnbus line receiver, is insufficient to reset the column bus.The temporary fix is to supply the current from an externalsource.

• Both the amplifier and the ADC ramp have non-linear re-gions, particularly at the long cycle times required by thetemporary printed circuit board used so far.

• The line receiver is now reset by closing S5 and S6. If S5alone is closed, the output voltage value

becomes

which depends, in part, on the setting of the I-internal DAC.If only S6 is closed, is set equal to . Thensolving for gives

since . In general this will give a different valuefor . The present chip requires S5 and S6 to operatetogether, and when both S5 and S6 are closed, the ampli-fier will try to go to , while the DAC, with lessdrive capability, will try to drive the output, via S5 and S6,to . The resulting voltage is not well determined, andwhen the reset is turned off, the relative timing of the twoswitches will affect the reset values.

• Due to a timing error, the ADC, which has an AC input,is still reset when the Vr1 to Vr2 step, shown in Fig. 5,takes place. This step, which consequently is not sensed,was intended to assure that all input pulses, no matter howsmall, trigger the comparator.

• The command decoder cannot recognize commands to pro-gram the internal registers of the chip unless the externalclock is turned off. The clock is not needed during this pro-gramming, so turning it off solves this problem.

Fig. 9. Map of the 8� 8 pixel area surrounding the aiming point of the X-raybeam.

• A fraction of the calibration pulse is seen on non-pulsedchannels, and large calibration signals affect the wholedetector.

• The voltage steps in the 5-bit DAC controlling V-pedare too coarse, allowing different pixel-to-pixel levels ofleakage currents to take a channel out of its linear range.This has been temporarily solved by cooling the sensor(and readout) to reduce the leakage current, and so, thevoltage shift it causes.

• The ADC ramp is not externally available, limiting calibra-tion possibilities.

• The 8-bit RAM that drives the output bus does not have anadequate current supply at speeds above 40 MHz. For nowwe are using an external supply to run at the nominal 66MHz readout speed.

Despite these, it was possible to operate the detector in theAugust 2004 test run. Fig. 9 is a map of an 8 8 pixel areaof our sensor, showing the positional response function from adirect beam of X-rays on our beam line. The central pixel re-sponse is scaled arbitrarily to 100%. Our initial impression wasthat the response was limited to a single pixel but that provednot to be the case. Rather, we observed some scattering from ourtantalum slits, in the horizontal direction to the right, and in thevertical direction up. In a normal protein crystallographic beamline, such scattering is normally captured by the beam stop. Asseen in Fig. 9 there is no response of the pixels immediately tothe bottom or to the left of our beam. The sensor apparatus wasapproximately 350 mm from the tantalum slits, and the pixelson the sensor are 150 m wide. If our beam was centered in thepixel we might have expected to see symmetric scatter. There-fore if the beam were striking the central pixel closer to its right,upper corner, the scatter we saw did not extend beyond about150 m (max 0.4 milliradian) to the left and down. Taken inthis light, this result clearly shows that pixels immediately ad-jacent to pixels with central X-ray hits do not respond to thosesignals.

1686 IEEE TRANSACTIONS ON NUCLEAR SCIENCE, VOL. 53, NO. 3, JUNE 2006

Fig. 10. Observed Spectral response (a), Pulse height spectrum for quantum-calibrated x axis (b). Data: dots with error bars, Gaussian fit: solid line, gammadistribution for hni = 2:46: dashed line.

Fig. 10(a) shows the number of readout ADC values, asa function of ADC channel, for a single pixel. Peaks corre-sponding to events with 0 through 7 photons are clearly visible.In this data set, charge shared with neighboring pixels, andin particular the pixel to the right in Fig. 9, was not saved foranalysis, and hence not added to the total signal.

The spectrum has three features:• The peaks are substantially distinct—given an ADC level,

we can derive a reliable quantum count for the numberof photons in each pixel of a readout event, even withoutrestoring charge that may have been shared with neigh-boring pixels.

• There is a significant amount of non-linearity in the spec-trum around channel 100. The main source of this non-lin-earity is in the differential amplifier of the line receiver. Itshould be corrected in the next version of the chip.

• The peak widths, measured in terms of collected charge ordeposited energy are nearly equal. This is consistent withthe expectation that the dominant noise source is withinthe readout electronics, and not anything from the sensorthat would increase with signal size, such as Fano effectfluctuations.

To demonstrate the basic energy resolution and count rate ca-pability of this system we have corrected the spectrum for thegain non-linearity. While the non-linearity could be compen-sated by using the electronic calibration-pulse input, it is moreprecise to do a self-calibration using the positions of the eightpeaks. The result is shown in Fig. 10(b).

The fit used the top 5–8 points on the first 6 peaks (0–5 pho-tons) and the top 3 on the last two, smaller peaks (6 and 7 pho-tons). These were fit to the sum of 8 equally spaced, equal width(on a photon number scale) Gaussians. Nine parameters de-scribed an 8th order polynomial that transformed the non-linearADC channel number (the x-axis) to the linear photon numberscale. The Gaussian and total area (which is proportional tothe total number of readout events), and the mean number ofX-rays in the pixel per readout event, , were all varied to op-timize the fit. The areas or peak heights of the Gaussians werenot individually varied, but were constrained to follow Poissonstatistics

PARKER et al.: 3DX: AN X-RAY PIXEL ARRAY DETECTOR 1687

where P(n) is the probability of observing n occurrences in anygiven measurement and was set to be equal to the meannumber of occurrences. Note that the areas of each Gaussianfunction are proportional to their respective P(n) value. Localx- and y-axis changes were reciprocal to preserve total area.

The best fit, where the spectrum is plotted as a function ofthe number of photons, gives keV for the 12 keVphoton pulses. Less than 0.2% of the area of each Gaussian liesbeyond the photon points in the valleys. For n greaterthan 1 however, extra counts above the Gaussians, about 7% ofthe total, are visible in the valley regions, and the percentage ofsuch extra counts tends to increase with photon number. Thisis expected to be due to the small loss from charge sharing toneighboring pixels (see Fig. 9), which for this run, were notrecorded. The parameter of the best Poisson distribution,

, corresponds to an average counting rate of persecond. The excellent fit of the data to the Poisson-weightedGaussians is just what one would expect for a detector that canhandle 6 or 7 hits per pixel per readout as easily as 1.

Further improvements in these spectra are expected from:• operating the ASIC at full speed which will provide better

compliance with design specifications, higher full-scalebeam intensity, and reduced influence of leakage currents;

• use of a companion field programmable gate array for datademultiplexing, clock distribution, level translation, andcalibration-pulse synchronization;

• a corrected baseline-shift compensation algorithm;• additional optimization of the ASIC internal settings;• the conversion from the 2.3 V CMOS digital-signal

voltage levels currently used to 0.7 V low voltage differ-ential signaling.

Work in the lab on such items has now significantly reducedthe non-linearity and reduced the noise from 1.9 keV to 1.6 keV.Further reductions in both are expected.

XIV. WHAT WE MUST DO NEXT

The major tasks remaining for this initial stage are:• complete test runs with existing and additional sensor-

readout chip units;• redesign the 8 64 pixel readout chip for another shared-

wafer run;• continue development of sensor fabrication and bonding

steps;• test redesigned chip—sensor units;• design and fabricate the 64 64 pixel readout chip;• design and fabricate the sensor/readout chip/mounting

plate—heat sink assembly;• design and fabricate the support bar/alignment block me-

chanical and cooling, system;• select, purchase and program the data acquisition

computer;• design and fabricate the module—computer interface

equipment;• design and test front-end data analysis software;• assemble and test the system, gradually increasing the

number of modules.

XV. CONCLUSION

We have fabricated a promising new kind of silicon pixel radi-ation-sensor. It features active edge sensors, and matching VLSIreadout chips. With these sensors, it should be possible to fab-ricate large, highly efficient, quantum-counting, fast detection,fast readout systems for X-rays. Data to be published in a sepa-rate, completed paper [31] show the sensor is sensitive to withinat least 4 microns of its physical edges. A number of small prob-lems in the VLSI readout chip were found and are expected tobe fixed in the next fabrication run. Tests with a narrow 12 keVX-ray beam have shown that the sensor and readout performwell and that events with 0 through 7 X-ray photons in one pixelhave cleanly separable pulse heights, ensuring a quantum X-raycount to that level. The next generation of this system will bethe basis for our first scientifically valuable detector system.

ACKNOWLEDGMENT

The authors would like to thank Dr. C. Da Via of Brunel Uni-versity for the support, interest, and encouragement from theearliest days of the work on 3D technology. They would alsolike to thank the staff of the Stanford Nanofabrication Facility,who helped in many different ways.

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