First experiments on the Australian Synchrotron Imaging and Medical beamline, including investigations of the effective source size in respect of X-ray imaging

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First experiments on the Australian Synchrotron Imaging and Medical beamline, including investigations of the effective source size in respect of X-ray imaging
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  electronic reprint  Journal of  SynchrotronRadiation ISSN 0909-0495 Editors:  G. Ice, A˚. Kvick and T. Ohta First experiments on the Australian Synchrotron Imaging andMedical beamline, including investigations of the effectivesource size in respect of X-ray imaging Andrew W. Stevenson, Sheridan C. Mayo, Daniel H ¨ausermann, AntonMaksimenko, Richard F. Garrett, Christopher J. Hall, Stephen W. Wilkins,Robert A. Lewis and Damian E. Myers  J. Synchrotron Rad.  (2010).  17 , 75–80 Copyright c  International Union of CrystallographyAuthor(s) of this paper may load this reprint on their own web site or institutional repository provided thatthis cover page is retained. Republication of this article or its storage in electronic databases other than asspecified above is not permitted without prior permission in writing from the IUCr.For further information see Synchrotron radiation research is rapidly expanding with many new sources of radiationbeing created globally. Synchrotron radiation plays a leading role in pure science andin emerging technologies. The  Journal of Synchrotron Radiation  provides comprehensivecoverage of the entire field of synchrotron radiation research including instrumentation,theory, computing and scientific applications in areas such as biology, nanoscience andmaterials science. Rapid publication ensures an up-to-date information resource for sci-entists and engineers in the field. Crystallography Journals Online  is available from  J. Synchrotron Rad.  (2010).  17 , 75–80 Andrew W. Stevenson  et al.  ·  First experiments on the Australian Synchrotron IMBL  research papers  J. Synchrotron Rad.  (2010).  17 , 75–80 doi:10.1107/S0909049509041788  75  Journal of  SynchrotronRadiation ISSN 0909-0495Received 18 February 2009Accepted 13 October 2009 # 2010 International Union of CrystallographyPrinted in Singapore – all rights reserved First experiments on the Australian SynchrotronImaging and Medical beamline, includinginvestigations of the effective source size inrespect of X-ray imaging Andrew W. Stevenson, a * Sheridan C. Mayo, a Daniel Ha¨usermann, a,b,c Anton Maksimenko, b Richard F. Garrett, b,d Christopher J. Hall, c,e Stephen W. Wilkins, a,e Robert A. Lewis c,e and Damian E. Myers a,f a CSIRO Materials Science and Engineering, Private Bag 33, Clayton South, Victoria 3169, Australia, b Australian Synchrotron, 800 Blackburn Road, Clayton, Victoria 3168, Australia,  c Monash Centrefor Synchrotron Science, Monash University, Melbourne, Victoria 3800, Australia,  d Bragg Institute,ANSTO, PMB 1, Menai, NSW 2234, Australia,  e School of Physics, Monash University, Melbourne,Victoria 3800, Australia, and  f Department of Medicine (RMH/WH), University of Melbourne,Parkville, Victoria 3050, Australia. E-mail: The Imaging and Medical beamline at the Australian Synchrotron achieved ‘firstlight’ in December 2008. Here, the first experiments performed on the beamlineare reported, which involved both X-ray imaging and tomography studiesfor a range of samples. The use of a plastic-edge phantom for quantitativemeasurements of contrast and resolution proved to be very instructive andhelped to confirm certain parameter values such as the effective horizontalsource size, detector resolution and average X-ray energy for the polychromaticbeam. Keywords: X-ray imaging; X-ray tomography; phase contrast; source size. 1. Introduction The Imaging and Medical beamline (IMBL) at the AustralianSynchrotron [3.0 GeV (1/    = 170  m rad); 200 mA; circumfer-ence 216 m; see Boldeman & Einfeld (2004) for a descriptionof the physics design] achieved ‘first light’ in December 2008.This paper reports the first experiments by a team fromCSIRO, Monash University and the Australian Synchrotron.These experiments involved both X-ray imaging and tomo-graphy studies for various samples, including medical/bio-medical and materials-science applications. The focus of thispaper is on the imaging results obtained, including somefundamental experiments aimed at estimating the effectiveX-ray source size.The experiments were performed in the second hutch (1B),with a minimum source-to-sample distance ( R 1 ) of 20 m.Sample-to-detector distances ( R 2 ) of up to 3 m were used. Thecurrent insertion device is an Advanced Photon Source (APS)type-A permanent-magnet wiggler, which was operated witha gap of 55 mm to protect a temporary Be window fromexcessive thermal loading. Given that hutch 2B (31.7–40.0 m)and the satellite building (including hutches 3A and 3B;sample position at 136 m) have already been constructed,there is interest in the quality of the X-ray imaging that can beachieved with this interim insertion device, and, ultimately,with the future superconducting multipole wiggler. The RMSelectron beam size in the straight sections at the AustralianSynchrotron is 320  m m horizontally and 16  m m vertically (1%coupling), with distributed dispersion of 0.1 m. These valuescorrespond to Gaussian FWHM of 754  m m and 38  m m,respectively. The electron-beam deviation caused by the fieldof the APS wiggler is small in comparison with the electron-beam size and so it is the latter which dictates the X-ray sourcesize. This large horizontal source size and the 20:1 aspect ratioare important factors to be investigated in respect of X-rayimaging on this beamline, especially with reference to spatialcoherence for propagation-based phase-contrast imaging. Inthe case of analyzer-based phase-contrast imaging, similarissues will arise if the plane of diffraction is vertical.The experiment end-station in the satellite building will notonly enable the use of a wide X-ray beam for imaging largeobjects but also significantly increase the demagnification of the source. Reduced source demagnification will significantlylimit the degree of phase contrast achievable in the horizontaldirection in hutch 1B.In conventional treatment of X-ray imaging, and implicit inthe above discussion, the X-ray source is regarded as totallyincoherent within the range of the source size. In reality, andespecially in the case of synchrotron radiation, some degree of coherence across the spatial extent of the source is possible.Such partial coherence of the source may affect image quality,and our aim is to measure the effective source size. electronic reprint  2. Experimental The synchrotron operated at 200 mA, with a beam decay toabout 150 mA in the 12 h between injections. The experimentswere performed in hutch 1B, with the beam delivered from theBe window in upstream hutch 1A through a He-filled tube.The He reduced ozone production and protected the 0.5 mmBe window in the aggressive environment caused by the whitebeam (no monochromators having been installed as yet). Thehigh X-ray flux also necessitated the use of polished Al filters(total thickness 6.0 mm) to protect the CCD detector andminimize damage to the more sensitive samples. The filterswere selected so that the X-ray image quality, after processing,was not noticeably compromised. Fig. 1 shows a schematicdiagram of the experimental configuration used.The CCD used was a 10 MHz 16M FDI-VHR camera,capable of 12-bit and 16-bit operation, supplied by PhotonicScience. It was operated at approximately 241 K  via  the multi-stage Peltier cooling, and with a chilled water supply toremove the heat generated by the Peltier. The CCD has 4872   3248 (horizontal    vertical) 7.4  m m pixels, is opticallybonded to a straight fibre-optic bundle (no magnification), andemploys a (P43) Tb-doped Gadox (gadolinium oxysulphide)input phosphor (5 mg cm  2 ). It is optimized for X-rays in the2–30 keV range. The images were pre-processed in conjunc-tion with flat-field and dark-current images,  i.e.  images withoutan object and without X-rays, respectively. Correlation of sequences of image frames from a static sample, collected overa period of time, showed no significant drift present,  i.e.  highcorrelation coefficients and (translational) movement of lessthan a single pixel.The APS wiggler has 28    8.5 cm periods with a total lengthof 2.4 m. At a gap of 55 mm, the field is approximately 0.24 Tand the deflection parameter  K   is 1.9 (see Lai  et al. , 1993; This quite small  K  -value means that this insertion deviceis behaving with considerable undulator character (see Clarke,2004, p. 43). The critical energy is 1.4 keV and the first-orderharmonic energy is 0.36 keV. The program  SPECTRA 8.0 (Tanaka & Kitamura, 2001; was used to calculate the spectralbrightness (Mills  et al. , 2005) as a function of energy in steps of 0.1 keV, using the storage-ring parameter values from This spectrum wasconverted into flux density within 1 mm 2 at the centre of thebeam and 20 m from the source. Allowance was then made forthe effect of the various filters, windows and materials presentin the beam path, and for the quantum efficiency of thedetector. The spectrum calculation was performed for both awiggler and an undulator; the final results shown in Fig. 2 havebeen smoothed by using a ‘running average’ over 11 datapoints. The undulator calculation yields, as expected, a (final)spectrum peak with considerable harmonic structure. Table 1shows the parameter values which characterize the (wiggler)spectrum at each stage after inclusion of the various factors(without applying the running average). The final results forthe corresponding undulator calculation are also given inTable 1. 3. Results Fig. 3 shows X-ray images collected for ( a ) a gum leaf ( R 1  =20.8 m;  R 2  = 155 cm) and ( b ) a coarse-fibre paper sample ( R 1  =20.3 m;  R 2  = 159 cm). The experimental magnification  M   =( R 1  +  R 2 )/ R 1  is approximately 1.08. There is little X-rayabsorption for these samples and the dominant contrastmechanism is phase contrast. The ‘salt and pepper’ noise nearthe edges of these images is due to the rapid drop in beam fluxhere, an effect exacerbated by the flat-field correction.In Fig. 4 the images of three fixed mouse tibiae are shown,one in each column [see Cornish  et al.  (2002) for details of thesamples]. The images reveal that the tibiae have quite distincttrabecular microstructures. The first row corresponds to  M   =1.00; the second row to  M   = 1.08; the third row to  M   = 1.15.Absorption- and phase-contrast effects are present in theseimages to varying degrees, with the  M   = 1.00 (essentially‘contact’) images being dominated by absorption contrast.Whilst the effects are quite subtle, the increase in phasecontrast and reduced demagnification of the X-ray source as R 2  increases from 158 cm to 305 cm can be detected. research papers 76  Andrew W. Stevenson  et al.   First experiments on the Australian Synchrotron IMBL  J. Synchrotron Rad.  (2010).  17 , 75–80 Figure 2 Calculated spectrum used for X-ray imaging and tomography experi-ments. The short solid line indicates the peak position (19.9 keV), theshort dashed line the weighted-average energy (21.2 keV), for the smoothcurve (wiggler-based calculation). The jagged curve is for the undulator-based calculation. Figure 1 Schematic diagram of the experimental layout used for these experimentsat IMBL. electronic reprint  The image of the dragon-flypresented in Fig. 5 is the result of combining more than 80 individualimages, obtained by scanning thesample in 2 mm steps verticallyand 6 mm steps horizontally acrossthe beam to create a montage ( R 1 = 20.8 m;  R 2  = 155 cm). The imagesto the right are magnified sectionsfrom a wing and the head. Whilstabsorption contrast is present,phase contrast is again the domi-nant mechanism, especially forthe delicate wing structure [seeSnigirev  et al.  (1995) and Wilkins  et al.  (1996) for the fundamentals of propagation-based X-ray phase-contrast imaging].A tomography data set wascollected for another mouse tibia.A total of 900 images werecollected over a 180  rotation in0.2  steps with  R 1  = 21.6 m and  R 2  = 23 cm ( M   = 1.01). Inaddition to the usual pre-processing steps mentioned earlier, aphase-retrieval step was included for the tomography data.The algorithm used was that of Paganin  et al.  (2002), whichassumes a homogeneous object and is based on the transport-of-intensity equation (Teague, 1983). It requires a value of    /  (=   2 ’ /  ) for the object, where the X-ray refractive index isgiven by  n  = 1      i  , ’ is the phase shift per unit length, and research papers  J. Synchrotron Rad.  (2010).  17 , 75–80 Andrew W. Stevenson  et al.   First experiments on the Australian Synchrotron IMBL  77 Table 1 Values of parameters used to characterize the X-ray spectrum after inclusion of the effects of windows,filters and other materials present in the beam path (wiggler-based calculation). The final row (in italics) corresponds to an undulator-based calculation of the spectrum. The Al filter thicknesssubsumes a 12  m m Al window in the CCD for excluding light. We also note that the number of visible photonsproduced in the CCD is a function not only of the number of X-ray photons but also of their energy. Allowancefor this energy dependence has little effect in the current context however,  e.g.  the final value of the weighted-average energy changes to 21.6 keV. NA = not applicable.Factor†Maximum flux density[photons s  1 (0.1%bandwidth)  1 mm  2 ]Energy (keV)for maximumflux densityFWHM(keV)Weighted-averageenergy (keV)None 3.4    10 13 1.9 NA NA+ He (6.5 m) 2.3    10 13 2.9 3.6 4.3+ Be (0.5 mm) 9.4    10 12 4.5 3.8 5.8+ Sigradur (0.1 mm)‡ 6.8    10 12 5.0 3.9 6.2+ Kapton (0.1 mm) 5.0    10 12 5.5 4.0 6.7+ graphite (1 mm) 9.3    10 11 7.8 4.5 8.9+ Al (6.0 mm) 9.1    10 6 21.3 6.7 22.2+ Gd 2 O 2 S:Tb (5 mg cm  2 )§ 1.4    10 6 19.9 6.2 21.2 + Gd  2 O  2 S:Tb (5 mg cm   2  )§ 8.3    10 6  22.5 4.0 21.3 † All absorption coefficients are calculated using total cross sections (Zschornack, 2007). ‡ Glassy carbon CCDwindow. § CCD quantum efficiency calculated as 1    exp(   m  s ), where   m  is the energy-dependent mass absorptioncoefficient and   s  is the ‘surface density’ (or ‘phosphor concentration’); a more rigorous calculation of the energy-dependentCCD response, to be reported elsewhere, does not have any significant effect in the current context Figure 5 X-ray image of a dragon-fly obtained by combining more than 80individual images to create a montage. Magnified sections from a wingand the head are shown on the right. Figure 4 X-ray images obtained for three fixed mouse tibiae. The tibiae wereobtained from mice treated with control (left column),   -MSH (middlecolumn) and leptin (right column). Details are provided by Cornish  et al. (2002). The rows correspond to, from top to bottom,  R 1  = 22.5 m and  R 2  =8 cm ( M   = 1.00);  R 1  = 20.5 m and  R 2  = 158 cm ( M   = 1.08);  R 1  = 20.5 m and R 2  = 305 cm ( M   = 1.15). Figure 3 X-ray phase-contrast images obtained for ( a ) a gum leaf and ( b ) a coarse-fibre paper sample. electronic reprint    is the linear absorption coefficient(all these quantities being energy-or wavelength-dependent). As theresults are not particularly sensitiveto this parameter, we used a spec-trally weighted average value (180)for hydroxylapatite [Ca 5 (PO 4 ) 3 OH;   = 3.18 g cm  3 ], the major compo-nent of osseous tissue. A cone-beamreconstruction was performed usingthe conventional  FDK   algorithm(Feldkamp  et al. , 1984). These dataprocessing and analysis operationswere all performed using the  X-TRACT   (version 4) software package; Figs. 6( a )–6( d ) show reconstructed (  xy ) slicesperpendicular to the direction of the tibia shaft at 1.72, 1.36,0.99 and 0.62 mm from the top of the tibia. Fig. 6( e ) is areconstructed  yz  slice and Fig. 6(  f  ) is a reconstructed  xz  slice,both at the longitudinal mid-line of the tibia.The images presented thus far are all remarkable in that therelatively large horizontal source size and 20:1 aspect ratiodo not appear to be significant factors for the geometricalconditions being employed. Close examination of the images,especially those for the tibiae in Fig. 4, do indicate that theresolution of fine details is superior in the vertical directionthan in the horizontal. However, the degree of improvement isnot consistent with a simplistic view of the effect of the X-raysource. Given that these observations are qualitative and to acertain extent subjective, it was decided that images should becollected for a plastic-edge phantom.The plastic-edge phantom was studied previously with alaboratory-based microfocus X-ray source (Gureyev  et al. ,2008). It provides a means of obtaining quantitative contrastand resolution values, and of simultaneously checking verticaland horizontal directions. This simple phantom consists of two 100  m m-thick polyethylene sheets, partially overlappedto have edges running vertical and horizontal. Given ourexperimental conditions, in particular the X-ray energy range,this phantom provides images with both absorption and phasecontrast, but dominated by the latter, in the form of char-acteristic single black–white fringes. The images were analysedto provide contrast and resolution values. The observed(experimental) contrast values are obtained from the differ-ence between the maximum and minimum intensity valuesdivided by their sum. The observed resolution values areobtained from the spatial separation of these features, referredto the object plane. The observed data values for vertical andhorizontal edges, affected by the horizontal and verticalsource dimensions, respectively, are listed in Table 2 as afunction of   R 2  ( R 1  = 21.6 m). The estimated standard devia-tions (e.s.d.s) for the contrast values are 0.3% and for theresolution values are 2  m m (these values are smaller than theeffective pixel size as the positions of the maximum andminimum intensities were extracted from the data by fitting).These e.s.d.s are consistent with the agreement between valuesof contrast and resolution obtained for a single polyethyleneedge and for a single polyethylene edge overlapped by a singlepolyethylene sheet.It can be shown that the contrast for a Gaussian-blurrededge can be expressed as C   ¼ R 0  ’ t   2  ð 2  e Þ 1 = 2   2tot ;  ð 1 Þ and the resolution as R  ¼  4   2tot  þ  R 0    1 = 2 ;  ð 2 Þ where   tot  ¼    2b  þ ð M     1 Þ 2   2s = M  2 þ    2d = M  2   1 = 2 :  ð 3 Þ The derivation of these formulae and the associated validityconditions are detailed by Gureyev  et al.  (2008).  R 0 =  R 1 R 2 /( R 1  +  R 2 ) =  R 2 / M   is the effective propagation or ‘defocus’distance,    is the X-ray wavelength,  t   is the thickness of thepolyethylene, and    b ,    s  and    d  are the standard deviationsassociated with the blurring of the edge, the source emissivity research papers 78  Andrew W. Stevenson  et al.   First experiments on the Australian Synchrotron IMBL  J. Synchrotron Rad.  (2010).  17 , 75–80 Table 2 Summary of experimental and theoretical (least-squares fitting) contrast and resolution values for aplastic-edge phantom. Errors associated with the experimental quantities are discussed in the text. R 2  (cm) [ M  ]Plastic-edgedispositionContrast  C   (%)experimentContrast  C   (%)calculatedResolution  R  ( m m)experimentResolution  R  ( m m)calculated19.8 [1.01] Vertical 1.2 0.82 40 3919.8 [1.01] Horizontal 1.3 0.84 41 3969.8 [1.03] Vertical 2.6 2.2 43 4469.8 [1.03] Horizontal 3.5 3.0 36 38119.8 [1.06] Vertical 3.0 2.6 55 54119.8 [1.06] Horizontal 5.2 5.3 37 38169.8 [1.08] Vertical 2.8 2.4 64 65169.8 [1.08] Horizontal 7.2 7.7 37 37 Figure 6 X-ray tomography reconstructed slices for a leptin-treated fixed mousetibia. ( a ), ( b ), ( c ) and ( d ) show  xy  slices perpendicular to the main shaft of the bone at 1.72, 1.36, 0.99 and 0.62 mm, respectively, from the top of thetibia. ( e ) and (  f  ) are  yz  and  xz  slices, respectively, at the longitudinal mid-line of the bone. electronic reprint
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