- Email: [email protected]
X-ray microtome by fluorescence tomography
Nuclear Instruments and Methods in Physics Research A 467–468 (2001) 889–892
X-ray microtome by fluorescence tomography c . A. Simionovicia,*, M. Chukalinab, F. Gunzler , Ch. Schroerc, A. Snigireva, a c . I. Snigireva , J. Tummler , T. Weitkampa a
ESRF, BP 220, 38043 Grenoble, France b IMT-RAS, Chernogolovka, Russia c RWTH, Univ. of Aachen, Germany
Abstract The X-ray fluorescence microtomography method is presented, which is capable of virtually slicing samples to obtain cross-sections of their inner structure. High precision experimental results of fluo-tomography in ‘‘pencil-beam’’ geometry with up to 1.2 mm resolution are described. Image reconstructions are based on either a simplified algebraic reconstruction method (ART) or the filtered back-projection method (FBP). Phantoms of inhomogenous test objects as well as biological samples are successfully analyzed. # 2001 Elsevier Science B.V. All rights reserved. PACS: 87.59.Fm; 78.70.En Keywords: X-ray fluorescence tomography; Synchrotron radiation
1. Introduction Over the past few years, a novel technique of imaging namely X-ray Fluorescence Computed Micro-Tomography (XFCMT) was introduced [1–3] and started to play an increasing role in microanalysis. XFCMT is an excellent complementary technique to phase contrast imaging in that it offers the much-needed elemental sensitivity down to trace element concentrations with the same micron-sized spatial resolution. Reconstruction techniques are used for the retrieval of quantitative 2D/3D images of the fluorescence signals in relatively short times. In this article we
*Corresponding author. Fax: +33-47688-2542. E-mail address: [email protected] (A. Simionovici).
describe high precision experiments performed at the ID22 beamline of ESRF on either test or real samples featuring inhomogenous elemental distributions.
2. Experimental set-up The ID 22 beamline is dedicated to micro X-ray fluorescence spectrometry and X-ray absorption imaging (XRF, XAS), X-ray diffraction and phase contrast imaging of samples with micron resolution at high energy [4,5]. The microtomography set-up includes several normalization detectors (PIN diodes, ionization chambers, etc.) and a lens assembly housing compound refractive lenses (CRL) [6]. A high precision sample stage with 7 degrees of freedom is used for positioning the
0168-9002/01/$ - see front matter # 2001 Elsevier Science B.V. All rights reserved. PII: S 0 1 6 8 - 9 0 0 2 ( 0 1 ) 0 0 5 1 2 - 5
890
A. Simionovici et al. / Nuclear Instruments and Methods in Physics Research A 467–468 (2001) 889–892
sample and rotating the sample axis perpendicular to the beam. A Si drift detector registers the fluorescence signal and an X-ray intensified CCD camera set behind the sample is used for alignment purposes with precisions of a few mm.
mahogany plant (Swietenia macrophylla). This is part of a study on ion channels and their influence on the long range transport of ions throughout the . plants, in collaboration with the IBI at FZ Julich. This is the first record of an X-ray 2D elemental imaging of the inner structure of a plant.
3. Measurements 4. Reconstruction For the first experiment, a 20 keV monochromatic beam was used for the excitation of the elements in the sample, the energy cut-off of the mirror being set at 22 keV. The focusing element is a set of 120 aluminum parabolic CRL lenses, which delivers a beam of approximately 9.108 ph/s in a beam spot of about 1 7 mm2. A PIN diode detector operated in the current integration mode is positioned before the sample to monitor the flux of the focused beam. The Si drift diode is set in the vertical plane at 908 with respect to the incident beam to minimize the scattering contribution. This particular geometry allows to make use of the horizontal rotation axis of the sample and to take advantage of the highly focused vertical beam size. The sample is scanned in this ‘‘pencil-beam’’ geometry as follows: the sample is translated vertically with a 1.2 mm step in front of the Si drift diode detector. At each end of the travel, the sample is brought back to the incident position and rotated around the horizontal axis by an angle of approximately 1.58 and the translation scan is restarted. At each individual step an X-ray fluorescence spectrum is acquired during 1 s and the intensity associated with K and L lines of elements of interest is measured. The phantom analyzed in this experiment consists of a quartz capillary of about 160 mm diameter and 10 mm thick walls which was filled with quartz dust grains (1410 mm) impregnated with 0.1–1% saline solutions of K, Fe, Cu, As and Yr whose K lines are measured. The capillary itself gives rise to Sr, Zr K and Ba L lines. The count rates of all the elements are normalized to the flux of the PIN diode and serve as the fluorescence signals used in the reconstruction algorithm described in the next section. The second sample imaged at 19.5 keV with lower resolution (6 mm) was a root of the
The reconstruction algorithms [3,7] used for the retrieval of the 2D fluorescence images are twofold: Filtered back-projection method [7] (FBP) and a modified Algebraic reconstruction technique (ART). Several simplifications were made to reduce the complexity of the problem and the required calculation time. The following approximations are made throughout the calculation: *
*
*
scattering from sample and scattering and absorption in the surrounding air are neglected, ‘‘enhancement effects’’ due to secondary/ternary fluorescence are not considered, the detector efficiency is considered 100%, regardless of the energy or angle of incidence. The detector-sample distance and the angle between incident and detected fluorescence photons are constant.
5. Results For the first sample we first performed a transmission microtomography, which gives a 3D map of the density with a resolution of about 1 mm. 2D slices of this volume were summed to obtain the exact slice thickness of the fluorescence tomography scan at the same position on the capillary. This allows a direct comparison of the observed features as well a test of the resolution, contrast and degree of noise in the reconstruction. In Fig. 1 the reconstructions obtained with the two methods are compared with the transmission tomogram. It is evident that the elemental maps well reproduce the features of the density map and allow a one-to-one matching of the maps. The FBP reconstruction, appears of better quality for
A. Simionovici et al. / Nuclear Instruments and Methods in Physics Research A 467–468 (2001) 889–892
891
Fig. 1. Comparison between FBP, respectively, ART elemental 2D reconstructions and a transmission tomogram of a capillary filled with mineral dust.
Fig. 2. Comparison between the FBP elemental 2D reconstruction and the transmission tomogram of a mahogany root.
the homogenous capillary tube with little structure and self-absorption. The overall resolution of the images seems higher than that of the ART reconstructed images but some radial artifacts appear. The graininess of the FBP images is probably a consequence of the 1808 collection range. The ART data which span 3608 (padded by fitting) show less artifacts. For the second sample (Fig. 2) the comparison transmission/fluorescence yields spectacular re-
sults. Here we employed the FBP reconstruction method for a relatively lower resolution (6 mm). In comparison, the very detailed transmission tomogram features a resolution close to 1 mm. With a resolution of 6 mm the cellular structures of the plant are clearly resolved. The Ca concentration is very high in the surrounding soil, but a much smaller Ca concentration barely distinguishable from the noise can be detected in the inner parts of the root. The Rb is incorporated by the plant in a
892
A. Simionovici et al. / Nuclear Instruments and Methods in Physics Research A 467–468 (2001) 889–892
similar way to K. However, it is about 103 less concentrated than it, which well illustrates the high sensitivity of the method.
6. Conclusions The combination of a tomographic set-up in the ‘‘pencil-beam’’ parallel collection geometry and the two reconstruction methods: one, based on a modification of ART and the other on the FBP, provided the highest resolution achieved so far in fluorescence tomography (1.2 mm). Furthermore, spectacular results obtained from plants fully qualify this method for detailed investigations in the inner structure of samples in a precise and non-destructive way. To further improve these results, we are currently considering: *
*
oversampling using smaller scanning steps (0.5 mm) and deconvoluting the full spectrum. correcting for incident beam absorption, selfabsorption and secondary fluorescence effects.
For the establishment of this technique as a fullfledged microanalysis method, it will be necessary to reduce the collection time below 0.5 s/pt and
also to perform limited-angle as well as partial volume data collection, enabling the recording of a small volume inside a large object, with a limited number of projections and thus a relatively short acquisition time. Such improvements will be included in a future campaign of measurements that will be extended to samples of more complex composition and heterogeneity.
References [1] R. Cesareo, S. Mascarenhas, Nucl. Instr. and Meth. A 277 (1989) 669. [2] G.F. Rust, J. Weigelt, IEEE Trans. Nucl. Sci. 45 (1) (1998) 75. [3] A. Simionovici, M. Chukalina, M. Drakopoulos, I. Snigireva, A. Snigirev, Ch. Schroer, B. Lengeler, K. Janssens, F. Adams, Developments in X-ray tomography 2, Ed. U. Bonse, SPIE, 1999, pp. 304–310. [4] http:// www.esrf.fr/exp facilities/ID22/ [5] S. Bohic, C. Camerani, M. Drakopoulos, W. Leitenberger, C. Rau, A. Simionovici, A. Snigirev, I. Snigireva, A. Somogy T. Weitkamp, Nucl. Instr. and Meth. A 467–468 (2001), these proceedings. . [6] B. Lengeler, C.G. Schroer, M. Richwin, J. Tummler, M. Drakopoulos, A. Snigirev, I. Snigireva, Appl. Phys. Lett. 74 (1999) 3924. [7] A.C. Kak, M. Slaney, Principles of Computerized Tomographic Imaging, IEEE Press, New York, 1988.
X-ray microtome by fluorescence tomography c . A. Simionovicia,*, M. Chukalinab, F. Gunzler , Ch. Schroerc, A. Snigireva, a c . I. Snigireva , J. Tummler , T. Weitkampa a
ESRF, BP 220, 38043 Grenoble, France b IMT-RAS, Chernogolovka, Russia c RWTH, Univ. of Aachen, Germany
Abstract The X-ray fluorescence microtomography method is presented, which is capable of virtually slicing samples to obtain cross-sections of their inner structure. High precision experimental results of fluo-tomography in ‘‘pencil-beam’’ geometry with up to 1.2 mm resolution are described. Image reconstructions are based on either a simplified algebraic reconstruction method (ART) or the filtered back-projection method (FBP). Phantoms of inhomogenous test objects as well as biological samples are successfully analyzed. # 2001 Elsevier Science B.V. All rights reserved. PACS: 87.59.Fm; 78.70.En Keywords: X-ray fluorescence tomography; Synchrotron radiation
1. Introduction Over the past few years, a novel technique of imaging namely X-ray Fluorescence Computed Micro-Tomography (XFCMT) was introduced [1–3] and started to play an increasing role in microanalysis. XFCMT is an excellent complementary technique to phase contrast imaging in that it offers the much-needed elemental sensitivity down to trace element concentrations with the same micron-sized spatial resolution. Reconstruction techniques are used for the retrieval of quantitative 2D/3D images of the fluorescence signals in relatively short times. In this article we
*Corresponding author. Fax: +33-47688-2542. E-mail address: [email protected] (A. Simionovici).
describe high precision experiments performed at the ID22 beamline of ESRF on either test or real samples featuring inhomogenous elemental distributions.
2. Experimental set-up The ID 22 beamline is dedicated to micro X-ray fluorescence spectrometry and X-ray absorption imaging (XRF, XAS), X-ray diffraction and phase contrast imaging of samples with micron resolution at high energy [4,5]. The microtomography set-up includes several normalization detectors (PIN diodes, ionization chambers, etc.) and a lens assembly housing compound refractive lenses (CRL) [6]. A high precision sample stage with 7 degrees of freedom is used for positioning the
0168-9002/01/$ - see front matter # 2001 Elsevier Science B.V. All rights reserved. PII: S 0 1 6 8 - 9 0 0 2 ( 0 1 ) 0 0 5 1 2 - 5
890
A. Simionovici et al. / Nuclear Instruments and Methods in Physics Research A 467–468 (2001) 889–892
sample and rotating the sample axis perpendicular to the beam. A Si drift detector registers the fluorescence signal and an X-ray intensified CCD camera set behind the sample is used for alignment purposes with precisions of a few mm.
mahogany plant (Swietenia macrophylla). This is part of a study on ion channels and their influence on the long range transport of ions throughout the . plants, in collaboration with the IBI at FZ Julich. This is the first record of an X-ray 2D elemental imaging of the inner structure of a plant.
3. Measurements 4. Reconstruction For the first experiment, a 20 keV monochromatic beam was used for the excitation of the elements in the sample, the energy cut-off of the mirror being set at 22 keV. The focusing element is a set of 120 aluminum parabolic CRL lenses, which delivers a beam of approximately 9.108 ph/s in a beam spot of about 1 7 mm2. A PIN diode detector operated in the current integration mode is positioned before the sample to monitor the flux of the focused beam. The Si drift diode is set in the vertical plane at 908 with respect to the incident beam to minimize the scattering contribution. This particular geometry allows to make use of the horizontal rotation axis of the sample and to take advantage of the highly focused vertical beam size. The sample is scanned in this ‘‘pencil-beam’’ geometry as follows: the sample is translated vertically with a 1.2 mm step in front of the Si drift diode detector. At each end of the travel, the sample is brought back to the incident position and rotated around the horizontal axis by an angle of approximately 1.58 and the translation scan is restarted. At each individual step an X-ray fluorescence spectrum is acquired during 1 s and the intensity associated with K and L lines of elements of interest is measured. The phantom analyzed in this experiment consists of a quartz capillary of about 160 mm diameter and 10 mm thick walls which was filled with quartz dust grains (1410 mm) impregnated with 0.1–1% saline solutions of K, Fe, Cu, As and Yr whose K lines are measured. The capillary itself gives rise to Sr, Zr K and Ba L lines. The count rates of all the elements are normalized to the flux of the PIN diode and serve as the fluorescence signals used in the reconstruction algorithm described in the next section. The second sample imaged at 19.5 keV with lower resolution (6 mm) was a root of the
The reconstruction algorithms [3,7] used for the retrieval of the 2D fluorescence images are twofold: Filtered back-projection method [7] (FBP) and a modified Algebraic reconstruction technique (ART). Several simplifications were made to reduce the complexity of the problem and the required calculation time. The following approximations are made throughout the calculation: *
*
*
scattering from sample and scattering and absorption in the surrounding air are neglected, ‘‘enhancement effects’’ due to secondary/ternary fluorescence are not considered, the detector efficiency is considered 100%, regardless of the energy or angle of incidence. The detector-sample distance and the angle between incident and detected fluorescence photons are constant.
5. Results For the first sample we first performed a transmission microtomography, which gives a 3D map of the density with a resolution of about 1 mm. 2D slices of this volume were summed to obtain the exact slice thickness of the fluorescence tomography scan at the same position on the capillary. This allows a direct comparison of the observed features as well a test of the resolution, contrast and degree of noise in the reconstruction. In Fig. 1 the reconstructions obtained with the two methods are compared with the transmission tomogram. It is evident that the elemental maps well reproduce the features of the density map and allow a one-to-one matching of the maps. The FBP reconstruction, appears of better quality for
A. Simionovici et al. / Nuclear Instruments and Methods in Physics Research A 467–468 (2001) 889–892
891
Fig. 1. Comparison between FBP, respectively, ART elemental 2D reconstructions and a transmission tomogram of a capillary filled with mineral dust.
Fig. 2. Comparison between the FBP elemental 2D reconstruction and the transmission tomogram of a mahogany root.
the homogenous capillary tube with little structure and self-absorption. The overall resolution of the images seems higher than that of the ART reconstructed images but some radial artifacts appear. The graininess of the FBP images is probably a consequence of the 1808 collection range. The ART data which span 3608 (padded by fitting) show less artifacts. For the second sample (Fig. 2) the comparison transmission/fluorescence yields spectacular re-
sults. Here we employed the FBP reconstruction method for a relatively lower resolution (6 mm). In comparison, the very detailed transmission tomogram features a resolution close to 1 mm. With a resolution of 6 mm the cellular structures of the plant are clearly resolved. The Ca concentration is very high in the surrounding soil, but a much smaller Ca concentration barely distinguishable from the noise can be detected in the inner parts of the root. The Rb is incorporated by the plant in a
892
A. Simionovici et al. / Nuclear Instruments and Methods in Physics Research A 467–468 (2001) 889–892
similar way to K. However, it is about 103 less concentrated than it, which well illustrates the high sensitivity of the method.
6. Conclusions The combination of a tomographic set-up in the ‘‘pencil-beam’’ parallel collection geometry and the two reconstruction methods: one, based on a modification of ART and the other on the FBP, provided the highest resolution achieved so far in fluorescence tomography (1.2 mm). Furthermore, spectacular results obtained from plants fully qualify this method for detailed investigations in the inner structure of samples in a precise and non-destructive way. To further improve these results, we are currently considering: *
*
oversampling using smaller scanning steps (0.5 mm) and deconvoluting the full spectrum. correcting for incident beam absorption, selfabsorption and secondary fluorescence effects.
For the establishment of this technique as a fullfledged microanalysis method, it will be necessary to reduce the collection time below 0.5 s/pt and
also to perform limited-angle as well as partial volume data collection, enabling the recording of a small volume inside a large object, with a limited number of projections and thus a relatively short acquisition time. Such improvements will be included in a future campaign of measurements that will be extended to samples of more complex composition and heterogeneity.
References [1] R. Cesareo, S. Mascarenhas, Nucl. Instr. and Meth. A 277 (1989) 669. [2] G.F. Rust, J. Weigelt, IEEE Trans. Nucl. Sci. 45 (1) (1998) 75. [3] A. Simionovici, M. Chukalina, M. Drakopoulos, I. Snigireva, A. Snigirev, Ch. Schroer, B. Lengeler, K. Janssens, F. Adams, Developments in X-ray tomography 2, Ed. U. Bonse, SPIE, 1999, pp. 304–310. [4] http:// www.esrf.fr/exp facilities/ID22/ [5] S. Bohic, C. Camerani, M. Drakopoulos, W. Leitenberger, C. Rau, A. Simionovici, A. Snigirev, I. Snigireva, A. Somogy T. Weitkamp, Nucl. Instr. and Meth. A 467–468 (2001), these proceedings. . [6] B. Lengeler, C.G. Schroer, M. Richwin, J. Tummler, M. Drakopoulos, A. Snigirev, I. Snigireva, Appl. Phys. Lett. 74 (1999) 3924. [7] A.C. Kak, M. Slaney, Principles of Computerized Tomographic Imaging, IEEE Press, New York, 1988.