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Investigation of Measurement Condition for 3Dimensional Spectroscopy by Scanning
Transmission X-ray Microscopy
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X-Ray Microscopy Conference 2016 (XRM 2016)
IOP Conf. Series: Journal of Physics: Conf. Series 1234567890
849 (2017) 012044

IOP Publishingdoi:10.1088/1742-6596/849/1/012044

Investigation of Measurement Condition for 3-Dimensional
Spectroscopy by Scanning Transmission X-ray Microscopy
T. Ohigashi1, Y. Inagaki1, A. Ito2, K. Shinohara2 and N. Kosugi1
1UVSOR Synchrotron, Institute for Molecular Science, NINS, Okazaki, Aichi 4448585 Japan
2
School of Engineering, Tokai University, Kitakaname, Hiratsuka, Kanagawa 2581292, Japanohigashi@ims.ac.jp
Abstract. A sample cell for performing computed tomography (CT) was developed. The 3dimensional (3D) structure of polystyrene spheres was observed and the fluctuation ofreconstructed linear absorption coefficients (LAC) was 9.3%. To improve the quality of data in
3D spectro-microscopy, required measurement condition is discussed.

1. Introduction
Combination of X-ray microscopy and computed tomography (CT) is one of the advanced techniques
to be realized in forth-coming diffraction limit synchrotron-based light sources, considering the hightransmittance of X-rays and the high spatial resolution of the X-ray microscopy. This combination
allows us to analyze 3-dimentional (3D) structures without any destructive process of samples. Among
several CT techniques, the full-field microscopy [1-5] may be more suitable methods than thescanning one from the viewpoint of data acquisition time. The scanning transmission X-ray
microscope (STXM) in the soft X-ray region has been established as a powerful tool for the 2D
chemical analysis based on near edge X-ray absorption fine structure (NEXAFS) and also been
applied to 3D chemical state mappings [6-8]. In the soft X-ray region, the thickness of typical samples
is around one micron; therefore, the spatial resolution of microscopy, a few tens nm, is suitable for
performing CT. In most cases, tomographic data by using scanning typemicroscopy have been acquired under the condition of restricted angleprojection due to the limitations of the measurement time and the shape andmounting of samples. In order to realize more quantitative analysis, the fullprojection (180° or 360°) measurement is highly required [9]. In this report,
an experimental result of CT measurements is shown. The feasibility and themeasurement condition to perform 3D spectroscopic measurements in STXM
are also discussed.
2. Development of a sample cell for the CT measurement
A sample cell for the CT measurement is shown in Fig.1. This cell consists ofa base plate, a small two phase stepper motor (AM-1020, Faulhaber) with aspur gearhead (12/5) and a sample clamp. Samples can be attached on a tip ofa needle or in a glass capillary tube, and then be held by the sample clamp.

10 mmSample

Fig. 1: The sample
cell for CT

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Published under licence by IOP Publishing Ltd1X-Ray Microscopy Conference 2016 (XRM 2016)
IOP Conf. Series: Journal of Physics: Conf. Series 1234567890
849 (2017) 012044

IOP Publishingdoi:10.1088/1742-6596/849/1/012044

The stepper motor is driven by a programmable stepping driver (AD PM 00, Faulhaber) via a
feedthrough. The controllable accuracy of the rotating angle is approximately 0.1°/full step. Design ofthe base plate is compatible with ALS-based STXM systems.
3. Experiments and results
3.1. STXM beamline, BL4U
The present measurement was performed at STXM beamline, BL4U, in UVSOR Synchrotron(Okazaki, Japan) [10]. In this experiment, a Fresnel zone plate (FZP) with a long focal length was used
for the long working distance and focal depth. Parameters of the FZP is as follows; diameter of 240µm, outermost zone width of 35 nm, diameter of a 0th order stop of 90 µm, pattern material of nickel
on a silicon nitride membrane (100 nm thick) support. Diameter of an order select aperture (OSA) is
65 µm. In this experiment, the photon energy was 280 eV, below the carbon K-edge, and the focal
length of the FZP is 1.90 mm. Size of a fixed exit slit used as a virtual source was set to 50×50 µm2. In
this geometry of the STXM, the working distance is ~400 µm, the spot size of the focused beam is
73×73 nm2 and the calculated focal depth is 2.2 µm.
3.2. Sample and data acquisition
A cross sectional image of polystyrene spheres with diameter of 5 µm wasobtained by CT. The spheres were fixed on a tip of tungsten needle withglue. In this experiment, the sample was rotated by 180° in total to get
quantitative reconstructed values. 50 STXM images were totally acquiredwith rotating the sample by 3.6° each. The dwell time was 3 ms, thescanning step size was 150 nm, and the size of the image was 100×100pixels. Due to wobbling of the sample position and refocusing, it took 2.5
hour to acquire all images. One of the STXM images is shown in Fig. 2.
The rotational axis of the CT sample cell is along the vertical direction ofthe image.

5 µm

Fig. 2: STXM imageof a sample

3.3. CT image reconstruction
The alignment of a series of 50 STXM images was done manually to extract sinograms. Cross
sectional images were reconstructed by a home-made filtered-back projection algorithm withassuming the incident X-rays are parallel beams. One of the reconstructed cross sectional images (CTimage) and a 3D volume image are shown in Fig. 3 (a) and (b), respectively. A profile along the radial
direction of Fig. 3(a) is shown in Fig. 3(c). Judging from 10-90% of the edge of the profile, the spatial
resolution is estimated as >300 nm. In Fig. 3(d), a histogram of the CT image is shown and a peak of
the linear attenuation coefficient (LAC) at 0.173 µm-1 implies polystyrene (cf. 0.185 µm-1 at 280 eV[11]). An FWHM of that peak is 0.016 µm-1, 9.3% of the peak LAC.
4. Discussion
In this experiment, structure of the sample is homogeneous so that the fluctuation of reconstructed
LACs (i.e. the FWHM of the peak) will become an error in spectroscopy by CT. The fluctuation ofLACs was 9.3% in this experiment and should be suppressed. There are several reasons for thisfluctuation; (a) resolving power of the monochromator, (b) beam hardening, (c) photon flux, (d)degradation of the spatial resolution and (e) error by reconstruction algorithm, where (a), (b) and (c)can be negligible. The resolving power of the monochromator at BL4U is >3,000 in this configuration[10] so that the fluctuation of the LAC is less than 0.01%. The effect of beam hardening due to thehigher order incident X-rays, such as bright edges on the CT image, is not clearly seen in Fig. 3(a) and3(c) [12]. The photon flux onto one pixel was 3.5×104 [photons/dwell] and the fluctuation is estimatedas 0.5%.

2X-Ray Microscopy Conference 2016 (XRM 2016)
IOP Conf. Series: Journal of Physics: Conf. Series 1234567890
849 (2017) 012044(a)

IOP Publishingdoi:10.1088/1742-6596/849/1/012044(b)

5 µm100	0.2	(d)	 
Number of pixels

LAC [µm^-1]	 

(c)	 

0.15	

0.1	

0.05	

0	-0.05	80	

0.173	 

60	40	

20	0	-0.05	

0	0.05	

Position [pixels]	 

0.1	

0.15	

0.2	

LAC [µm^-1]

Fig. 3: Reconstructed images of the polystyrene spheres; (a) a cross sectional image and (b) 3dimensional volume image. (c) A profile along radial direction and (d) a histogram of (a).
To estimate (d) error by the reconstruction algorithm and the required number of rotations, thereconstruction of a phantom with the same size as in the experiment, 100×100 pixels, is simulated.
The distributions of LACs of the phantom is shown in Fig. 4(a). Sinograms are extracted from thephantom with 25, 50, 100, 150, 200 and 250 rotations per 180°, respectively. The phantoms arereconstructed and their FWHMs at the peak at 0.185 µm-1 are plotted in 4(c). In this plot, the FWHM
saturates at 0.0021 µm-1 above 100 rotations and the fluctuation is 1.1%. Therefore, we can improve
the fluctuation caused by reconstruction algorithm from 2.2% to 1.1% by increasing the number ofrotation from 50 to 100.
1400	

0.012	(b)1200	

FWHM [µm^-1]	 

(a)Pixels	 

1000	

800	

600	

400	

200	

0	-0.05	0	0.05	

0.1	0.15	

LAC [µm^-1]	 

0.2	

0.25	

0.3	(c)0.01	0.008	

0.006	

0.004	

0.002	

0	0	

100	200	

Number of rotation	 Fig. 4: (a) Distribution of LAC of the phantom and (c) a histogram of the reconstructed sinogram with100 rotations. (c) The FWHMs of the peak at 0.185 µm-1 are plotted against the number of rotations.
In the experiment, the expected spatial resolution was around 150 nm, similar to the scanning stepsize, but >300 nm in fact. This degradation of the spatial resolution was caused by mechanical issues,
such as insufficient focal depth of the FZP, instability of the sample and wobbling of a rotational axisof the stepper motor. Effect of the degraded resolution is simulated by reconstructing the phantom
which is filtered by Gaussian with radius of 1 pixel. The histograms of the reconstructed normal andfiltered phantoms are shown in Fig. 5(a) and the detail of the peaks around 0.185 µm-1 is shown ininset. The FWHM of the filtered phantom becomes slightly larger than the normal one, 0.0024 and0.0020, respectively. Furthermore, the peak of the filtered phantom has a tail to the higher LAC and its
peak shifts toward the higher LAC. Profiles of the reconstructed phantoms are shown in Fig. 5(b). The
profiles are extracted from center of the phantom, shown in Fig. 4(a) as a dashed line. Even though3X-Ray Microscopy Conference 2016 (XRM 2016)
IOP Conf. Series: Journal of Physics: Conf. Series 1234567890
849 (2017) 012044

IOP Publishingdoi:10.1088/1742-6596/849/1/012044

integrated intensities of normal and filtered phantoms are same, reconstructed LACs of the filtered one
are slightly higher than normal one. This result is due to the smaller diameter of the profile of thefiltered phantom in Fig. 5(b). Therefore, density of the reconstructed LACs of the filtered phantom
becomes higher than the normal one.
1400	(a)Normal	Filtered	1000	

Pixels	 (b)800	

LAC [µm^-1]	 

1200	

600	

400	

200	0	-0.05	

0	0.05	

0.1	

0.15	

0.2	

0.25	

0.25	

0.2	

0.15	

0.1	

0.05	

Normal	Filtered	0	0.3	

LAC [µm^-1]	 

-0.05	

Position	 Fig. 5: (a) Histograms of the CT image of the normal and Gaussian filtered phantoms and inset showsdetail of the peak around 0.185 µm-1, (b) profiles of reconstructed images
5. Conclusion
The first trial of CT by STXM was performed and the fluctuation of the reconstructed LAC of 9.3%
was obtained. This fluctuation should be suppressed to perform spectroscopic measurement by CT.
Then, we investigated the measurement condition by simulation to obtain more reliable reconstructed
LACs and 100 rotations per 180° is necessary for data acquisition. The spatial resolution of STXM isalso effective to obtain reliable LACs so that the FZP with suitable parameters, spatial resolution andsufficient focal depth, has to be improved. For performing actual 3D spectro-microscopy, the new CT
sample cell should be developed for high stability and low wobbling. That reduces the measurement
time remarkably (e.g. 17.5 hour is estimated in current condition).
Acknowledgement
This work was partly supported by Nanotechnology Platform Program (Molecule and MaterialSynthesis) of the Ministry of Education, Culture, Sports, Science and Technology (MEXT), Japan, andalso by JSPS Grants-in-Aid for Scientific Research (JSPS KAKENHI Grant Nos. 16K05022 and26248010).
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