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Compact Soft X-Ray Microscopy: Image Processing and Instrumentation
KTH, School of Engineering Sciences (SCI), Applied Physics, Biomedical and X-ray Physics.
2006 (English)Doctoral thesis, comprehensive summary (Other scientific)
Abstract [en]

Soft x-ray microscopy is a powerful technique for natural-contrast, high-resolution imaging of organic materials. This Thesis describes new instrumentational and new image-processing methods to improve the image quality of the compact x-ray microscope at the Biomedical & X-Ray Physics division at KTH. The microscope is based on a laser-plasma source combined with different condenser optics, either multilayer mirrors or zone plates. Imaging is performed by micro zone plates. The microscope works in the water window (\lambda = 2.3-4.4 nm), where the attenuation lengths of oxygen and carbon differ strongly, providing high natural contrast for carbon-containing specimens in an aqueous environment.

By optimizing the properties of the laser-plasma source and fabricating multilayer mirrors with high, uniform reflectivity, the performance of the microscope's illumination system could be improved and exposure times decreased significantly to about 2 min for imaging dry samples and 5 min for imaging wet samples. For imaging of wet samples, a wet-specimen chamber was developed, which is vacuum-compatible. Since it is horizontally mounted in the microscope, it offers advantages for investigations in polymer and soil science.

To improve the quality of images taken by the compact x-ray microscope an image-restoration algorithm was developed. Denoising is performed by a filtering algorithm based on the discrete wavelet transform. This algorithm shows advantages compared to Fourier-based algorithms, since the filtering of spatial frequencies is done locally. An improvement in exposure time by a factor of about 2 could be realized without loss of image information.

To stimulate experiments on functional imaging in x-ray microscopy an image-analysis algorithm for identifying colloidal-gold particles was developed. This algorithm is based on a combination of a threshold with respect to the local absorption and a shape discrimination, realized by fitting a Gaussian profile to the potential particles. The algorithm was evaluated and optimized on images taken by the transmission x-ray microscope at BESSY II. The size-selective identification and localization of single gold particles down to a diameter of 50 nm was demonstrated.

Place, publisher, year, edition, pages
Stockholm: KTH , 2006. , viii, 51 p.
Series
Trita-FYS, ISSN 0280-316X ; 2006:60
Keyword [en]
X-ray microscopy
National Category
Physical Sciences
Identifiers
URN: urn:nbn:se:kth:diva-4128ISBN: 91-7178-458-6 (print)OAI: oai:DiVA.org:kth-4128DiVA: diva2:10849
Public defence
2006-10-20, FD 5, Albanova, 10:30
Opponent
Supervisors
Note
QC 20100920Available from: 2006-10-03 Created: 2006-10-03 Last updated: 2010-09-20Bibliographically approved
List of papers
1. Wavelet-based image restoration for compact x-ray microscopy
Open this publication in new window or tab >>Wavelet-based image restoration for compact x-ray microscopy
2003 (English)In: Journal of Microscopy, ISSN 0022-2720, E-ISSN 1365-2818, Vol. 211, no 2, 154-160 p.Article in journal (Refereed) Published
Abstract [en]

Compact water-window X-ray microscopy with short exposure times will always be limited on photons owing to sources of limited power in combination with low-efficency X-ray optics. Thus, it is important to investigate methods for improving the signal-to-noise ratio in the images. We show that a wavelet-based denoising procedure significantly improves the quality and contrast in compact X-ray microscopy images. A non-decimated, discrete wavelet transform (DWT) is applied to original, noisy images. After applying a thresholding procedure to the finest scales of the DWT, by setting to zero all wavelet coefficients of magnitude below a prescribed value, the inverse DWT to the thresholded DWT produces denoised images. It is concluded that the denoising procedure has potential to reduce the exposure time by a factor of 2 without loss of relevant image information.

Keyword
compact X-ray microscopy, image restoration, wavelet denoising
National Category
Physical Sciences
Identifiers
urn:nbn:se:kth:diva-6199 (URN)000184468300006 ()
Note
QC 20100616Available from: 2006-10-03 Created: 2006-10-03 Last updated: 2017-12-14Bibliographically approved
2. High-resolution spatial characterization of laser produced plasmas at soft x-ray wavelengths
Open this publication in new window or tab >>High-resolution spatial characterization of laser produced plasmas at soft x-ray wavelengths
Show others...
2004 (English)In: Applied physics. B, Lasers and optics (Print), ISSN 0946-2171, E-ISSN 1432-0649, Vol. 78, no 1, 53-58 p.Article in journal (Refereed) Published
Abstract [en]

In this article, we describe the setup and application of a system for the spatial characterization of laser-produced plasma x-ray sources. While pinhole cameras are normally used for this purpose, we employed a zone plate to act as the x-ray lens. Together with an x-ray CCD camera as the detector, a spatial resolution of up to 2 mum was achieved. Due to the wavelength-dependent focal length of a zone plate, the monochromaticity of the image was better than lambda/Deltalambda=150, and the large aperture of the zone plate allowed single-laser-shot images to be collected. Methanol and ethanol were used as liquid-jet target systems. Two different Nd:YAG lasers with pulse durations of 3 ns and 10 ns produced the plasmas. Our measurements concentrated on the line emission of carbon in the soft x-ray spectral range, namely, the hydrogen-like alpha-line at 3.37 nm and the helium-like alpha-line at 4.03 nm. We investigated the influence of different nozzle sizes, laser energies, and pulse durations on the source size of the plasma. Depending on the experimental conditions, plasma diameters of 17-60 mum were measured.

Keyword
Ethanol; Image quality; Lenses; Light emission; Light sources; Methanol; Neodymium lasers; Nozzles; X rays; High resolution spatial characterization; Liquid jet target systems; Plasma diameters; Soft x ray wavelengths; Laser produced plasmas
National Category
Physical Sciences
Identifiers
urn:nbn:se:kth:diva-6200 (URN)10.1007/s00340-003-1338-9 (DOI)000187014400011 ()2-s2.0-0742321216 (Scopus ID)
Note
QC 20100819Available from: 2006-10-03 Created: 2006-10-03 Last updated: 2017-12-14Bibliographically approved
3. Size-selective colloidal-gold localization in transmission x-ray microscopy
Open this publication in new window or tab >>Size-selective colloidal-gold localization in transmission x-ray microscopy
2007 (English)In: Journal of Microscopy, ISSN 0022-2720, E-ISSN 1365-2818, Vol. 225, no 1, 80-87 p.Article in journal (Refereed) Published
Abstract [en]

Colloidal gold is a useful marker for functional-imaging experiments in transmission X-ray microscopy. Due to the low contrast of gold particles with small diameters it is necessary to develop a powerful algorithm to localize the single gold particles. The presented image-analysis algorithm for identifying colloidal gold particles is based on the combination of a threshold with respect to the local absorption and shape discrimination, realized by fitting a Gaussian profile to the identified regions of interest. The shape discrimination provides the possibility of size-selective identification and localization of single colloidal gold particles down to a diameter of 50 nm. The image-analysis algorithm, therefore, has potential for localization studies of several proteins simultaneously and for localization of fiducial markers in X-ray tomography.

Keyword
Colloidal gold; Image analysis; Soft X-ray microscopy; algorithm; article; image analysis; microscopy; normal distribution; particle size; priority journal; protein localization; transmission X ray microscopy; X ray microanalysis
National Category
Physical Sciences
Identifiers
urn:nbn:se:kth:diva-6201 (URN)10.1111/j.1365-2818.2007.01717.x (DOI)000243974000008 ()2-s2.0-33846829091 (Scopus ID)
Note
QC 20100820. Uppdaterad från Accepted till Published 20100820.Available from: 2006-10-03 Created: 2006-10-03 Last updated: 2017-12-14Bibliographically approved
4. High-reflectivity Cr/Sc multilayer condenser for compact soft x-ray microscopy
Open this publication in new window or tab >>High-reflectivity Cr/Sc multilayer condenser for compact soft x-ray microscopy
2006 (English)In: Review of Scientific Instruments, ISSN 0034-6748, E-ISSN 1089-7623, Vol. 77, no 12, 123101- p.Article in journal (Refereed) Published
Abstract [en]

The condenser is a critical component in compact water-window x-ray microscopes as it influences the exposure time via its efficiency and the resolution via its numerical aperture. Normal-incidence multilayer mirrors can reach large geometrical collection efficiencies and match the numerical aperture of the zone plate but require advanced processing for high total reflectivity. In the present article we demonstrate large-diameter normal-incidence spherical Cr/Sc multilayer condensers with high and uniform reflectivity. Dc-magnetron sputtering was used to deposit 300 bilayers of Cr/Sc with a predetermined d-spacing matching the lambda=3.374 nm operating wavelength on spherical substrates. The mirrors show a uniform reflectivity of similar to 3% over the full 58 mm diameter condenser area. With these mirrors an improvement in exposure time by a factor of 10 was achieved, thereby improving the performance of the compact x-ray microscope significantly.

Keyword
Chromium compounds; Magnetron sputtering; Multilayers; Numerical analysis; Optical microscopy; Reflection; d-spacing matching; Multilayer mirrors; Water-window x-ray microscopes; Capacitors
National Category
Physical Sciences
Identifiers
urn:nbn:se:kth:diva-6202 (URN)10.1063/1.2400665 (DOI)000243159100001 ()2-s2.0-33846081459 (Scopus ID)
Note
QC 20100820. Uppdaterad från Submitted till Published 20100820.Available from: 2006-10-03 Created: 2006-10-03 Last updated: 2017-12-14Bibliographically approved
5. Sub 30-nm resolution compact x-ray microscopy
Open this publication in new window or tab >>Sub 30-nm resolution compact x-ray microscopy
Show others...
2006 (English)In: Journal of Microscopy, ISSN 0022-2720, E-ISSN 1365-2818Article in journal (Other academic) Submitted
National Category
Physical Sciences
Identifiers
urn:nbn:se:kth:diva-6203 (URN)
Note
QS 20120316Available from: 2006-10-03 Created: 2006-10-03 Last updated: 2017-12-14Bibliographically approved
6. A vacuum-compatible wet-specimen chamber for compact x-ray microscopy
Open this publication in new window or tab >>A vacuum-compatible wet-specimen chamber for compact x-ray microscopy
2007 (English)In: Journal of Microscopy, ISSN 0022-2720, E-ISSN 1365-2818, Journal of Microscopy, Vol. 226, no 1, 71-73 p.Article in journal (Refereed) Published
Abstract [en]

Soft X-ray microscopy is a powerful tool for investigations of, for example, polymers or soils in their natural liquid environment. This requires a wet-specimen chamber. Compact X-ray microscopy allows the horizontal mounting of such samples, thereby reducing the influence of gravitational forces. We have developed a wet-specimen chamber for such compact X-ray microscope. The chamber is vacuum compatible, which reduces the exposure time. The vacuum sealing is achieved by a combination of mechanical sealing and sealing by bio-compatible glue. With the wet-specimen chamber the specimens can be kept in an aqueous environment in a vacuum of 10(-4) mbar for several hours. Imaging of lipid droplets in water demonstrates the function of the wet-specimen chamber.

Keyword
compact X-ray microscopy, wet cell, wet-specimen chamber
National Category
Physical Sciences
Identifiers
urn:nbn:se:kth:diva-6204 (URN)000245101000009 ()2-s2.0-33947397151 (Scopus ID)
Note
Uppdaterad från manuskript till artikel: 20100920 QC 20100920Available from: 2006-10-03 Created: 2006-10-03 Last updated: 2017-12-14Bibliographically approved

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