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Size-selective colloidal-gold localization in transmission x-ray microscopy
KTH, Skolan för teknikvetenskap (SCI), Tillämpad fysik, Biomedicinsk fysik och röntgenfysik.
Institut für Röntgenphysik, Georg-August-Universität Göttingen, Berlin.
KTH, Skolan för teknikvetenskap (SCI), Tillämpad fysik, Biomedicinsk fysik och röntgenfysik.
KTH, Skolan för teknikvetenskap (SCI), Tillämpad fysik, Biomedicinsk fysik och röntgenfysik.ORCID-id: 0000-0003-2723-6622
2007 (engelsk)Inngår i: Journal of Microscopy, ISSN 0022-2720, E-ISSN 1365-2818, Vol. 225, nr 1, s. 80-87Artikkel i tidsskrift (Fagfellevurdert) 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.

sted, utgiver, år, opplag, sider
2007. Vol. 225, nr 1, s. 80-87
Emneord [en]
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
HSV kategori
Identifikatorer
URN: urn:nbn:se:kth:diva-6201DOI: 10.1111/j.1365-2818.2007.01717.xISI: 000243974000008Scopus ID: 2-s2.0-33846829091OAI: oai:DiVA.org:kth-6201DiVA, id: diva2:10845
Merknad
QC 20100820. Uppdaterad från Accepted till Published 20100820.Tilgjengelig fra: 2006-10-03 Laget: 2006-10-03 Sist oppdatert: 2017-12-14bibliografisk kontrollert
Inngår i avhandling
1. Compact Soft X-Ray Microscopy: Image Processing and Instrumentation
Åpne denne publikasjonen i ny fane eller vindu >>Compact Soft X-Ray Microscopy: Image Processing and Instrumentation
2006 (engelsk)Doktoravhandling, med artikler (Annet vitenskapelig)
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.

sted, utgiver, år, opplag, sider
Stockholm: KTH, 2006. s. viii, 51
Serie
Trita-FYS, ISSN 0280-316X ; 2006:60
Emneord
X-ray microscopy
HSV kategori
Identifikatorer
urn:nbn:se:kth:diva-4128 (URN)91-7178-458-6 (ISBN)
Disputas
2006-10-20, FD 5, Albanova, 10:30
Opponent
Veileder
Merknad
QC 20100920Tilgjengelig fra: 2006-10-03 Laget: 2006-10-03 Sist oppdatert: 2010-09-20bibliografisk kontrollert
2. Compact Soft X-Ray Microscopy: Sources, Optics and Instrumentation
Åpne denne publikasjonen i ny fane eller vindu >>Compact Soft X-Ray Microscopy: Sources, Optics and Instrumentation
2007 (engelsk)Doktoravhandling, med artikler (Annet vitenskapelig)
Abstract [en]

This thesis describes the development of a sub-60-nm full-period resolution compact soft x-ray microscope operating in the water-window region (2.3-4.4 nm). Soft x-ray water-window microscopy is a powerful technique for high-resolution imaging of organic materials exploiting the natural contrast mechanism between carbon and oxygen, cf. Sect. 4.1. The thesis discusses the components of, as well as the integration of the microscope, including liquid-jet laser-plasma x-ray sources, optics, simulations, and image-processing tools.

Liquid-jet-target laser-plasma sources for generation of soft x-rays and extreme-ultraviolet radiation are compact sources with high brightness. The work focused on improved target stability, decreased debris, and accurate source characterization. For x ray microscopy applications a liquid-jet target delivery system allowing cryogenic liquids was developed. Source characterization was performed for two different liquid-jet targets: Methanol and liquid nitrogen. For extreme-ultraviolet lithography applications, the potential use of a liquid-tin-jet laser-plasma source was explored including conversion efficiency and debris measurements.

High quality optics are essential in the development of compact x-ray microscopes. For soft x-ray wavelengths, zone plates and multilayer mirrors are used to focus or redirect radiation. This thesis describes the development and characterization of a condenser zone plate suitable for use in a compact soft x-ray microscope operating at λ = 2.478 nm. It also investigates the possibility to perform differential interference contrast microscopy in the water window using a single diffractive optical element. An arrangement for rapid and accurate determination of absolute and local diffraction efficiency of soft x-ray zone plates using a compact laser-plasma source has been developed. The instrument is used to characterize the zone plates fabricated at the Biomedical & X-Ray Physics division at KTH. Through a collaboration with the Fraunhofer-Institut in Jena, Germany, a large diameter spherical Cr/Sc multilayer mirror, suitable as condenser in the compact x-ray microscope, was developed and characterized. The mirror is designed for λ = 3.374 nm and shows a high, and uniform reflectivity of 3%. This increases the photon flux by an order of magnitude compared to the W/B4C mirrors previously used.

The thesis describes the development of a compact soft x-ray microscope with sub-60-nm full-period resolution. It can operate at two different wavelengths in the water window using the soft x-ray laser-plasma sources combined with the condenser optics described above. Imaging is performed by zone plate objectives. The microscope is capable of imaging hydrated biological samples with thicknesses up to ~10 μm. Improvements made to the mechanical design has turned it into a user friendly instrument allowing daily operation. A numerical method was developed to study the effects of partially coherent illumination on 2D imaging. To stimulate experiments on functional imaging in x-ray microscopy an image-analysis algorithm for identifying colloidal-gold particles was developed. Size selective identification and localization of single gold particles down to a diameter of 50 nm was demonstrated.

sted, utgiver, år, opplag, sider
Stockholm: KTH, 2007. s. x, 59
Serie
Trita-FYS, ISSN 0280-316X ; 2007:25
Emneord
soft x-ray microscopy, water window, compact, laser plasma, liquid jet, zone plate optics
HSV kategori
Identifikatorer
urn:nbn:se:kth:diva-4342 (URN)978-91-7178-613-5 (ISBN)
Disputas
2007-05-04, FD 5, Albanova, Roslagstullsbacken 21, Stockholm, 13:00
Opponent
Veileder
Merknad
QC 20100819Tilgjengelig fra: 2007-04-20 Laget: 2007-04-20 Sist oppdatert: 2010-08-20bibliografisk kontrollert

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