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Laboratory soft x-ray microscopy and tomography
KTH, School of Engineering Sciences (SCI), Applied Physics, Biomedical and X-ray Physics.
2011 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Soft x-ray microscopy in the water-window (λ = 2.28 nm – 4.36 nm) is based on zone-plate optics and allows high-resolution imaging of, e.g., cells and soils in their natural or near-natural environment. Three-dimensional imaging is provided via tomographic techniques, soft x-ray cryo tomography. However, soft x-ray microscopes with such capabilities have been based on large-scale synchrotron x‑ray facilities, thereby limiting their accessibility for a wider scientific community.

This Thesis describes the development of the Stockholm laboratory soft x-ray microscope to three-dimensional cryo tomography and to new optics-based contrast mechanisms. The microscope relies on a methanol or nitrogen liquid-jet laser-plasma source, normal-incidence multilayer or zone-plate condenser optics, in-house fabricated zone-plate objectives, and allows operation at two wavelengths in the water-window, λ = 2.48 nm and λ = 2.48 nm. With the implementation of a new state-of-the-art normal-incidence multilayer condenser for operation at λ = 2.48 nm and a tiltable cryogenic sample stage the microscope now allows imaging of dry, wet or cryo-fixed samples. This arrangement was used for the first demonstration of laboratory soft x-ray cryo microscopy and tomography. The performance of the microscope has been demonstrated in a number of experiments described in this Thesis, including, tomographic imaging with a resolution of 140 nm, cryo microscopy and tomography of various cells and parasites, and for studies of aqueous soils and clays. The Thesis also describes the development and implementation of single-element differential-interference and Zernike phase-contrast zone-plate objectives. The enhanced contrast provided by these optics reduce exposure times or lowers the dose in samples and are of major importance for harder x-ray microscopy. The implementation of a high-resolution 50 nm compound zone-plate objective for sub-25-nm resolution imaging is also described. All experiments are supported by extensive numerical modelling for improved understanding of partially coherent image formation and stray light in soft x-ray microscopes. The models are useful tools for studying effects of zone plate optics or optical design of the microscope on image formation and quantitative accuracy in soft x-ray tomography.

Place, publisher, year, edition, pages
Stockholm: KTH Royal Institute of Technology , 2011. , x, 76 p.
Series
Trita-FYS, ISSN 0280-316X ; 2011:03
Keyword [en]
Microscopy, X-ray optics, Diffractive optics, Zone plates, X-ray microscopy, Soft X-ray physics, Tomography
National Category
Atom and Molecular Physics and Optics Physical Sciences
Identifiers
URN: urn:nbn:se:kth:diva-29950ISBN: 978-91-7415-874-8 (print)OAI: oai:DiVA.org:kth-29950DiVA: diva2:398800
Public defence
2011-02-25, FB42, AlbaNova Universitetscentrum, Roslagstullsbacken 21, Stockholm, 13:00 (English)
Opponent
Supervisors
Note
QC 20110221Available from: 2011-02-21 Created: 2011-02-18 Last updated: 2011-02-21Bibliographically approved
List of papers
1. Laboratory arrangement for soft x-ray zone-plate efficiency measurements
Open this publication in new window or tab >>Laboratory arrangement for soft x-ray zone-plate efficiency measurements
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2007 (English)In: Review of Scientific Instruments, ISSN 0034-6748, E-ISSN 1089-7623, Vol. 78, no 2, 026103- p.Article in journal (Refereed) Published
Abstract [en]

We demonstrate a laboratory-scale arrangement for rapid and accurate measurements of the absolute and local efficiency of soft x-ray micro zone plates in the water window. This in-house instrument is based on a single-line lambda=2.88 nm liquid-jet laser-plasma source. Measurements are performed by a simultaneous comparison of first diffraction-order photon flux with the flux in a calibrated reference signal. This arrangement eliminates existing source emission fluctuations. The performance of the method is demonstrated by the result from measurements of two similar to 55 mu m diameter nickel micro zone plates, showing a groove efficiency of 12.9%+/- 1.1% and 11.7%+/- 1.0%. Furthermore, we show that spatially resolved efficiency mapping is an effective tool for a detailed characterization of local zone plate properties. Thus, this laboratory-scale instrument allows rapid feedback to the fabrication process which is important for future improvements.

Keyword
Electron diffraction; Laser beams; Photons; Plasma theory; X rays; Emission fluctuations; Micro zone plates; Reference signals; Plates (structural components)
National Category
Physical Sciences
Identifiers
urn:nbn:se:kth:diva-7018 (URN)10.1063/1.2472590 (DOI)000244531600057 ()2-s2.0-33847677594 (Scopus ID)
Note
QC 20100820Available from: 2007-04-20 Created: 2007-04-20 Last updated: 2017-12-14Bibliographically approved
2. Simulation of partially coherent image formation in x-ray microscopy - art. no. 67050I
Open this publication in new window or tab >>Simulation of partially coherent image formation in x-ray microscopy - art. no. 67050I
2007 (English)In: Advances in X-Ray/EUV Optics and Components II, SPIE - International Society for Optical Engineering, 2007, Vol. 6705, I7050-I7050 p.Conference paper, Published paper (Refereed)
Abstract [en]

We present the theory and implementation of a numerical model capable of simulating two-dimensional images for an x-ray microscope using partially coherent illumination considerations. Partially coherent illumination is found in all x-ray microscopes and particularly in the latest generation of our in-house compact soft x-ray microscope. This is due to an introduced mismatch in numerical aperture of the condenser and objective zone plate, and will yield diffraction-like artifacts in phase-shifting objects. The numerical model approximates the condenser zone plate as a secondary incoherent source represented by individually coherent but mutually incoherent source emitters, each giving rise to a separate image. A final image is obtained by adding up the image intensities of the individual contributions. The simulation has been a useful tool for investigating the influence of coherence on images in both the mirror and zone plate condenser arrangement of the in-house compact soft x-ray microscope. The latest development included in the program is the effect of astigmatism and partial coherence, where the calculated results show good qualitative agreement with respect to the microscope images.

Place, publisher, year, edition, pages
SPIE - International Society for Optical Engineering, 2007
Series
Proceedings of the society of photo-optical instrumentation engineers (spie), ISSN 0277-786X ; 6705
Keyword
x-ray microscopy, zone plates, partial coherence, image formation
National Category
Atom and Molecular Physics and Optics
Identifiers
urn:nbn:se:kth:diva-29734 (URN)10.1117/12.734003 (DOI)000252146700015 ()2-s2.0-42149185208 (Scopus ID)978-0-8194-6853-6 (ISBN)
Conference
Advances in X-Ray/EUV Optics and Components II; San Diego, CA; United States; 27 August 2007 through 28 August 2007
Note

QC 20110214

Available from: 2011-02-14 Created: 2011-02-14 Last updated: 2014-11-07Bibliographically approved
3. Theoretical development of a high-resolution differential-interference-contrast optic for x-ray microscopy
Open this publication in new window or tab >>Theoretical development of a high-resolution differential-interference-contrast optic for x-ray microscopy
2008 (English)In: Optics Express, ISSN 1094-4087, E-ISSN 1094-4087, Vol. 16, no 2, 1132-1141 p.Article in journal (Refereed) Published
Abstract [en]

In this paper, the theoretical background and development of a differential-interference contrast (DIC) x-ray optic is presented. The single-element optic is capable of high-resolution phase contrast imaging and is compatible with compact sources. It is shown that an understanding of the coherence requirements in this type of imaging is imperative and is explained in detail. The optic is capable of a wavefront separation equal to the resolution of the optic which places only minor constraints on the object illumination.

Keyword
phase-contrast
National Category
Condensed Matter Physics
Identifiers
urn:nbn:se:kth:diva-17274 (URN)10.1364/OE.16.001132 (DOI)000252479700064 ()2-s2.0-38549088419 (Scopus ID)
Note
QC 20100525Available from: 2010-08-05 Created: 2010-08-05 Last updated: 2017-12-12Bibliographically approved
4. Compact high-resolution differential interference contrast soft x-ray microscopy
Open this publication in new window or tab >>Compact high-resolution differential interference contrast soft x-ray microscopy
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2008 (English)In: Applied Physics Letters, ISSN 0003-6951, E-ISSN 1077-3118, Vol. 92, no 064104Article in journal (Refereed) Published
Abstract [en]

We demonstrate high-resolution x-ray differential interference contrast (DIC) in a compact soft x-ray microscope. Phase contrast imaging is enabled by the use of a diffractive optical element objective which is matched to the coherence conditions in the microscope setup. The performance of the diffractive optical element objective is evaluated in comparison with a normal zone plate by imaging of a nickel siemens star pattern and linear grating test objects. Images obtained with the DIC optic exhibit typical DIC enhancement in addition to the normal absorption contrast. Contrast transfer functions based on modulation measurements in the obtained images show that the DIC optic gives a significant increase in contrast without reducing the spatial resolution. The phase contrast operation mode now available for our compact soft x-ray microscope will be a useful tool for future studies of samples with low absorption contrast.

Keyword
diffractive optical-elements, zone plates, phase-contrast, fabrication, condenser
National Category
Physical Sciences
Identifiers
urn:nbn:se:kth:diva-9811 (URN)10.1063/1.2842422 (DOI)000253237900123 ()2-s2.0-39349084101 (Scopus ID)
Note
QC 20100728Available from: 2009-01-07 Created: 2009-01-07 Last updated: 2017-12-14Bibliographically approved
5. Compact Zernike phase contrast x-ray microscopy using a single-element optic
Open this publication in new window or tab >>Compact Zernike phase contrast x-ray microscopy using a single-element optic
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2008 (English)In: Optics Letters, ISSN 0146-9592, E-ISSN 1539-4794, Vol. 33, no 9, 932-934 p.Article in journal (Refereed) Published
Abstract [en]

We demonstrate Zernike phase contrast in a compact soft x-ray microscope using a single-element optic. The optic is a combined imaging zone plate and a Zernike phase plate and does not require any additional alignment or components. Contrast is increased and inversed in an image of a test object using the Zernike zone plate. This type of optic may be implemented into any existing x-ray microscope where phase contrast is of interest.

Keyword
spatial-resolution, zone plates
National Category
Biomedical Laboratory Science/Technology
Identifiers
urn:nbn:se:kth:diva-17561 (URN)000256166900014 ()2-s2.0-44949260817 (Scopus ID)
Note
QC 20100525Available from: 2010-08-05 Created: 2010-08-05 Last updated: 2017-12-12Bibliographically approved
6. High-resolution computed tomography with a compact soft x-ray microscope
Open this publication in new window or tab >>High-resolution computed tomography with a compact soft x-ray microscope
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2009 (English)In: Optics Express, ISSN 1094-4087, E-ISSN 1094-4087, Vol. 17, no 13, 11057-11065 p.Article in journal (Refereed) Published
Abstract [en]

Computed tomography based on high-resolution soft x-ray microscopy utilizes the natural contrast for biological specimens provided by the water window (lambda = 2.4 - 4.4 nm) and the high resolving power of zone plate objectives. It is capable of revealing the 3D structure of biological specimens at sub-visible-microscopic resolution. To date, the technique has only been available at synchrotron-based microscopes, which limits the researchers access. In the present paper we demonstrate high-resolution soft x-ray tomography with a laboratory zone-plate-based soft x-ray microscope. The specimen, a diatom mounted on a glass capillary, was reconstructed from a tilt series of 53 images covering 180 using a filtered back projection algorithm. The resolution of the tomogram was estimated to a half period of 140 nm using a differential-phase-residual method. Cryo-fixation, increased source brightness and extended-depth-of-focus objectives are important for pushing the resolution of compact systems for biological samples.

Identifiers
urn:nbn:se:kth:diva-18584 (URN)000267761100066 ()2-s2.0-67649271251 (Scopus ID)
Note
QC 20100525Available from: 2010-08-05 Created: 2010-08-05 Last updated: 2017-12-12Bibliographically approved
7. Sub-25-nm laboratory x-ray microscopy using a compound Fresnel zone plate
Open this publication in new window or tab >>Sub-25-nm laboratory x-ray microscopy using a compound Fresnel zone plate
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2009 (English)In: Optics Letters, ISSN 0146-9592, E-ISSN 1539-4794, Vol. 34, no 17, 2631-2633 p.Article in journal (Refereed) Published
Abstract [en]

Improving the resolution in x-ray microscopes is of high priority to enable future applications in nanoscience. However, high-resolution zone-plate optics often have low efficiency, which makes implementation in laboratory microscopes difficult. We present a laboratory x-ray microscope based on a compound zone plate. The compound zone plate utilizes multiple diffraction orders to achieve high resolution while maintaining reasonable efficiency. We analyze the illumination conditions necessary for this type of optics in order to suppress stray light and demonstrate microscopic imaging resolving 25 nm features.

Keyword
resolution
Identifiers
urn:nbn:se:kth:diva-18788 (URN)000270114400031 ()2-s2.0-69549105762 (Scopus ID)
Note
QC 20100525Available from: 2010-08-05 Created: 2010-08-05 Last updated: 2017-12-12Bibliographically approved
8. Laboratory X-ray microscopy for high-resolution imaging of environmental colloid structure
Open this publication in new window or tab >>Laboratory X-ray microscopy for high-resolution imaging of environmental colloid structure
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2012 (English)In: Chemical Geology, ISSN 0009-2541, E-ISSN 1872-6836, Vol. 329, no SI, 26-31 p.Article in journal (Refereed) Published
Abstract [en]

Transmission X-ray microscopy is a uniquely suited technique for studies of environmental colloids since it allows imaging in aqueous media with high spatial resolution, presently down to the 20 nm range. Such nanoscale morphological description of these high-specific-surface-area compounds show promise for improved understanding of soils, sediments or groundwater aquifers. However, present high-quality X-ray microscopes are located at synchrotron radiation facilities resulting in limited applicability and accessibility for colloid scientists. Here we investigate the applicability of a laboratory-scale transmission X-ray microscope for studies of colloids of the environment. The microscope is based on a laser-plasma source in combination with multilayer and zone plate optics. Samples are held at atmospheric pressure in their natural wet state. We show images revealing the nano-scale morphology of the clay nontronite, soils such as chernozem and luvisol, and the mineral hematite, an iron oxide. Comparative studies of dried substances clearly show the need for imaging in the wet state. The image quality approaches that of synchrotron-based microscopes, albeit at longer exposure times. Stereo imaging is investigated as a means for giving 3D information with shorter exposure times than tomography requires. Finally the future development of the laboratory X-ray microscope is discussed, especially with regard to the reduction of exposure times.

Keyword
X-ray microscopy, Laser plasma, Diffractive optics, Laboratory scale, environmental colloids, soils
National Category
Other Physics Topics
Identifiers
urn:nbn:se:kth:diva-26952 (URN)10.1016/j.chemgeo.2011.07.012 (DOI)000310125000005 ()2-s2.0-84866508020 (Scopus ID)
Funder
Swedish Research Council
Note

QC 20121127

Available from: 2010-11-30 Created: 2010-11-30 Last updated: 2017-12-12Bibliographically approved
9. Laboratory Soft X-Ray Cryo Tomography
Open this publication in new window or tab >>Laboratory Soft X-Ray Cryo Tomography
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(English)Manuscript (preprint) (Other academic)
Abstract [en]

X-rays allow quantitative high-spatial-resolution three-dimensional (3D) imaging of intact unstained cells. Such 3D imaging is provided by soft x-ray lens-based methods (water-window cryo tomography) and hard x-ray lens-less methods (coherent diffraction imaging) are emerging. However, both methods rely on high-brightness synchrotron-radiation sources, which limit the accessibility of a wider scientific community. Here we show 3D water-window cryo tomography with a laboratory-source-based microscope arrangement. The system relies on a λ=2.48-nm liquid-jet laser-plasma source, normal- incidence multilayer condenser optics, 30-nm zone-plate optics, and a cryo sample chamber. We demonstrate imaging of intact unstained yeast, protozoan parasites and mammalian cells. 3D images show noise-limited features close to ~100 nm and intra-cellular structure is classified based on the local absorption coefficient. A comprehensive theoretical model of the tomographic imaging system allows optimization of system parameters and a quantitative estimate of the 3D imaging accuracy. The model includes issues such as non-geometric projections of the thick samples and stray light, and is applicable to laboratory as well as synchrotron-based x-ray microscopes. The model shows that laboratory x-ray cryo tomography will allow quantitative 3D imaging with ~30-nm (half-period) resolution over a full 5 µm object.

 

National Category
Physical Sciences
Identifiers
urn:nbn:se:kth:diva-29938 (URN)
Note
QC 20110217Available from: 2011-02-17 Created: 2011-02-17 Last updated: 2011-02-21Bibliographically approved

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