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3D X-ray microscopy: image formation, tomography and instrumentation
KTH, School of Engineering Sciences (SCI), Applied Physics, Biomedical and X-ray Physics. (Biomedical and X-ray Physics)ORCID iD: 0000-0001-8604-735X
2016 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Tomography in soft X-ray microscopy is an emerging technique for obtaining quantitative 3D structural information about cells. One of its strengths, compared with other techniques, is that it can image intact cells in their near-native state at a few 10 nm’s resolution, without staining. However, the methods for reconstructing 3D-data rely on algorithms that assume projection data, which the images are generally not due to the imaging systems’ limited depth of focus. To bring out the full potential of tomography in soft X-ray microscopy an improved understanding of the image formation is desired.

This Thesis reviews zone plate-based X-ray microscopy for biological imaging and the theory necessary for a numerical implementation of a 3D image formation model. Furthermore, a novel reconstruction approach is proposed that improves the overall resolution in a reconstruction of a tomographically imaged object. This is demonstrated by simulations and experiments. Finally, this Thesis covers work on the Stockholm X-ray microscope, including an upgrade of the X-ray source yielding unprecedented brightness for a compact system. With this upgrade it was possible to do high-quality imaging of cells in their near-native state with only 10 second exposures.

Abstract [sv]

Tomografi i mjukröntgenmikroskopi är en ny teknik för att få ut kvantitativ strukturell 3D information om celler. Dess styrka jämfört med andra tekniker är att den kan avbilda intakta celler i deras nära naturliga tillstånd med ett par 10 nm upplösning, utan omfattande preparering. Dock är metoderna för att rekonstruera 3D-data beroende av algoritmer som antar projektionsdata, vilket bilderna i allmänhet inte är på grund av avbildningsystemens begränsade skärpedjup. För att få ut den fulla potentialen av tomografi i röntgenmikroskopi behövs en ökad förståelse för avbildningsprocessen.

Denna avhandling behandlar zonplatte-baserad röntgenmikroskopi för biologisk avbildning och den nödvändiga teorin för en numerisk implementering av en avbildningsmodell i 3D. En ny rekonstruktionsmetod föreslås som förbättrar upplösningen i rekonstruktionen för ett tomografiskt avbildat objekt. Detta visas i simuleringar och experiment. Slutligen omfattar denna avhandling arbete på Stockholms mjukröntgenmikroskop, inklusive en uppgradering av röntgenkällan som ger oöverträffad ljusstyrka för ett kompakt system. Denna uppgradering möjliggör högkvalitativ avbildning av celler i deras nästan naturliga tillstånd med endast 10 sekunders exponering.

Place, publisher, year, edition, pages
Stockholm: KTH Royal Institute of Technology, 2016. , viii, 75 p.
Series
TRITA-FYS, ISSN 0280-316X ; 2016:15
Keyword [en]
X-ray microscopy, image formation theory, partial coherence in imaging, wave propagation, tomography, instrumentation
National Category
Physical Sciences
Research subject
Physics
Identifiers
URN: urn:nbn:se:kth:diva-184095ISBN: 978-91-7595-914-6 (print)OAI: oai:DiVA.org:kth-184095DiVA: diva2:914483
Public defence
2016-04-22, FD5, Albanova universitetscentrum, Roslagstullsbacken 21, Stockholm, 13:00 (English)
Opponent
Supervisors
Funder
Swedish Research CouncilKnut and Alice Wallenberg Foundation
Note

QC 20160324

Available from: 2016-03-24 Created: 2016-03-23 Last updated: 2016-03-24Bibliographically approved
List of papers
1. 3D simulation of the image formation in soft x-ray microscopes
Open this publication in new window or tab >>3D simulation of the image formation in soft x-ray microscopes
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2014 (English)In: Optics Express, ISSN 1094-4087, E-ISSN 1094-4087, Vol. 22, no 25, 30756-30768 p.Article in journal (Refereed) Published
Abstract [en]

In water-window soft x-ray microscopy the studied object is typically larger than the depth of focus and the sample illumination is often partially coherent. This blurs out-of-focus features and may introduce considerable fringing. Understanding the influence of these phenomena on the image formation is therefore important when interpreting experimental data. Here we present a wave-propagation model operating in 3D for simulating the image formation of thick objects in partially coherent soft x-ray microscopes. The model is compared with present simulation methods as well as with experiments. The results show that our model predicts the image formation of transmission soft x-ray microscopes more accurately than previous models.

Place, publisher, year, edition, pages
Optical Society of America, 2014
Keyword
Wave propagation, X ray microscopes, 3D simulations, Depth of focus, Out-of-focus, Partially coherent, Propagation modeling, Soft X-ray, Soft x-ray microscopy
National Category
Atom and Molecular Physics and Optics
Identifiers
urn:nbn:se:kth:diva-160068 (URN)10.1364/OE.22.030756 (DOI)000346368800068 ()2-s2.0-84919663855 (Scopus ID)
Funder
Swedish Research Council
Note

QC 20150227

QC 20160324

Available from: 2015-02-27 Created: 2015-02-13 Last updated: 2017-12-04Bibliographically approved
2. Tomographic reconstruction in soft x-ray microscopy using focus-stack back-projection
Open this publication in new window or tab >>Tomographic reconstruction in soft x-ray microscopy using focus-stack back-projection
2015 (English)In: Optics Letters, ISSN 0146-9592, E-ISSN 1539-4794, Vol. 40, no 10, 2201-2204 p.Article in journal (Refereed) Published
Abstract [en]

Tomographic reconstruction in soft x-ray microscopy is a powerful technique for obtaining high-resolution 3D images of biological samples. However, the depth of focus of such zone-plate-based microscopes is typically shorter than the thickness of many relevant biological objects, challenging the validity of the projection assumption used in conventional reconstruction algorithms. In order to make full use of the soft x-ray microscopes' high resolution, the tomographic reconstruction needs to take the depth of focus into account. Here we present a method to achieve high resolution in the full sample when the depth of focus is short compared to the sample thickness. The method relies on the back-projection of focus-stacked image data from x-ray microscopy. We demonstrate the method on theoretical and experimental data.

Place, publisher, year, edition, pages
Optical Society of America, 2015
Keyword
Image-Formation, Beamline
National Category
Other Physics Topics
Identifiers
urn:nbn:se:kth:diva-169265 (URN)10.1364/OL.40.002201 (DOI)000354708300012 ()2-s2.0-84981357563 (Scopus ID)
Funder
Swedish Research Council
Note

QC 20150615

Available from: 2015-06-15 Created: 2015-06-12 Last updated: 2017-12-04Bibliographically approved
3. High average brightness water window source for short-exposure cryomicroscopy
Open this publication in new window or tab >>High average brightness water window source for short-exposure cryomicroscopy
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2012 (English)In: Optics Letters, ISSN 0146-9592, E-ISSN 1539-4794, Vol. 37, no 21, 4425-4427 p.Article in journal (Refereed) Published
Abstract [en]

Laboratory water window cryomicroscopy has recently demonstrated similar image quality as synchrotron-based microscopy but still with much longer exposure times, prohibiting the spread to a wider scientific community. Here we demonstrate high-resolution laboratory water window imaging of cryofrozen cells with 10 s range exposure times. The major improvement is the operation of a lambda = 2.48 nm, 2 kHz liquid nitrogen jet laser plasma source with high spatial and temporal stability at high average brightness >1.5 x 10(12) ph/(s x sr x mu m(2) x line), i.e., close to that of early synchrotrons. Thus, this source enables not only biological x-ray microscopy in the home laboratory but potentially other applications previously only accessible at synchrotron facilities.

Place, publisher, year, edition, pages
Optical Society of America, 2012
Keyword
X-Ray Microscopy
National Category
Other Physics Topics
Identifiers
urn:nbn:se:kth:diva-107087 (URN)10.1364/OL.37.004425 (DOI)000310577700024 ()2-s2.0-84868308552 (Scopus ID)
Funder
Swedish Research CouncilSwedish Foundation for Strategic Research
Note

QC 20121207

Available from: 2012-12-07 Created: 2012-12-06 Last updated: 2017-12-07Bibliographically approved
4. DiffractX: A Simulation Toolbox for Diffractive X-ray Optics
Open this publication in new window or tab >>DiffractX: A Simulation Toolbox for Diffractive X-ray Optics
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2011 (English)In: 10TH INTERNATIONAL CONFERENCE ON X-RAY MICROSCOPY / [ed] McNulty, I; Eyberger, C; Lai, B, American Institute of Physics (AIP), 2011, Vol. 1365, 341-344 p.Conference paper, Published paper (Refereed)
Abstract [en]

X-ray wavefront propagation is a powerful technique when simulating the performance of x-ray optical components. Using various numerical methods, interesting parameters such as focusing capability and efficiency can be investigated. Here we present the toolbox DiffractX, implemented in MATLAB. It contains many different wave propagation methods for the simulation of diffractive x-ray optics, including Fresnel propagation, the finite difference method (FDM), the thin object approximation, the rigorous coupled wave theory (RCWT), and the finite element method (FEM). All tools are accessed through a graphical interface, making the design of simulations fast and intuitive, even for users with little or no programming experience. The tools have been utilized to characterize realistic as well as idealized optical components. This will aid further developments of diffractive x-ray optics.

Place, publisher, year, edition, pages
American Institute of Physics (AIP), 2011
Series
AIP Conference Proceedings, ISSN 0094-243X ; 1365
Keyword
wavefront-reconstruction imaging; X-ray diffraction; wave propagation; simulation
National Category
Atom and Molecular Physics and Optics
Identifiers
urn:nbn:se:kth:diva-73363 (URN)10.1063/1.3625374 (DOI)000298672400081 ()2-s2.0-80053310440 (Scopus ID)
Conference
10th International Conference on X-ray Microscopy. Univ Chicago, Chicago, IL. AUG 15-20, 2010
Note

QC 20120202

Available from: 2012-02-02 Created: 2012-02-02 Last updated: 2016-03-24Bibliographically approved
5. Stability of liquid-nitrogen-jet laser-plasma targets
Open this publication in new window or tab >>Stability of liquid-nitrogen-jet laser-plasma targets
2015 (English)In: Journal of Applied Physics, ISSN 0021-8979, E-ISSN 1089-7550, Vol. 118, no 17, 174902Article in journal (Refereed) Published
Abstract [en]

Microscopic jets of cryogenic substances such as liquid nitrogen are important regenerative high-density targets for high-repetition rate, high-brightness laser-plasma soft x-ray sources. When operated in vacuum such liquid jets exhibit several non-classical instabilities that negatively influence the x-ray source's spatial and temporal stability, yield, and brightness, parameters that all are important for applications such as water-window microscopy. In the present paper, we investigate liquid-nitrogen jets with a flash-illumination imaging system that allows for a quantitative stability analysis with high spatial and temporal resolution. Direct and indirect consequences of evaporation are identified as the key reasons for the observed instabilities. Operating the jets in an approximately 100 mbar ambient atmosphere counteracts the effects of evaporation and produces highly stable liquid nitrogen jets. For operation in vacuum, which is necessary for the laser plasmas, we improve the stability by introducing an external radiative heating element. The method significantly extends the distance from the nozzle that can be used for liquid-jet laser plasmas, which is of importance for high-average-power applications. Finally, we show that laser-plasma operation with the heating-element-stabilized jet shows improved short-term and long-term temporal stability in its water-window x-ray emission.

Place, publisher, year, edition, pages
American Institute of Physics (AIP), 2015
Keyword
Electric heating elements, Electron sources, Evaporation, Fighter aircraft, Image resolution, Jets, Laser beams, Laser produced plasmas, Liquid nitrogen, Liquids, Luminance, Nitrogen, Nitrogen plasma, Plasma stability, Stability, Vacuum applications, X ray apparatus, X ray optics, Ambient atmosphere, High average power, High brightness lasers, High repetition rate, Quantitative stability analysis, Radiative heating, Spatial and temporal resolutions, Temporal stability, Plasma interactions
National Category
Physical Sciences
Identifiers
urn:nbn:se:kth:diva-181201 (URN)10.1063/1.4935143 (DOI)000364584200024 ()2-s2.0-84946811961 (Scopus ID)
Funder
Swedish Research Council
Note

QC 20160205

Available from: 2016-02-05 Created: 2016-01-29 Last updated: 2017-11-30Bibliographically approved
6. Instrumentation in the Stockholm XRM lab
Open this publication in new window or tab >>Instrumentation in the Stockholm XRM lab
2016 (English)Report (Other academic)
Abstract [en]

A software platform is presented that brings the instruments of the Stockholm X-ray microscope (XRM) together. The code is designed with flexibility and extensibility in mind. Its features are reported and promise to make the microscope operation more comfortable to the user.

Place, publisher, year, edition, pages
KTH Royal Institute of Technology, 2016. 6 p.
Keyword
Instrumentation, LabVIEW, X-ray microscope
National Category
Other Physics Topics
Research subject
Physics
Identifiers
urn:nbn:se:kth:diva-184094 (URN)
Note

QC 20160323

Available from: 2016-03-23 Created: 2016-03-23 Last updated: 2016-03-24Bibliographically approved

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  • en-US
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Output format
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