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Publications (10 of 11) Show all publications
Selin, M. (2016). 3D X-ray microscopy: image formation, tomography and instrumentation. (Doctoral dissertation). Stockholm: KTH Royal Institute of Technology
Open this publication in new window or tab >>3D X-ray microscopy: image formation, tomography and instrumentation
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. p. viii, 75
Series
TRITA-FYS, ISSN 0280-316X ; 2016:15
Keywords
X-ray microscopy, image formation theory, partial coherence in imaging, wave propagation, tomography, instrumentation
National Category
Physical Sciences
Research subject
Physics
Identifiers
urn:nbn:se:kth:diva-184095 (URN)978-91-7595-914-6 (ISBN)
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
Selin, M. (2016). Instrumentation in the Stockholm XRM lab. KTH Royal Institute of Technology
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. p. 6
Keywords
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
Fogelqvist, E., Kördel, M., Selin, M. & Hertz, H. M. (2015). Stability of liquid-nitrogen-jet laser-plasma targets. Journal of Applied Physics, 118(17), Article ID 174902.
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, article id 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
Keywords
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
Selin, M., Fogelqvist, E., Werner, S. & Hertz, H. M. (2015). Tomographic reconstruction in soft x-ray microscopy using focus-stack back-projection. Optics Letters, 40(10), 2201-2204
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, p. 2201-2204Article 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
Keywords
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
Selin, M., Fogelqvist, E., Holmberg, A., Guttmann, P., Vogt, U. & Hertz, H. M. (2014). 3D simulation of the image formation in soft x-ray microscopes. Optics Express, 22(25), 30756-30768
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, p. 30756-30768Article 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
Keywords
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: 2020-01-30Bibliographically approved
Fogelqvist, E., Selin, M., Martz, D. H., Christakou, A. E. & Hertz, H. M. (2013). The Stockholm laboratory cryo x-ray microscope: towards cell-cell interaction studies. In: 11th International Conference On X-Ray Microscopy (XRM2012): . Paper presented at 11th International Conference on X-ray Microscopy (XRM), AUG 05-10, 2012, Shanghai, China (pp. 012054). Institute of Physics (IOP)
Open this publication in new window or tab >>The Stockholm laboratory cryo x-ray microscope: towards cell-cell interaction studies
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2013 (English)In: 11th International Conference On X-Ray Microscopy (XRM2012), Institute of Physics (IOP), 2013, p. 012054-Conference paper, Published paper (Refereed)
Abstract [en]

We describe recent improvements in the Stockholm laboratory x-ray microscope and the first experiments aiming towards studies of cell-cell interaction. The shorter exposure time due to a higher brightness laser-plasma source will become of large importance for tomography while the reproducible cryo preparation of few-cell samples is essential for the interaction studies.

Place, publisher, year, edition, pages
Institute of Physics (IOP), 2013
Series
Journal of Physics Conference Series, ISSN 1742-6588 ; 463
National Category
Other Physics Topics
Identifiers
urn:nbn:se:kth:diva-139243 (URN)10.1088/1742-6596/463/1/012054 (DOI)000327949000054 ()2-s2.0-84891288729 (Scopus ID)
Conference
11th International Conference on X-ray Microscopy (XRM), AUG 05-10, 2012, Shanghai, China
Note

QC 20140113

Available from: 2014-01-13 Created: 2014-01-08 Last updated: 2017-05-04Bibliographically approved
Legall, H., Blobel, G., Stiel, H., Sandner, W., Seim, C., Takman, P., . . . Diete, W. (2012). Compact X-ray microscope for the water window based on a high brightness laser plasma source. Optics Express, 20(16), 18362-18369
Open this publication in new window or tab >>Compact X-ray microscope for the water window based on a high brightness laser plasma source
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2012 (English)In: Optics Express, ISSN 1094-4087, E-ISSN 1094-4087, Vol. 20, no 16, p. 18362-18369Article in journal (Refereed) Published
Abstract [en]

We present a laser plasma based x-ray microscope for the water window employing a high-average power laser system for plasma generation. At 90 W laser power a brightness of 7.4 x 10(11) photons/(s x sr x mu m(2)) was measured for the nitrogen Ly alpha line emission at 2.478 nm. Using a multilayer condenser mirror with 0.3 % reflectivity 10(6) photons/(mu m(2) x s) were obtained in the object plane. Microscopy performed at a laser power of 60 W resolves 40 nm lines with an exposure time of 60 s. The exposure time can be further reduced to 20 s by the use of new multilayer condenser optics and operating the laser at its full power of 130 W.

Keywords
Spatial-Resolution, Contrast
National Category
Other Physics Topics
Identifiers
urn:nbn:se:kth:diva-101568 (URN)10.1364/OE.20.018362 (DOI)000307356300107 ()2-s2.0-84864590889 (Scopus ID)
Note

QC 20120831

Available from: 2012-08-31 Created: 2012-08-30 Last updated: 2017-12-07Bibliographically approved
Martz, D. H., Selin, M., von Hofsten, O., Fogelqvist, E., Holmberg, A., Vogt, U., . . . Hertz, H. M. (2012). High average brightness water window source for short-exposure cryomicroscopy. Optics Letters, 37(21), 4425-4427
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, p. 4425-4427Article 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
Keywords
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: 2020-01-30Bibliographically approved
Hertz, H., von Hofsten, O., Bertilson, M., Vogt, U., Holmberg, A., Reinspach, J. A., . . . Svärd, S. (2012). Laboratory cryo soft X-ray microscopy. Journal of Structural Biology, 177(2), 267-272
Open this publication in new window or tab >>Laboratory cryo soft X-ray microscopy
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2012 (English)In: Journal of Structural Biology, ISSN 1047-8477, E-ISSN 1095-8657, Vol. 177, no 2, p. 267-272Article in journal (Refereed) Published
Abstract [en]

Lens-based water-window X-ray microscopy allows two- and three-dimensional (2D and 3D) imaging of intact unstained cells in their near-native state with unprecedented contrast and resolution. Cryofixation is essential to avoid radiation damage to the sample. Present cryo X-ray microscopes rely on synchrotron radiation sources, thereby limiting the accessibility for a wider community of biologists. In the present paper we demonstrate water-window cryo X-ray microscopy with a laboratory-source-based arrangement. The microscope relies on a lambda = 2.48-nm liquid-jet high-brightness laser-plasma source, normal-incidence multilayer condenser optics, 30-nm zone-plate optics, and a cryo sample chamber. We demonstrate 2D imaging of test patterns, and intact unstained yeast, protozoan parasites and mammalian cells. Overview 3D information is obtained by stereo imaging while complete 3D microscopy is provided by full tomographic reconstruction. The laboratory microscope image quality approaches that of the synchrotron microscopes, but with longer exposure times. The experimental image quality is analyzed from a numerical wave-propagation model of the imaging system and a path to reach synchrotron-like exposure times in laboratory microscopy is outlined.

Keywords
X-ray microscopy, Cryo fixation, Laboratory, Parasites
National Category
Other Physics Topics
Identifiers
urn:nbn:se:kth:diva-73759 (URN)10.1016/j.jsb.2011.11.015 (DOI)000300755400011 ()22119891 (PubMedID)2-s2.0-84857033171 (Scopus ID)
Funder
Swedish Research Council
Note
QC 20120326Available from: 2012-02-02 Created: 2012-02-02 Last updated: 2017-12-08Bibliographically approved
Selin, M., Bertilson, M., Nilsson, D., von Hofsten, O., Hertz, H. & Vogt, U. (2011). DiffractX: A Simulation Toolbox for Diffractive X-ray Optics. In: McNulty, I; Eyberger, C; Lai, B (Ed.), 10TH INTERNATIONAL CONFERENCE ON X-RAY MICROSCOPY: . Paper presented at 10th International Conference on X-ray Microscopy. Univ Chicago, Chicago, IL. AUG 15-20, 2010 (pp. 341-344). American Institute of Physics (AIP), 1365
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, p. 341-344Conference 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
Keywords
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
Organisations
Identifiers
ORCID iD: ORCID iD iconorcid.org/0000-0001-8604-735X

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