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3D simulation of the image formation in soft x-ray microscopes
KTH, School of Engineering Sciences (SCI), Applied Physics, Biomedical and X-ray Physics.ORCID iD: 0000-0001-8604-735X
KTH, School of Engineering Sciences (SCI), Applied Physics, Biomedical and X-ray Physics.
KTH, School of Engineering Sciences (SCI), Applied Physics, Biomedical and X-ray Physics.ORCID iD: 0000-0003-2745-6289
Show others and affiliations
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. Vol. 22, no 25, 30756-30768 p.
Keyword [en]
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: urn:nbn:se:kth:diva-160068DOI: 10.1364/OE.22.030756ISI: 000346368800068Scopus ID: 2-s2.0-84919663855OAI: oai:DiVA.org:kth-160068DiVA: diva2:791244
Funder
Swedish Research Council
Note

QC 20150227

QC 20160324

Available from: 2015-02-27 Created: 2015-02-13 Last updated: 2017-12-04Bibliographically approved
In thesis
1. 3D X-ray microscopy: image formation, tomography and instrumentation
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. viii, 75 p.
Series
TRITA-FYS, ISSN 0280-316X ; 2016:15
Keyword
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
2. Laboratory Soft X-Ray Cryo Microscopy: Source, System and Bio Applications
Open this publication in new window or tab >>Laboratory Soft X-Ray Cryo Microscopy: Source, System and Bio Applications
2017 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Soft x-ray microscopes routinely perform high-resolution 3D imaging of biological cells in their near-native environment with short exposure times at synchrotron radiation facilities. Some laboratory-sized microscopes are aiming to make this imaging technique more accessible to a wider scientific community. However, these systems have been hampered by source instabilities hindering routine imaging of biological samples with short exposure times.

This Thesis presents work performed on the Stockholm laboratory x-ray microscope. A novel heat control system has been implemented, improving the stability of the laser-produced plasma source. In combination with recent upgrades to the imaging system and an improved cryofixation method, the microscope now has the capability to routinely produce images with 10-second exposure time of cryofixed biological samples. This has allowed for tomographic imaging of cell autophagy and cell-cell interactions. Furthermore, a numerical 3D image formation model is presented as well as a novel reconstruction approach dealing with the limited depth of focus in x-ray microscopes.

Place, publisher, year, edition, pages
Stockholm: KTH Royal Institute of Technology, 2017. 63 p.
Series
TRITA-FYS, ISSN 0280-316X ; 2017:21
Keyword
X-ray microscopy, X-ray optics, Instrumentation, Laser plasma, Cryofixation, Tomography, Tomographic reconstruction, Autophagy, Immune synapse, Physics
National Category
Physical Sciences
Research subject
Physics
Identifiers
urn:nbn:se:kth:diva-206428 (URN)978-91-7729-369-9 (ISBN)
Public defence
2017-06-02, FD5, Roslagstullsbacken 21, Stockholm, 13:00 (English)
Opponent
Supervisors
Funder
Swedish Research CouncilKnut and Alice Wallenberg Foundation
Note

QC 20170505

Available from: 2017-05-05 Created: 2017-05-04 Last updated: 2017-05-05Bibliographically approved

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Selin, MårtenHolmberg, AndersVogt, UlrichHertz, Hans M.

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