Change search
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf
Object plane detection and phase retrieval from single-shot holograms using multi-wavelength in-line holography
Umeå University, Faculty of Science and Technology, Department of Physics. (Biophysics & Biophotonics group)
Umeå University, Faculty of Science and Technology, Department of Physics.
Umeå University, Faculty of Science and Technology, Department of Physics.
Umeå University, Faculty of Science and Technology, Department of Physics. Umeå University, Faculty of Medicine, Umeå Centre for Microbial Research (UCMR).
(English)Manuscript (preprint) (Other academic)
Abstract [en]

Phase retrieval and the twin-image problem in digital in-line holographic microscopy can be resolvedby iterative reconstruction routines. However, recovering the phase properties of an object in a hologramneeds an object plane to be chosen correctly for reconstruction. In this work, we present a novelmulti-wavelength Gerchberg-Saxton algorithm to determine the object plane using single-shot hologramsrecorded with multiple wavelengths in an in-line holographic microscope. For micro-sized objects, weverify the object positioning capabilities of the method for various shapes and derive the phase informationusing synthetic and experimental data. Experimentally, we built a compact digital in-line holographicmicroscopy setup around a standard optical microscope with a regular RGB-CCD camera andacquire holograms of micro-spheres, E. coli and red blood cells, that are illuminated using three lasersoperating at 491nm, 532nm and 633nm, respectively. We demonstrate that our method provides accurateobject plane detection and phase retrieval under noisy conditions, e.g., using low-contrast hologramswithout background normalization. This method allows for automatic positioning and phase retrievalsuitable for holographic particle velocimetry, and object tracking in biophysical or colloidal research.

Keywords [en]
digital holographic microscopy, image reconstruction, multiple wavelengths
National Category
Biophysics
Research subject
Physics
Identifiers
URN: urn:nbn:se:umu:diva-150685OAI: oai:DiVA.org:umu-150685DiVA, id: diva2:1239192
Available from: 2018-08-15 Created: 2018-08-15 Last updated: 2018-08-15
In thesis
1. Digital holography and image processing methods for applications in biophysics
Open this publication in new window or tab >>Digital holography and image processing methods for applications in biophysics
2018 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Understanding dynamic mechanisms, morphology and behavior of bacteria are important to develop new therapeutics to cure diseases. For example, bacterial adhesion mechanisms are prerequisites for initiation of infections and for several bacterial strains this adhesion process is mediated by adhesive surface organelles, also known as fimbriae. Escherichia coli (E. coli) is a bacterium expressing fimbriae of which pathogenic strains can cause severe diseases in fluidic environments such as the urinary tract and intestine. To better understand how E. coli cells attach and remain attached to surfaces when exposed to a fluid flow using their fimbriae, experiments using microfluidic channels are important; and to assess quantitative information of the adhesion process and cellular information of morphology, location and orientation, the imaging capability of the experimental technique is vital.

In-line digital holographic microscopy (DHM) is a powerful imaging technique that can be realized around a conventional light microscope. It is a non-invasive technique without the need of staining or sectioning of the sample to be observed in vitro. DHM provides holograms containing three-dimensional (3D) intensity and phase information of cells under study with high temporal and spatial resolution. By applying image processing algorithms to the holograms, quantitative measurements can provide information of position, shape, orientation, optical thickness of the cell, as well as dynamic cell properties such as speed, growing rate, etc.

In this thesis, we aim to improve the DHM technique and develop image processing methods to track and assess cellular properties in microfluidic channels to shed light on bacterial adhesion and cell morphology. To achieve this, we implemented a DHM technique and developed image processing algorithms to provide for a robust and quantitative analysis of holograms. We improved the cell detection accuracy and efficiency in DHM holograms by developing an algorithm for detection of cell diffraction patterns. To improve the 3D detection accuracy using in-line digital holography, we developed a novel iterative algorithm that use multiple-wavelengths. We verified our algorithms using synthetic, colloidal and cell data and applied the algorithms for detecting, tracking and analysis. We demonstrated the performance when tracking bacteria with sub-micrometer accuracy and kHz temporal resolution, as well as how DHM can be used to profile a microfluidic flow using a large number of colloidal particles. We also demonstrated how the results of cell shape analysis based on image segmentation can be used to estimate the hydrodynamic force on tethered capsule-shaped cells in micro-fluidic flows near a surface.

Place, publisher, year, edition, pages
Umeå: Umeå University, 2018. p. 59
Keywords
Digital holographic microscopy, image processing, image reconstruction, bacterial adhesion, cell morphology, algorithm development, software design, quantitative measurement, microfluidics, multidisciplinary research
National Category
Biophysics Computer Vision and Robotics (Autonomous Systems)
Research subject
Signal Processing; Technical Physics
Identifiers
urn:nbn:se:umu:diva-150687 (URN)978-91-7601-915-3 (ISBN)
Public defence
2018-09-07, Naturvetarhuset, N430, Umeå, 13:15 (English)
Opponent
Supervisors
Available from: 2018-08-17 Created: 2018-08-15 Last updated: 2018-08-16Bibliographically approved

Open Access in DiVA

No full text in DiVA

Search in DiVA

By author/editor
Zhang, HanqingStangner, TimWiklund, KristerAndersson, Magnus
By organisation
Department of PhysicsUmeå Centre for Microbial Research (UCMR)
Biophysics

Search outside of DiVA

GoogleGoogle Scholar

urn-nbn

Altmetric score

urn-nbn
Total: 258 hits
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf