umu.sePublikationer
Ändra sökning
RefereraExporteraLänk till posten
Permanent länk

Direktlänk
Referera
Referensformat
  • apa
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Annat format
Fler format
Språk
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Annat språk
Fler språk
Utmatningsformat
  • html
  • text
  • asciidoc
  • rtf
Refining particle positions using circular symmetry
Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysik.
Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysik.
Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysik.
Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap.
Visa övriga samt affilieringar
2017 (Engelska)Ingår i: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 12, nr 4, artikel-id e0175015Artikel i tidskrift (Refereegranskat) Published
Abstract [en]

Particle and object tracking is gaining attention in industrial applications and is commonly applied in: colloidal, biophysical, ecological, and micro-fluidic research. Reliable tracking information is heavily dependent on the system under study and algorithms that correctly determine particle position between images. However, in a real environmental context with the presence of noise including particular or dissolved matter in water, and low and fluctuating light conditions, many algorithms fail to obtain reliable information. We propose a new algorithm, the Circular Symmetry algorithm (C-Sym), for detecting the position of a circular particle with high accuracy and precision in noisy conditions. The algorithm takes advantage of the spatial symmetry of the particle allowing for subpixel accuracy. We compare the proposed algorithm with four different methods using both synthetic and experimental datasets. The results show that C-Sym is the most accurate and precise algorithm when tracking micro-particles in all tested conditions and it has the potential for use in applications including tracking biota in their environment.

Ort, förlag, år, upplaga, sidor
2017. Vol. 12, nr 4, artikel-id e0175015
Nationell ämneskategori
Datorseende och robotik (autonoma system)
Identifikatorer
URN: urn:nbn:se:umu:diva-135283DOI: 10.1371/journal.pone.0175015ISI: 000399955200030OAI: oai:DiVA.org:umu-135283DiVA, id: diva2:1098736
Forskningsfinansiär
Vetenskapsrådet, 2013-5379Tillgänglig från: 2017-05-26 Skapad: 2017-05-26 Senast uppdaterad: 2018-08-15Bibliografiskt granskad
Ingår i avhandling
1. Digital holography and image processing methods for applications in biophysics
Öppna denna publikation i ny flik eller fönster >>Digital holography and image processing methods for applications in biophysics
2018 (Engelska)Doktorsavhandling, sammanläggning (Övrigt vetenskapligt)
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.

Ort, förlag, år, upplaga, sidor
Umeå: Umeå University, 2018. s. 59
Nyckelord
Digital holographic microscopy, image processing, image reconstruction, bacterial adhesion, cell morphology, algorithm development, software design, quantitative measurement, microfluidics, multidisciplinary research
Nationell ämneskategori
Biofysik Datorseende och robotik (autonoma system)
Forskningsämne
signalbehandling; teknisk fysik med inriktningen mikrosystemteknik
Identifikatorer
urn:nbn:se:umu:diva-150687 (URN)978-91-7601-915-3 (ISBN)
Disputation
2018-09-07, Naturvetarhuset, N430, Umeå, 13:15 (Engelska)
Opponent
Handledare
Tillgänglig från: 2018-08-17 Skapad: 2018-08-15 Senast uppdaterad: 2018-08-16Bibliografiskt granskad

Open Access i DiVA

fulltext(6987 kB)215 nedladdningar
Filinformation
Filnamn FULLTEXT01.pdfFilstorlek 6987 kBChecksumma SHA-512
92fda2525714a659978dd9503f3aaf47e6ba0b4de13522ae0c274b7faf39dc53e0dc9b1035b032d442f951edd8beaf125d0514ccc98fd1e34b77b87f66b5332b
Typ fulltextMimetyp application/pdf

Övriga länkar

Förlagets fulltext

Personposter BETA

Rodriguez, AlvaroZhang, HanqingWiklund, KristerBrodin, TomasKlaminder, JonatanAndersson, PatrikAndersson, Magnus

Sök vidare i DiVA

Av författaren/redaktören
Rodriguez, AlvaroZhang, HanqingWiklund, KristerBrodin, TomasKlaminder, JonatanAndersson, PatrikAndersson, Magnus
Av organisationen
Institutionen för fysikInstitutionen för ekologi, miljö och geovetenskapKemiska institutionen
I samma tidskrift
PLoS ONE
Datorseende och robotik (autonoma system)

Sök vidare utanför DiVA

GoogleGoogle Scholar
Totalt: 215 nedladdningar
Antalet nedladdningar är summan av nedladdningar för alla fulltexter. Det kan inkludera t.ex tidigare versioner som nu inte längre är tillgängliga.

doi
urn-nbn

Altmetricpoäng

doi
urn-nbn
Totalt: 938 träffar
RefereraExporteraLänk till posten
Permanent länk

Direktlänk
Referera
Referensformat
  • apa
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Annat format
Fler format
Språk
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Annat språk
Fler språk
Utmatningsformat
  • html
  • text
  • asciidoc
  • rtf