Fiber finding algorithm using stepwise tracing to identify biopolymer fibers in noisy 3D images
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Fiber finding algorithm using stepwise tracing to identify biopolymer fibers in noisy 3D images. / Rossen, Ninna Struck; Kyrsting, Anders; Giaccia, Amato J.; Erler, Janine Terra; Oddershede, Lene Broeng.
I: Biophysical Journal, Bind 120, Nr. 18, 2021, s. 3860-3868.Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › fagfællebedømt
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TY - JOUR
T1 - Fiber finding algorithm using stepwise tracing to identify biopolymer fibers in noisy 3D images
AU - Rossen, Ninna Struck
AU - Kyrsting, Anders
AU - Giaccia, Amato J.
AU - Erler, Janine Terra
AU - Oddershede, Lene Broeng
PY - 2021
Y1 - 2021
N2 - We present a novel fiber finding algorithm (FFA) that will permit researchers to detect and return traces of individual biopolymers. Determining the biophysical properties and structural cues of biopolymers can permit researchers to assess the progression and severity of disease. Confocal microscopy images are a useful method for observing biopolymer structures in three dimensions, but their utility for identifying individual biopolymers is impaired by noise inherent in the acquisition process, including convolution from the point spread function (PSF). The new, iterative FFA we present here 1) measures a microscope's PSF and uses it as a metric for identifying fibers against the background; 2) traces each fiber within a cone angle; and 3) blots out the identified trace before identifying another fiber. Blotting out the identified traces in each iteration allows the FFA to detect and return traces of single fibers accurately and efficiently-even within fiber bundles. We used the FFA to trace unlabeled collagen type I fibers-a biopolymer used to mimic the extracellular matrix in in vitro cancer assays-imaged by confocal reflectance microscopy in three dimensions, enabling quantification of fiber contour length, persistence length, and three-dimensional (3D) mesh size. Based on 3D confocal reflectance microscopy images and the PSF, we traced and measured the fibers to confirm that colder gelation temperatures increased fiber contour length, persistence length, and 3D mesh size-thereby demonstrating the FFA's use in quantifying biopolymers' structural and physical cues from noisy microscope images.
AB - We present a novel fiber finding algorithm (FFA) that will permit researchers to detect and return traces of individual biopolymers. Determining the biophysical properties and structural cues of biopolymers can permit researchers to assess the progression and severity of disease. Confocal microscopy images are a useful method for observing biopolymer structures in three dimensions, but their utility for identifying individual biopolymers is impaired by noise inherent in the acquisition process, including convolution from the point spread function (PSF). The new, iterative FFA we present here 1) measures a microscope's PSF and uses it as a metric for identifying fibers against the background; 2) traces each fiber within a cone angle; and 3) blots out the identified trace before identifying another fiber. Blotting out the identified traces in each iteration allows the FFA to detect and return traces of single fibers accurately and efficiently-even within fiber bundles. We used the FFA to trace unlabeled collagen type I fibers-a biopolymer used to mimic the extracellular matrix in in vitro cancer assays-imaged by confocal reflectance microscopy in three dimensions, enabling quantification of fiber contour length, persistence length, and three-dimensional (3D) mesh size. Based on 3D confocal reflectance microscopy images and the PSF, we traced and measured the fibers to confirm that colder gelation temperatures increased fiber contour length, persistence length, and 3D mesh size-thereby demonstrating the FFA's use in quantifying biopolymers' structural and physical cues from noisy microscope images.
KW - EXTRACELLULAR-MATRIX STIFFNESS
KW - PORE-SIZE
KW - FILAMENTOUS NETWORKS
KW - CONFOCAL MICROSCOPY
KW - COLLAGEN GELS
KW - RHEOLOGY
U2 - 10.1016/j.bpj.2021.08.017
DO - 10.1016/j.bpj.2021.08.017
M3 - Journal article
C2 - 34411578
VL - 120
SP - 3860
EP - 3868
JO - Biophysical Society. Annual Meeting. Abstracts
JF - Biophysical Society. Annual Meeting. Abstracts
SN - 0523-6800
IS - 18
ER -
ID: 282478187