PMID- 34411578
OWN - NLM
STAT- MEDLINE
DCOM- 20211028
LR  - 20220922
IS  - 1542-0086 (Electronic)
IS  - 0006-3495 (Print)
IS  - 0006-3495 (Linking)
VI  - 120
IP  - 18
DP  - 2021 Sep 21
TI  - Fiber finding algorithm using stepwise tracing to identify biopolymer fibers in 
      noisy 3D images.
PG  - 3860-3868
LID - S0006-3495(21)00683-4 [pii]
LID - 10.1016/j.bpj.2021.08.017 [doi]
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.
CI  - Copyright (c) 2021. Published by Elsevier Inc.
FAU - Rossen, Ninna Struck
AU  - Rossen NS
AD  - Biotech Research & Innovation Center, University of Copenhagen (UCPH), 
      Copenhagen, Denmark; Department of Radiation Oncology, Stanford University, Palo 
      Alto, California; Niels Bohr Institute, University of Copenhagen (UCPH), 
      Copenhagen, Denmark. Electronic address: ninna.s.rossen@gmail.com.
FAU - Kyrsting, Anders
AU  - Kyrsting A
AD  - Niels Bohr Institute, University of Copenhagen (UCPH), Copenhagen, Denmark.
FAU - Giaccia, Amato J
AU  - Giaccia AJ
AD  - Department of Radiation Oncology, Stanford University, Palo Alto, California.
FAU - Erler, Janine Terra
AU  - Erler JT
AD  - Biotech Research & Innovation Center, University of Copenhagen (UCPH), 
      Copenhagen, Denmark.
FAU - Oddershede, Lene Broeng
AU  - Oddershede LB
AD  - Niels Bohr Institute, University of Copenhagen (UCPH), Copenhagen, Denmark. 
      Electronic address: oddershede@nbi.ku.dk.
LA  - eng
GR  - 28736/CRUK_/Cancer Research UK/United Kingdom
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20210817
PL  - United States
TA  - Biophys J
JT  - Biophysical journal
JID - 0370626
RN  - 0 (Biopolymers)
RN  - 0 (Collagen Type I)
SB  - IM
MH  - *Algorithms
MH  - Biopolymers
MH  - Collagen Type I
MH  - *Imaging, Three-Dimensional
MH  - Microscopy, Confocal
PMC - PMC8511358
EDAT- 2021/08/20 06:00
MHDA- 2021/10/29 06:00
PMCR- 2022/09/21
CRDT- 2021/08/19 20:14
PHST- 2021/02/23 00:00 [received]
PHST- 2021/05/22 00:00 [revised]
PHST- 2021/08/11 00:00 [accepted]
PHST- 2021/08/20 06:00 [pubmed]
PHST- 2021/10/29 06:00 [medline]
PHST- 2021/08/19 20:14 [entrez]
PHST- 2022/09/21 00:00 [pmc-release]
AID - S0006-3495(21)00683-4 [pii]
AID - 10.1016/j.bpj.2021.08.017 [doi]
PST - ppublish
SO  - Biophys J. 2021 Sep 21;120(18):3860-3868. doi: 10.1016/j.bpj.2021.08.017. Epub 
      2021 Aug 17.