FibrilJ: ImageJ Plugin for Fibrils' Diameter and Persistence Length Determination

Research output

4 Citations (Scopus)

Abstract

Application of microscopy to evaluate the morphology and size of filamentous proteins and amyloids requires new and creative approaches to simplify and automate the image processing. The estimation of mean values of fibrils diameter, length and bending stiffness on micrographs is a major challenge. For this purpose we developed an open-source FibrilJ plugin for the ImageJ/FiJi program. It automatically recognizes the fibrils on the surface of a mica, silicon, gold or formvar film and further analyzes them to calculate the distribution of fibrils by diameters, lengths and persistence lengths. The plugin has been validated by the processing of TEM images of fibrils formed by Sup35NM yeast protein and artificially created images of rod-shape objects with predefined parameters. Novel data obtained by SEM for Sup35NM protein fibrils immobilized on silicon and gold substrates are also presented and analyzed.
Original languageUndefined
Pages (from-to)199-206
JournalComputer Physics Communications
Volume214
DOIs
Publication statusPublished - 2017
Externally publishedYes

Cite this

@article{5d0d9b9415f34d79a9f7898edced53e2,
title = "FibrilJ: ImageJ Plugin for Fibrils' Diameter and Persistence Length Determination",
abstract = "Application of microscopy to evaluate the morphology and size of filamentous proteins and amyloids requires new and creative approaches to simplify and automate the image processing. The estimation of mean values of fibrils diameter, length and bending stiffness on micrographs is a major challenge. For this purpose we developed an open-source FibrilJ plugin for the ImageJ/FiJi program. It automatically recognizes the fibrils on the surface of a mica, silicon, gold or formvar film and further analyzes them to calculate the distribution of fibrils by diameters, lengths and persistence lengths. The plugin has been validated by the processing of TEM images of fibrils formed by Sup35NM yeast protein and artificially created images of rod-shape objects with predefined parameters. Novel data obtained by SEM for Sup35NM protein fibrils immobilized on silicon and gold substrates are also presented and analyzed.",
keywords = "Amyloid, Fibril, Diameter, Persistence length, Bending stiffness, Image processing, Sup35, Prion",
author = "Sokolov, {P. A.} and Belousov, {M. V.} and Bondarev, {S. A.} and Zhouravleva, {G. A.} and N.A. Kasyanenko",
year = "2017",
doi = "10.1016/j.cpc.2017.01.011",
language = "не определен",
volume = "214",
pages = "199--206",
journal = "Computer Physics Communications",
issn = "0010-4655",
publisher = "Elsevier",

}

TY - JOUR

T1 - FibrilJ: ImageJ Plugin for Fibrils' Diameter and Persistence Length Determination

AU - Sokolov, P. A.

AU - Belousov, M. V.

AU - Bondarev, S. A.

AU - Zhouravleva, G. A.

AU - Kasyanenko, N.A.

PY - 2017

Y1 - 2017

N2 - Application of microscopy to evaluate the morphology and size of filamentous proteins and amyloids requires new and creative approaches to simplify and automate the image processing. The estimation of mean values of fibrils diameter, length and bending stiffness on micrographs is a major challenge. For this purpose we developed an open-source FibrilJ plugin for the ImageJ/FiJi program. It automatically recognizes the fibrils on the surface of a mica, silicon, gold or formvar film and further analyzes them to calculate the distribution of fibrils by diameters, lengths and persistence lengths. The plugin has been validated by the processing of TEM images of fibrils formed by Sup35NM yeast protein and artificially created images of rod-shape objects with predefined parameters. Novel data obtained by SEM for Sup35NM protein fibrils immobilized on silicon and gold substrates are also presented and analyzed.

AB - Application of microscopy to evaluate the morphology and size of filamentous proteins and amyloids requires new and creative approaches to simplify and automate the image processing. The estimation of mean values of fibrils diameter, length and bending stiffness on micrographs is a major challenge. For this purpose we developed an open-source FibrilJ plugin for the ImageJ/FiJi program. It automatically recognizes the fibrils on the surface of a mica, silicon, gold or formvar film and further analyzes them to calculate the distribution of fibrils by diameters, lengths and persistence lengths. The plugin has been validated by the processing of TEM images of fibrils formed by Sup35NM yeast protein and artificially created images of rod-shape objects with predefined parameters. Novel data obtained by SEM for Sup35NM protein fibrils immobilized on silicon and gold substrates are also presented and analyzed.

KW - Amyloid

KW - Fibril

KW - Diameter

KW - Persistence length

KW - Bending stiffness

KW - Image processing

KW - Sup35

KW - Prion

U2 - 10.1016/j.cpc.2017.01.011

DO - 10.1016/j.cpc.2017.01.011

M3 - статья

VL - 214

SP - 199

EP - 206

JO - Computer Physics Communications

JF - Computer Physics Communications

SN - 0010-4655

ER -