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Biomat

SYSNO ASEP	0522714
Document Type	L4 - Software
R&D Document Type	Software
Title	Biomat
Author(s)	Janáček, Jiří (FGU-C)_{RID, ORCID}
Year of issue	2019
Int.Code	BM_2020_1.0.1
Technical parameters	Pluginy v Biomat jsou nástroje pro detekci a analýzu kapilárního řečiště a převodního systému v srdci
Economic parameters	Jedná se o volně dostupný software
Owner Name	Fyziologický ústav AV ČR, v. v. i.
Registration Number of the result owner	67985823
License fee fee	N - Poskytovatel licence nepožaduje licenční poplatek
Internal identification code of the product assigned by its creator, Regulation no.,	BM_2020_1.0.1
Language	eng - English
Country	CZ - Czech Republic
Keywords	tensor images ; ImageJ ; fiber networks ; Lipschitz envelope ; heat equation ; Crank-Nicolson method
Subject RIV	FP - Other Medical Disciplines
OECD category	Anatomy and morphology (plant science to be 1.6)
R&D Projects	LTC17023 GA MŠMT - Ministry of Education, Youth and Sports (MEYS)
Institutional support	FGU-C - RVO:67985823
Annotation	Biomat is collection of ImageJ plugins distributed in FiJi. 1) Plugins for 3D image preprocessing. Stack Linear Contrast - multiplies images in stack by coefficient obtained by linear interpolation of the “first” and “last” coefficient. A simple tool for compensation of contrast decreasing with depth within thick sample. Lipschitz 3D Filter - top hat - subtracts slowly varying background calculated as lower Lipschitz envelope from the image. 2) Plugins for detection of fibres in 3D image. Tensor Line 3D Filter - enhances white fibers of uniform width sparsely distributed on dark background. Vector Line 3D Filter - enhances white fibers of varying thickness. Crossection of the fibers need not be circular. 3) Plugins for evaluation of 2D images using heat equation. 2D Tensor Color Coding - standard color coding of 2D tensor image. Symmetric tensor is coded as channels of 32 bit image stacks. 2D Heat Kernel Tensor - second order moments of heat kernel calculated from 8 bit binary image by Crank-Nicolson method. 2D Tensor Statistics - summary of tensor image (in ROI). “Value” is average trace of the tensor, “shape” is the ratio of its eigenvalues and “angle” of the first eigenvector is measured counterclockwise from the horizontal axis.
Workplace	Institute of Physiology
Contact	Lucie Trajhanová, lucie.trajhanova@fgu.cas.cz, Tel.: 241 062 400
Year of Publishing	2020
Electronic address	https://imagej.net/Biomat

Number of the records: 1