Orientation and the degree of isotropy are important in many biological systems such as the sarcomeres of cardiomyocytes and other fibrillar structures of the cytoskeleton. Image based analysis of such structures is often limited to qualitative evaluation by human experts, hampering the throughput, repeatability and reliability of the analyses.
Characterizes the orientation and isotropy properties of a region of interest (ROI) in an image, based on the evaluation of the structure tensor in a local neighborhood. The software OrientationJ automates the orientation analysis. It is a Java plug-in for ImageJ. OrientationJ has four functionalities: visual representation of the orientation, quantitative orientation measurement, making distribution of orientations and corner detection.
An ImageJ plug-in based on the concept of nematic tensor, which can provide a quantitative description of the anisotropy of fiber arrays and their average orientation in cells, directly from raw images obtained by any form of microscopy. FibrilTool has been validated on microtubules, actin and cellulose microfibrils, but it may also help analyze other fibrillar structures, such as collagen, or the texture of various materials. The tool is ImageJ-based, and it is therefore freely accessible to the scientific community and does not require specific computational setup. The tool provides the average orientation and anisotropy of fiber arrays in a given region of interest (ROI) in a few seconds.
An automated tool based on spectral analysis, allowing the quantification of orientation and also size distributions of structures in microscopy images. CytoSpectre utilizes the Fourier transform to estimate the power spectrum of an image and based on the spectrum, computes parameter values describing, among others, the mean orientation, isotropy and size of target structures. The analysis can be further tuned to focus on targets of particular size at cellular or subcellular scales. The software can be operated via a graphical user interface without any programming expertise. The tool is compatible with most 2D images and can be used to analyze targets at different scales.
Provides tools for simulating the diffraction patterns from fibrillar assemblies of biomolecules and optimizing the fibrillar models for experimental diffraction data. DISORDER is able to simulate diffraction patterns from fibrillar assemblies with orientation disorder. The software can be used for building of fibrillar molecular structures, simulation of the diffraction patterns for these structures, or visual and quantitative comparison of the simulated and experimental diffraction data.
Infers the preferred orientation of structures present in an input image. Directionality is a plugin for the image analysis software ImageJ. It computes a histogram indicating the amount of structures in a given direction. The interface allows to specify: (i) the number of bins, (ii) the starting angle for analysis, (iii) the debug flag, (iv) the result table flag and (v) the orientation map flag.
Reads and displays diffraction patterns. WCEN is a program for preliminary analysis of fiber diffraction data, that allows the determination of experimental parameters, and correction for geometric effects, polarization, and for film data, film absorption. The software can be used to determine experimental and specimen parameters and to convert diffraction data from detector to reciprocal space. It is designed for use with fiber diffraction data, but can have some applicability to other types of diffraction data, including solution scattering data.