Find and compare the best bioinformatics software tools for analysing oriented structures on cellular and subcellular levels on conventional fluorescence microscopy images. Tools are ranked by the biomedical research community.
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.
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.
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