The OrientationJ plugins are recordable on ImageJ. Automatic installation (Fiji, Image2): Using the built-in updater of Fiji, check the site BIG-EPFL ().Manual installation: Download the last version of the plugin: OrientationJ_.jar and put the file OrientationJ_.jar into the "plugins" folder of ImageJ.OrientationJ Vector Field: Evaluate the direction by regular patches.OrientationJ Corner Harris: Find corners in an image based the Harris corner detection.OrientationJ Distribution: Build a histogram of orientations based on selected structures.OrientationJ Measure: Make measurement of the orientation and the coherency inside reion of interest.OrientationJ Analysis: Full interface to access to all features of the structure tensor and create color survey.ImageJ has a public domain licence it runs on several plateforms: Linux, Windows, Mac OSX. This software package is a series of plugin running onĪ general purpose image-processing package. We provide a software OrientationJ to produce to visualize and to measure the orientation in the images. 219, Springer International Publishing, ch. Püspöki et al., Transforms and Operators for Directional Bioimage Analysis: A Survey, Advances in Anatomy, Embryology and Cell Biology, vol. The feature are gather in color map in HSB mode, e.g, hue is orientation, saturation is coherency, and brigthness is the source image. The program computes the local orientation and the local coherency. In the left example, the original image ( source) is used as input of the structure tensor computation. With the orientation being typically encoded in the color (hue). The equations above and are then visualized as gray level or color images The local orientation properties are computed according to The structure tensor for each pixel in the image by sliding the Gaussian analysis window Size of a Gaussian-shaped window, and the program computes Qualitative or visual mode: the user specifies the OrientationJ has a companion plugin MonogenicJ that performs multiresolutionĬircular color map coding, Courtesy of Urszula Zajaczkowska. It is a open source project available on GitHub. OrientationJ is a software package which consists of a series of plugins for ImageJ and Fiji. The computation of the dominant orientation, the alignment of images based on the gradient structure tensor OrientationJ has also others tools: the manual measurement of the orientation and coherency in a ROI, Plotting the distribution of orientations,Īnd detection of keypoints (Harris Corner). Performing a visual representation of the orientation of a image, The software package OrientationJ automates the orientation analysis with four functionalities: The theoretical background is fully described in this PDF document. On the evaluation of the gradient structure tensor in a local neighborhood. More explanationsĪnalyse series of 3 greyscale images taken through red, green, and blue filters (ex: GFP, Hcred, Dapi) (metafluor format) to construct a color image (with or without a fourth fluorescent image).The aim is to characterize the orientation and isotropy properties of a region of interest (ROI) in an image, based Macro to measure mean intensity of one large object (ex: artery) at two wavelength (pairs of images), using each image to create a mask and measuring both images with both masks. Macro for calculating empty surfaces on histological slices (ex: tubules in a kidney). Macro for detecting and measuring external (ex: adventis) and internal (ex: intima) perimeter and area of a ring-like structure (ex: artery). More explanationsĪnalyse series of images and perform multiple length measurements. More explanationsĪnalyse series of images and perform multiple objects measurements. Macro for quantifying gels (or any black spots on a white background). Macro to set the global scale according to the used microscope and objective. Create you own script with the ImageJ Macroblocks generator csd_analysisĪnalysis of a intrinsic optical signal from brain slices for Cortical Spreading Depression (Fiji macro).
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