Analyzes, processes and visualizes multi-dimensional microscopy images. BioImageXD puts open-source computer science tools for three-dimensional visualization and analysis into the hands of all researchers, through a user-friendly graphical interface tuned to the needs of biologists. BioImageXD has no restrictive licenses or undisclosed algorithms and enables publication of precise, reproducible and modifiable workflows. It allows simple construction of processing pipelines and should enable biologists to perform challenging analyses of complex processes.
Performs 2D image registration based on elastic deformations represented by B-splines. bUnwarpJ is an ImageJ plugin that works on registration of two images, A and B: Image A is elastically deformed to look as similar as possible to image B, and, at the same time, the "inverse" transformation (from B to A) is also calculated. As a result, two images are given: the deformed versions of A and B images.
Serves for effective segmentation of multidimensional datasets. MIB can recognize several number of imaging formats and offers a variety of image processing tools. It also simplifies utilization and quantification of acquired data. It permits users to segment large datasets, to realize 3D visualization, and to quantify images and models. Its parameters enable users to insert plugin s to customize the program for specific needs.
Provides a method for elastic and consistent registration of histological sections. Register Virtual Stack Slices is an ImageJ plugin that uses a sequence of image slices stored in a folder, and offers a list of registered image slices (with enlarged canvas). It can perform six types of image registration techniques: (i) translation, (ii) rigid (translation + rotation), (iii) similarity (translation + rotation + isotropic scaling), (iv) affine, (v) elastic and (vi) moving least squares.
Serves for interactive and deformable alignment of large 2D and 3D images. BigWarp enables landmark pair placement and displays the effects of the warp on-the-fly. It builds upon BigDataViewer for visualization and data sources which enables navigation of large images with arbitrary 3D reslicing and zoom. Moreover, it uses a Thin Plate Spline implemented in Java to build a deformation from point correspondences.
Performs image segmentation and registration. CMP-BIA is dedicated to ImageJ/Fiji and contains a plugin named jSLIC. This plugin is a segmentation method for clustering, in a given image, similar regions (as known as superpixels) which are usually used for other segmentation techniques, classification and registration. It gives reliable superpixels shapes, with no need of decreasing their size.
Allows users to visualize, analyze and restore neuronal morphologies reassembled from microscopy stacks. NeuroMorphoVis is a framework composed of five principal modules for (i) data handling, (ii) simulation of three-dimensional somata profiles, (iii) building, repair and analysis of morphological skeletons, (iv) creation of polygonal surface meshes and (v) reconstruction of volumetric models that reflect the geometrical description of the skeletons.