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.
It is an organized collection of software modules for image data handling, pre-processing, segmentation, inspection and editing, post-processing, and secondary analysis. These modules can be scripted to accomplish a variety of automated image analysis tasks.
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.
A program that automatically finds the corresponding landmarks in a subject brain and maps it to the coordinate system of the target brain via a deformable warp. BrainAligner registers 3D images of adult Drosophila brain into a common coordinate System. It generates an image pattern atlas of 2,954 registered brains containing 470 different expression patterns that cover all the major compartments of the fly brain.
Creates a unified volumetric dataset by merging multiple stacks of tiled optical sections from laser scanning microscopy (LSM). VIAS enables the picking of individual image stacks coupled to an interactive adjustment. The application also provides features for auto alignment, gamma correction for contrast and a 2D distance measurement tool. However, the program is suited for 8 and 16 bit grayscale images processing only.
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.