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.
Provides assistance for elastic volume reconstruction via series of ultra-thin microscopy sections. Elastic Alignment and Montage works for the ImageJ software through the TrakEM2 toolkit. This elastic alignment method is appropriate for groups of overlapping 2D-images. It enables the montage of mosaics from overlapping tiles and the alignment of deformed section series from serially sectioned volumes.
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.
Allows to track populations of neurons with single neuron resolution in the brain of a freely moving C. elegans undergoing large motion and deformation. NeRVEclustering uses non-rigid point-set registration in order to match each segmented neuron in each volume with a set of reference volumes taken from throughout the recording. This tool primarily serves for tracking neurons in brains undergoing large deformations.
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.
Consists in a collection of tools developed to achieve group-wise elastic registration of 3D objects by decomposing the alignment problem into a sequence of orthogonal 2D elastic registrations. Atlas Toolkit furnishes methods for landmark-free alignment of 3D imaging datasets. It aims to make registration of 3D morphological datasets readily accessible to both experimental and computational biologists.
Provides a method for exposing gene expression patterns from different larval brains in a common reference space. Larvalign is an open source computational framework that mainly focuses on allowing the registration of microscope images of the central nervous system (CNS) of the third instar Drosophila larva. It includes functionalities for image processing and quality assessment. The software can be applied for help generate a curated database of registered expression patterns.
Permits to align images in a multi-tag fluorescence image stack. RAMTaB is a block-based registration method that can select a reference image with maximal overlap. It is able to determine sub-pixel shifts between phase contrast images in a multi-tag fluorescence image stack. The tool is not sensible to brightness and contrast variations. It has difficulties with poor quality phase contrast images containing blur due to the changes in the plane at which camera sets its focus while taking the images.
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.
A three-dimensional (3D) reconstruction and modeling software. Free-D allows to generate, process and analyze 3D point and surface models from stacks of 2D images. It is an integrated software tool, offering in a single graphical user interface all the functionalities required for 3D modeling.
Co-registers pairs of morphologies. Reg-MaxS is based on maximizing spatial overlap by applying a sequence of transformations. It can estimate transformation differences between morphologies with a multi-scale estimation method. This tool is useful for registering stereotypic neuron morphologies that show considerable spatial variability in their fine structures as long as they are similarly scaled along different axes.
A 4-D image processing platform for the work with laser scanning and wide field microscopes. TIKAL provides a registration software for correcting global movements and local deformations of cells as well as 2-D and 3-D tracking software.
Serves for montaging, alignment, analysis and visualization of serial sections. Reconstruct allows users to organize, transform and display different types of data. It is able to analyze series with large number of sections and images over a large range of magnifications. Moreover, this tool includes functionalities that simplify cropping, scaling and comparison of images.
Aims to embed photon counting into most existing multi-photon imaging systems. PySight is a program dedicated to perform planar and volumetric imaging. It can calculate the difference between photon arrival times and the respective synchronization signals from the laser beam steering element. It integrates features for solving distinct laminar dynamics simultaneously sampled by the variofocal lens, rather than merely extending the effective depth of field using Bessel beams.
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.
Reconstructs and makes complex datasets easily accessible. BigStitcher is an ImageJ plugin that enables interactive visualization, precise alignment, real-time fusion, deconvolution, support for alignment of multi-tile acquisition taken from different physical orientations, or so-called multi-tile views. It can also be used for doubling the size of specimens that can be imaged, while further orthogonal views can render the resolution isotropic.
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.
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.
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.
Aligns images in a multi-channel hyperstack. The HyperStackReg purpose is to apply the same transformation matrix to each channel of a hyperstack. This tool is an ImageJ plugin, offering a graphical user interface. It permits users to select the transformation type applicable to the images, such as translation, rigid body, scaled rotation, or affine.
Allows users to visualize, manipulate, and understand data from imaging modalities such as computed tomography, microscopy or Magnetic resonance imaging (MRI). Amira 3D Software for Life Sciences provides features to import and process 2D and 3D images data, visualization techniques and tools for visual analysis. Users can also create and share presentations. The base product can be customized by adding functional extensions to fit special needs in different application areas.
Manages instrument control, image processing and data analysis. SlideBook can drive hundreds of devices including microscopes, stages, lasers, wheels, piezos, scanners or shutters. It acquires data in 3D format over time, color, and specimen locations in customizable experiment protocols. This tool offers a solution to investigate images and obtain statistical data via a wide variety of algorithms while maintaining original data integrity.
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.
0 - 0 of 0
1 - 2 of 2