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.
Offers a plugin for unusual biological samples mapping. µ-Magellan is an open-source program allowing users to perform high-throughput imaging on various levels of space and time in three dimensions. The application gives users the possibility to alter a wide range of settings including spatial regions or automated excitation calculations and to generate files which can be exported towards many software such as Vaa3D/TeraFly or Imaris.
Provides general purpose functionality for reading, writing, processing and analysis of images. In the context of microscopy-based cellular assays, EBImage offers tools to segment cells and extract quantitative cellular descriptors. This allows the automation of such tasks using the R programming language and use of existing tools in the R environment for signal processing, statistical modeling, machine learning and data visualization. It uses ImageMagick to read and save images, and supports more than 80 image formats, including JPEG, TIFF, TGA, GIF and PNG. EBImage also supports standard geometric transformations such as rotation, reflection, cropping, translation and resizing. Classical image processing tools are available: linear filtering, morphological erosion and dilation, fast distance map computation, contour delineation and area filling.
Allows to navigate, share and collaboratively annotate massive image data sets of biological specimens. CATMAID combines three main components: a centralized data server, decentralized image servers and the client-side user interface. The interface is applicable to any 2D or 3D multimodal biological image datasets, as shown in examples of stitched confocal 3D volumes. Additionally, the interface can be used to navigate, annotate and bookmark locations in any large image canvas.
Estimates the positions and spacing between sections (or at local points) of three dimensional image data. Z-Spacing is an image-based method for the correction of continuous and discontinuous non-planar axial distortions in serial section microscopy. It may be applied to any imaging modality that acquires 3-dimensional data as a stack of 2-dimensional sections. It also provides plugins for both Fiji and TrakEM2.
A FIJI plugin for fusing bi-directionally recorded microscopic image volumes. BiDiFuse merges image stacks via 3D rigid transformations. The method is broadly applicable, considering its compatibility with all optical sectioning microscopes and does not rely on fiducial markers for image registration.
Enables users to reconstruct big images/stacks from an arbitrary number of tiled input images/stacks. Stitching is based on the Fourier Shift Theorem, and computes all possible translations between pairs of 3D images. It avoids the propagation of errors by consecutive registration steps. Moreover, this tool uses phase correlation to find the translation between all image pairs and registers multi-tile acquisitions globally minimizing all pairwise registration errors.
Provides solutions to users for viewing, modeling, and analyzing 3-D image data for structural biology. IMOD is designed for observing data from tomographic, serial section, and optical section reconstructions. Moreover, this program is also able to measure areas, volumes, and contour lengths, and to count objects of any model class.
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.
Allows users to implement and assemble control software for custom-built microscope systems. Helio provides a framework, built around a collection of components arrangeable according user needs, which can support multiple hardware and functional combinations. The application is able to handle a wide range of laser-scanning including galvanometric scan mirrors or resonant scanners as well as camera images.
Allows automatic 3D stitching of teravoxel-sized tiled images. TeraStitcher was initially developed for stitching images generated by the confocal laser scanning microscopy (CLSM) microscope. The software specifies the requirements of the stitching problem when teravoxel-sized images are involved, and then use the system resources to perform the stitching of these images. It is available both as standalone application and as plugin of the free software Vaa3D.
Stabilizes in vivo intravital microscopy images that suffer from soft-tissue background movement. StabiTissue quantifies the coincidence between image pairs from randomly distributed image regions. The method stabilizes the full 3D stack, aligning images within and across stacks. It provides an easy to use interface for the specific problem of stabilization. The method is more immune to noise and provides better performance for datasets’ possessing nonlinear tissue deformations.
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.
Provides methods that combines multiple microscopic recordings. XuvTools is an automated 3D stitching software developed for biomedical image data, typically confocal microscopy images. It permits to obtain a large field of view, a high dynamic range or good resolution. This software does not require a priori information on the stage positions. It is split into core library, command line tools for batch processing and a graphical user interface.
Allows users to perform phase correlation registration to correct movement that occurs as a result of sample drift in three-dimensional (3D) time lapse experiments. Correct 3D Drift is a Fiji plug-in assisting in the correction of the sample drift. It compensates for sample translation or alterations in focal position by utilizing phase correlation to register each time-point of a four dimensional (4D) confocal datasets.
Tracks iteratively the potential neuronal termini to the soma center. Rivuletpy is a Python toolkit for automatically reconstructing single neuron models from 3D microscopic image stacks. This algorithm supports large-scale batch-processing by requiring only a background threshold. It was also able to generate topologically acceptable neuronal models in a majority of cases without human intervention.
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.
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.
Assists in the creation and visualization of 3D fluorescence volume rendering. MicroSCoBioJ contains three plugins: (1) Mesh Maker MicroSCoBioJ that computes the triangles or tetrahedra mesh corresponding to an user-defined treshold; (2) Mesh Viewer MicroSCoBioJ that shows up to four different meshes and displays the mesh as points, lines, or fill surface; and (3) WAT MicroSCoBioJ Weight Adaptive Threshold.
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.
Assists in focusing microscopic images of 3D objects and organisms. Extended Depth of Field is based on different wavelet algorithms. This ImageJ plugin offers users two interfaces: a simplified mode and an expert mode with a complete set of parameters. It benefits from a RGB to grayscale conversion method that assures contrast and intensity in order to process color data.
0 - 0 of 0