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.
Permits surface rendering, multivariate statistical analysis (MSA), automatic classification, projection matching, angular reconstitution, automatic particle selection. IMAGIC can be employed for real data processing run for educational or testing purposes. This tool can exploit the properties of cheap graphic processors. It is useful for 4D analysis at atomic resolution or for refining towards multiple 3D structures.
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 users to determine nanofiber diameter. DiameterJ is an image analysis tool that enables automatic measurement of nanofiber diameters in scanning electron micrographs. This ImageJ/FIJI plug-in can be used for: (1) digital synthetic image files made with black and white lines of known pixel diameters; and (2) scanning electron micrographs of stainless steel wires of nominally monodispersed diameter.
Offers an assortment of features for treating centerlines of tubular structures. NeuroMorph_CenterLine_Processing is a module that allows users to add functionalities to Blender for handling files produced by the Vascular Modeling Toolkit (VMTK) software. The plugin also provides functionalities for: (i) cleansing meshes or (ii) discovering bouton swellings; (iii) creating cross-sectional surfaces, or (iv) computing surface areas of meshes or along center line. The application can also be downloaded as part of the NeuroMorph software.
Provides an additional set of features for the Blender software. NeuroMorph_Measurement_Tools is a module supplying characteristics to compute surface areas, volumes, and lengths of regions of meshes. The application enables users to select the desired vertices for measurements. It produces outputs that can be exported to be read through Excel.
Allows users to add features for the Blender’s software that analyzes proximity. NeuroMorph_Proximity Analysis includes two characteristics enabling : (i) the evaluation of surfaces from two different ones that are at a given distance of each other and (ii) the calculation of the closest distance from a given vesicle sphere to a synapse mesh. The application is part of the NeuroMorph software.
Supplies an environment for handling data from electron cryo-microscopy (cryoEM) and low-resolution X-ray crystallography. Gorgon aims to provide a modeling environment for subnanometer to near-atomic resolution density maps. The platform includes features such as a visualization framework for volumetric data, geometric operations as well as methods for refining molecular models.
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.
Offers a platform dedicated to image processing. VolumeRover is a toolkit able to handle 3D imaging data and to visualize datasets of arbitrary size. It provides multiple features to treat, improve, and analyze volumetric data as well as generating computational models. For instance, it can perform anisotropic diffusion, generalized digitized total variation (GDTV) filtering, secondary structure elucidation or boundary-free image skeletonization.
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.
A computational method to quantitatively assess the morphological defects in the Drosophila eye resulting from genetic alterations affecting basic cellular and developmental processes. Flynotyper utilizes a series of image processing operations to automatically detect the fly eye and the individual ommatidium, and calculates a phenotypic score as a measure of the disorderliness of ommatidial arrangement in the fly eye.
Automatically and semi-automatically detects exosomes in 2D images from transmission electron microscopy (TEM). TEM Exosome Analyzer enables identification of exosomes, their boundaries, and reports, and provides information about their size and shape. The software consists of two stages: (1) detection of the initial exosome seeds in the image, and (2) segmentation of the exosomes using the seeded watershed transform.
Offers a platform for fractal analysis and morphology functions. FracLac is a module that can be used as an ImageJ or FIJI plugin. The application includes features such as: (i) analyzing complexity and heterogeneity, (ii) measuring difficult to describe geometrical forms; (iii) extracting of pattern from several types of images for analysis. The software is suitable for images of biological cells as well as for other structures such as branching structures or known fractals.
A version of the public domain image analysis software NIH Image that has been extended to handle the loading, display and analysis of scanning microscope images. Image SXM supports SAM, SCM, SEM, SFM, SLM, SNOM, SPM and STM images.
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.
Allows users to determine Fourier descriptors and the curvature starting from a closed curve. Fourier Shape analysis is a module that can be run through the ImageJ software. The application consists of three main features allowing the computation of Fourier descriptors, the generation of elliptic Fourier descriptors including a normalized set of coefficients such as rotation or scale invariant, as well as the calculation of curvature.
Calculates standard bone histomorphometry parameters on a digitized trabecular-bone surface, according to the parallel plates model. Map_BoneMicrostructure is an ImageJ plugin for calculating bone area fraction (BA/TA), trabecular thickness (TbTh), trabecular separation (TbSp) and trabecular number per length unit (TbN). The software processes 8-bit grayscale images with black-colored bone-trabeculae on white background.
Permits scientific evaluation of 2D images. GSA Image Analyser is a program that allows (1) automatic surface calculation of the surfaces of all recognized objects, (2) direct length calculation of very complex and very ramified objects, and (3) object counting with an automatic count-function, a grid-intersection-count-function and two manual count-procedures.
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