Three-dimensional image surfacing software tools | Laser scanning microscopy image analysis

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.

A modular software tool for efficient quantification of biological tissues based on volume data obtained by biomedical image modalities. TiQuant includes a number of versatile image and volume processing chains tailored to the analysis of different tissue types which have been experimentally verified. It implements a novel method for the reconstruction of three-dimensional surfaces of biological systems, data that often cannot be obtained experimentally but which is of utmost importance for tissue modelling in systems biology.

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.

An interactive Qt4 analysis tool for attaching the intrinsic root coordinate system to 3-D confocal recordings of the Arabidopsis root apical meristem. This allows quantitative comparative studies of root populations in a sound and intuitive context. iRoCS Toolbox consists of the data browser labelling and a set of command line tools for batch processing. Main features are: (i) 3-D Visualization of the volume in an orthographic view; (ii) manual annotation of anatomical reference structures (QC, nuclei); (iii) automatic detection and annotation of cells and/or nuclei with several meaningful properties, like position, radius, tissue, cell file, cell cycle state, volume; (iv) full control. Any step can be manually corrected and re-fed into the modeling; (v) retrieval and localization of key events like cell divisions.

Computes a 3D triangular mesh of the tissue. DRACO-STEM is based on the dualization of a simplicial complex of adjacency, and the triangulation and optimization of the resulting polyhedral geometry to proceed. This tool follows three steps for the processing: delaunay complex creation, adjacency complex optimization and dual reconstruction. It was applied to triangular tissue meshes generated from a dataset of segmented tissue images.

A software application on MATLAB to visualize surface data from 3D fluorescence microscopy. Map3-2D accurately accurately projects up to five-dimensional (5D) fluorescence microscopy image data onto full-content 2D maps. Similar to the Earth's projection onto cartographic maps, Map3-2D unfolds surface information from a stack of images onto a single, structurally interconnected map. By cross-referencing between the 2D map and the original image stack, precise quantitative analyses of intensities and shapes are easily and intuitively executable.

Serves for the processing of 3D laser scanning multiphoton microscopy images. CANDLE is a program that performs about low signal-to-noise ratio (SNR) conditions typically encountered when imaging deep in scattering biological specimens. It locally adapts the amount of smoothing to deal with the noise inhomogeneity inherent to laser scanning fluorescence microscopy images.

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.

An automated algorithm for 3D cell nuclei segmentation based on gradient flow tracking. The proposed algorithm is able to segment closely juxtaposed or touching cell nuclei obtained from 3D microscopy imaging with reasonable accuracy. To validate the efficacy and performance of the proposed segmentation algorithm, we evaluated it by using synthesized and real biological images. The results show that the algorithm is able to segment juxtaposed nuclei correctly, a persistent problem in the field of cellular image analysis.

Restores images from microscopic data. Huygens is based on the deconvolution approach that reassigns out-of-focus light to its origin, thus improves signal-to-noise in images. It can use physically-acquired or simulated point-spread functions (PSFs) for characterization of optical system being deconvolved. The tool shows high-performance in in-house tests on deconvolution compared to other software packages. It provides intuitive wizards for parameter selection and processing.

A live cell imaging, tracking & analysis software that rises to the challenge of monitoring temporal changes in biological systems (2D and 3D images over time). ImarisTrack is based on a choice of multiple sophisticated manual and automatic tracking algorithms and also includes an intuitive and interactive track editing tool if manual correction is necessary.

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.

Creates interactive surface plots from all image types. Interactive 3D Surface Plot assists in interpreting the luminance of an image, and in viewing the position of the plot. The plugin has several modes for displaying surface plots: (1) drawing mode; (2) display colors; (3) axes; and (4) invert. It allows users to realize 3D projection.

Contains functionalities for processing and analysis image data. GoFigure2 is a platform which allows users to visualize and navigate through 4D multichannels bio-images. Besides, it aims to provide an automatic segmentation of nuclei and cell membranes and to enable the way of extracting data from bio-images.