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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.
iRoCS Toolbox
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.
DRACO-STEM / Dual Reconstruction by Adjacency Complex- SAM Tissue Enhanced Mesh
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.
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.
Amira 3D Software for Life Sciences
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.
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