Image-based modeling and simulation aims at using systematic, quantitative image data to build predictive models of biological systems that can be simulated with a computer. This allows one to disentangle molecular mechanisms from effects of shape and geometry. Questions like "what is the functional role of shape" or "how are biological shapes generated and regulated" can be addressed in the framework of image-based systems biology.
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.
Displays datasets from confocal laser scanning microscopy (CLSM). PView offers a graphical platform that allows users to interplay with pre-computed models as well as to figure large objects. It includes several features coupled to speed up techniques for picking up multiple models’ resolutions and changing scene colors or grid step.
Provides tools for learning generative models of cell organization directly from images, storing and retrieving those models in XML files and synthesizing cell images (or other representations) from one or more models.
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