Collection

Amira is 3D visualization and analysis software for life sciences.
 

" Amira software is a powerful, multifaceted 3D platform for visualizing, manipulating, and understanding life sciences data from computed tomography, microscopy, MRI, and many other imaging modalities. 
With incredible speed and flexibility, Amira software enables advanced 3D imaging workflows for specialists in research areas ranging from molecular and cellular biology to neuroscience and bioengineering. "

OpenCV is released under a BSD license and hence it’s free for both academic and commercial use. It has C++, C, Python and Java interfaces and supports Windows, Linux, Mac OS, iOS and Android. OpenCV was designed for computational efficiency and with a strong focus on real-time applications. Written in optimized C/C++, the library can take advantage of multi-core processing. Adopted all around the world, OpenCV has more than 47 thousand people of user community and estimated number of downloads exceeding 6 million. Usage ranges from interactive art, to mines inspection, stitching maps on the web or through advanced robotics.

OpenMOLE (Open MOdeL Experiment) is a workflow engine designed to leverage the computing power of distributed execution environments for naturally parallel processes. A process is told naturally parallel if the same computation runs many times for a set of different inputs, such as model experiment or data processing… It is free software distributed under the AGPLv3 free software license.

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Neuron studio is a software package to reconstruct neurons from 3D confocal images. Reconstruction can be done manually, semi-manually or fully automatic. The images as well as the detected objects are rendered in 3D. A spine detection and classification function is also included. Results can be exported as a text file with coords of the spines. It seems that active development has stopped in 2009. NeuronStudio is being developed at the Computational Neurobiology and Imaging Center (CNIC), a research laboratory at the Neuroscience Department of the Mount Sinai School of Medicine in New York.

NeuronStudio can be used with default parameters or user-defined parameters (Fully or semi-automated).