Collection

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).

**Python(x,y)** is a free scientific and engineering development software for numerical computations, data analysis and data visualization based on Python programming language, Qt graphical user interfaces and Spyder interactive scientific development environment. Many python libraries related to numerical calculation are packaged, so you do not need to search and install them individually. Included libraries are listed **[here](https://code.google.com/p/pythonxy/wiki/StandardPlugins).**

IMOD is a set of image processing, modeling and display programs used for tomographic reconstruction and for 3D reconstruction of EM serial sections and optical sections. The package contains tools for assembling and aligning data within multiple types and sizes of image stacks, viewing 3-D data from any orientation, and modeling and display of the image files.

Included are two programs with graphical interface: 3dmod, for displaying and segmenting 2D images and 3D volumes; etomo, for reconstructing tomographic volumes from tilt series of images.

Processing can be distributed on multiple cores and executed in batch mode.

MATLAB is famous, so this page is only for being the landing page for components and workflows.

Acquiarium is for carrying out the common pipeline of many spatial cell studies using fluorescence microscopy. It addresses image capture, raw image correction, image segmentation, quantification of segmented objects and their spatial arrangement, volume rendering, and statistical evaluation. It is focused on quantification of spatial properties of many objects and their mutual spatial relations in a collection of many 3D images. It can be used for analysis of a collection of 2D images or time lapse series of 2D or 3D images as well. It has a modular design and is extensible via plug-ins. It is a stand-alone, easy to install application written in C++ language. The GUI is written using cross-platform wxWidgets library.