Software Tools

If you encounter a recurring error and/or bug and do not know how to fix it, please contact:

NeuronStudio (Beta)

This program is designed to allow reconstruction of neuronal structures from confocal and multi-photon images. It is a self-contained software package that is free, easy to use, and available for 64-bit computers. Download

Online help manual.
View change log.
Windows Source Code (no technical support).

* Voxel Size (x,y,z): 0.05μm, 0.05μm, 0.10μm

Sample dataset, model, and spines #1.

* Voxel Size (x,y,z): 0.05μm, 0.05μm, 0.10μm

Sample dataset, model, and spines #2.

* After opening the dataset, the above voxel sizes must be entered into the settings dialog before importing the model and spines.

Rayburst (with dynamic refinement) Open-Source Code

Source code for the Rayburst Algorithm. This fully automated algorithm casts rays in a 2D/3D dataset without the use of pre-generated ray tables. Implemented in ANSI C as a single module. Includes test module for example use of the library routines. Download

Online documentation.

Volume Integration and Alignment System (VIAS)

This program allows multiple stacks of tiled optical sections obtained to be interactively tiled in 3D and integrated into a single volumetric dataset. Download

Online help manual.
Sample project #1.
Sample project #2.
Sample project #3.

Volume Integration and Alignment System (VIAS) Source Code

Source code for the VIAS software. The code is written in the C programming language and uses Win32 for the graphical user interface. Download

Online documentation.

Polygonized Viewer (P-View)

A tool for visualizing 3D datasets. The program allows you to look at files in .PVO format as generated by the pmake utility (packaged with the program). Download

Online help manual.
Sample .pvo file #1.
Sample .pvo file #2.

NeuroGL

NeuroGL is a software tool for the visualization of neural structures using OpenGL. The current version of the program accepts only NeuroZoom ASCII files as input (see also the CNIC repository). Download

Sample ASCII file #1.
Sample ASCII file #2.
Sample ASCII file #3.

TIFF Stack Sub-Sampler (TSS)

A tool for reducing the number of voxels used to represent a volumetric dataset by means of sub-sampling, while accurately preserving small features and gradients in the data. Download

Online help manual.