# CIBC:Documentation:SCIRun:UserGuide:Packages

## Overview

Packages are collections of modules organized by category. SCIRun's packages and their categories are listed below.

## SCIRun Core

Because SCIRun core is required, it is not technically a package. Like a package, SCIRun core provides a set of datatypes, algorithms, and modules. Unlike packages, SCIRun core is required and SCIRun would not function without it. Its modules are divided into the following categories:

- Bundle
- ChangeFieldData
- ChangeMesh
- Converters
- DataArrayMath
- DataIO
- Examples
- Math
- MiscField
- NewField
- Render
- String
- Visualization

## BioPSE

The BioPSE package supplies a set of modules for interactively constructing bioelectric field simulations.

BioPSE modules comprise a set of modeling tools for building finite element, finite difference, and boundary element models and allow for solving both forward and inverse bioelectric problems. Visualization tools are provided for interactively investigating scalar and vector field data. BioPSE allows for rapidly prototyping new modeling, simulation, and visualization components and well as providing a flexible method for using external packages. BioPSE provides support for source localization, focusing inversion, and electrical impedance imaging of neural and cardiac simulations.

- DataIO
- Forward
- Inverse
- LeadField
- Modeling
- NeuroFEM
- Visualization

## Teem

Modules of the Teem package provide functionality of the Teem project's unu and tend command-line programs and corresponding NRRD and Ten libraries.

The Teem project's NRRD library provides data types and functions for representing and processing N-dimensional raster data. The teem library provides types and functions for diffusion tensor processing, analysis, and visualization.

Typically, multiple instances of commands unu and tend are connected by pipes to solve a problem--the data-flow network equivalent is available in SCIRun using the Teem package. In other words, the Teem package provides a ``visual* programming equivalent to the unu and tend command-line tools.*

The Teem package is divided into the following categories:

- Converters
- DataIO Modules read/write NRRD data from/to files and modules that transform data to/from the NRRD representation.
- Misc - Modules for displaying and setting NRRD property values and for performing miscellaneous operations on NRRD data.
- Tend - equivalent to commands of the tend program. For example, module TendAnhist implements the command tend anhist
- UnuAtoM - Unu Modules equivalent to commands of the unu program. For example, module UnuMinMax implements the command unu minmax
- UnuNtoZ - Unu Modules equivalent to commands of the unu program. For example, module UnuMinMax implements the command unu minmax

## MatlabInterface

Modules of the Matlabinterface package allow SCIRun to use the facilities of Matlab via interactive commands and Matlab scripts.

Matlabinterface modules can be used to convert data files between SCIRun and Matlab formats. Matlabinterface modules can be part of SCIRun networks that invoke Matlab scripts to perform complex calculations.

Via a sockets interface SCIRun passes scripts and matrix data to Matlab, which executes scripts and returns matrix data to SCIRun. Matrix data returned from Matlab can be sent to other modules for further processing and visualization.

The Matlab process can run on the same computer as does SCIRun or it can run on a separate computer, helping to distribute the load and resolving potential licensing conflicts with Matlab.

Available categories:

- DataIO
- Interface

## Insight Toolkit

The Insight package provides an interface to the National Library of Medicine Insight Segmentation and Registration Toolkit (ITK). SCI has wrapped several ITK filters into SCIRun modules. This gives SCIRun users access to ITK filters, which provide image-processing capabilities ranging from fundamental algorithms to advanced segmentation and registration tools.

- Converters
- DataIO
- Filters