Introduction

This project looks for a set of routines commonly used to do neuronal data analysis. Initially we will explore the neuronal coding for sensory objects on primary sensory cortices and hippocampus.

We defined a set of reusable Java components that can be incorporated in another application. Each component is fully tested and has a separate documentation page in our Wiki. As of now, they are:

• SpikeHandler
  • And the spike data file format
• SpikeRateMatrix and CountMatrix
• BehaviorHandler
  • And the behavior data file format
• PatternHandler
  • And the pattern data file format

The elements outlined above form the core of our project. We have also built components for the specific user case of applying supervised learning techniques to identify behavior in neuron activity (the nda.analysis package). The later components have yet to be documented.

If you are new to this project and want to know what problems our project can help you with, we have set up a FAQ wiki page.

Code Organization

The project lives in the SVN repository as an Eclipse IDE project in the root tree. The directory layout is as follows:

• src/: Main source code folder
• test/: Source code folder for all test code (unit and integration tests)
• setup/: Real and made up data files used to test the code
• wiki/: Source code for our wiki pages
• lib/: Third party libraries used in this project
• doc/: Automatically generated documentation (Doxygen)
• legacy/: Old legacy code that we are currently improving by refactoring and pulling into src/

Dependencies

• JUnit: our testing framework
• Apache Commons Math: general math and statistics library
• Weka: machine learning algorithms

Using as a library

You have two options:

1. Use one of our generated JAR files in the Downloads tab in this page and import it in your project
2. Download the code from our SVN repository (see the Source tab) and use the newest version available

Contributing

There are several ways you can contribute to the project. As an user of this library, you can report bugs and issues at our Issue Tracker, or maybe just show us some idea you have about a cool feature we could implement.

You could also become an active contributer to the project. For one time changes, the easiest way is to contribute a patch. You can download our code using SVN (follow the instructions depicted on the Source tab in this page) and then make some changes, generate a patch, and send it to us through the Issue Tracker. If you want to contribute more actively, we encourage you to become an official comitter of the project, having direct access to our source code repository.

Documentation

The main documentation of the project consists of the Wiki pages in this site. Read then carefully and choose which components you will use in your application. After that, you can download our code and access the Javadoc documentation directly in your IDE or you can use the Doxygen tool to automatically generate HTML pages with documentation extracted from our source code.

Contact

This project is in active development and is currently being used for research at the Brain Institute, UFRN - Brazil. We are eager to hear about your interest in this project. How are you using it, your impressions, suggestions and complaints. Get in touch with us through our issue tracker or our project email: neurobjects@neuro.ufrn.br.

We look forward to hearing from you and maybe welcome you as a contributor to the project.