Scientific Software
In the course of my work, I developed some software that may be of use to other researchers:
- CSchem and CPCB are a pair of programs for drawing electronic circuit diagrams and laying those circuits out on a printed circuit board.
- VScope is a tool for data acquisition and analysis of voltage-sensitive dye imaging experiments.
- ELN is an Electronic Lab Notebook. The software is described in Wagenaar (2014).
- QPlot is an alternative 2D plotting library for Matlab and Octave that facilitates beautiful typography and precise axis scaling. QPlot is described in an article titled “Publication Quality 2D Graphs with Less Manual Effort due to Explicit Use of Dual Coordinate Systems,” (Wagenaar, 2014b).
- Wormfinder is a Matlab GUI for tracking leeches and other quasilinear animals in video sequences. The algorithm used by the software was described in Wagenaar and Kristan (2010).
- MEABench is a suite of programs to acquire and analyze recordings from multi-electrode arrays. It can be used for real-time as well as off-line analysis, and is written with extendibility in mind.
All of this software was developed for the Linux operating system. Porting it to other Unix variants should be straightforward. This software is free, and licensed using the GPL.
Matlab/Octave code library
Over the years, I have written quite a few functions for Matlab and Octave that others in the lab have found useful. You may find them useful too. The latest release is available on github. If you are using Ubuntu or Debian Linux, you can simply install the “deb” package on that page. Otherwise, please download the latest “zip” or “tar” archive and add the results to your Matlab or Octave search path. In that case, you may have to rerun “mex” on some of the more esoteric functions.
Other software and computer related things
In this space are listed some other bits and pieces that might be of use to others. These have no relation to my scientific work.
- vmcut-0.0.1: A program to cut Ogg Vorbis sound files into many segments, based on Michael Smith’s vcut (part of vorbis-tools). Currently the only documentation is obtained by running the program with “–help”, but it is really straightforward, so just take a look and you’ll figure it out.