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. [Github]
• VScope is a tool for data acquisition and analysis of voltage-sensitive dye imaging experiments. [Github]
• NotedELN is an Electronic Lab Notebook. The software is described in Wagenaar (2014). [Github]
• QPlot is an alternative 2D plotting library for Python, Octave, and Matlab 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). [Github]
• 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. (An older homepage is still available for those needing to download versions that predate the github era.) [Github]

Python Packages

• ephysio is a package for loading electrophysiology data from OpenEphys and KiloSort. Get it using “pip install ephysio”.
• ppersist is a package that makes saving and loading of multiple Python variables as easy as Matlab’s “save” and “load” commands. Get it using “pip install ppersist”.
• physfit is a package for curve fitting that understands about uncertains on the x-axis as well as the y-axis. Get it using “pip install physfit”.
• salpa is a package for suppressing stimulation artifacts in (multichannel) extracellular recordings. Get it using “pip install salpa”.
• shards is a package for ray tracing that incorporates a library of publicly available lens data from Thorlabs and Edmund Optics. (Not yet available on PyPi.)
• spectralign is a package for aligning large collections of microscopy images using spectral methods, based on the “SWiFT-IR” package by Art Wetzel at the Pittsburgh Supercomputer Center (Wetzel et al., 2016). Get it using “pip install spectralign”.

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. [Github]

Other software

These have no direct relation to my scientific work:

• Photohoard: An open-source non-destructive photo editor and digital asset menagement system. [Github]
• vmcut: An ancient but still functional program to cut Ogg Vorbis sound files into 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.