Software
Over the years I've written a number of software tools for processing neuronal data, which people occasionally find useful. Most of it is covered under a Creative Commons license which lets you do pretty much whatever you want with it. None of it exactly supported, but if you fix a bug please feel free to let me know. Also, if you use the software in any substantial way in published research, please include an acknowledgement or citation. I would also appreciate a note letting me know how you're using it!
Also see my code blog for potentially helpful bits of code.
Bioacoustic signal decomposition
Figure 1. Spectrogram of a European starling motif.
Vocalizations often consist of spectrotemporally disjoint, discrete elements (e.g. Fig. 1), and it is often desirable to extract and manipulate these elements separately. However, because they often overlap temporally, the separation can only be achieved in the spectrotemporal domain. Znote is a software package for identifying components in bioacoustic signals and extracting the sound pressure waveforms associated with them.
znote is hosted on github: git://github.com/dmeliza/znote.git
Copyright C Daniel Meliza and Zhiyi Chi. Use of the code is free for non-commercial purposes under the Creative Commons Attribution-Noncommercial-Share Alike 3.0 United States License. Publications using the algorithm should cite the following paper:
Meliza CD, Chi Z, Margoliash D, "Representations of Conspecific Song by Starling Secondary Forebrain Auditory Neurons: Towards a Hierarchical Framework". J Neurophysiology, doi:10.1152/jn.00464.2009
Multitaper time-frequency reassignment spectrograms
Time-frequency reassignment is a technique for sharpening spectrographic representations of sounds (e.g. Fig. 1). For relatively simple non-stationary processes, TFR can provide substantial improvements in detecting fine structure. Further improvements can be realized by using multiple windowing functions (similar to the multitaper method for calculating the spectra of stationary processes), but the algorithms are computationally intensive. libtfrspec is a library for calculating multitaper TFR spectrograms which is implemented in C and uses the extremely fast FFTW library. It also supports calculating standard multitaper spectrograms and spectra, and comes with python/numpy and MATLAB interfaces. Licensed under the GPL.
libtfrspec is hosted on github: git://github.com/dmeliza/libtfr.git
Intracellular data acquisition in MATLAB
My dissertation work involved measuring intracellular responses in vivo to visual stimuli. In order to synchronize stimulus presentation with acquisition, I wrote a custom data acquisition suite using MATLAB and the MATLAB Data Acquisition Toolkit, loosely based on the Exper toolbox from Zach Mainen's lab. Given the price and closed source of the commercially available software for this sort of thing, this may be a useful alternative.
There are two versions available here. wholecell was written first, while I was collecting data, so many of the algorithms are ad hoc. metaphys is a complete rewrite, with better support for adding new modules, improved event handling, and support for instrument telegraphs and multiple DAQ devices. It's being used in the lab of my former advisor, Yang Dan.
Source: Metaphys is hosted on github: git://github.com/dmeliza/metaphys.git. Written and tested on MATLAB R14SP3 (DAQ toolkit 2.7) on a PC running Windows XP SP2. Also runs on Windows 2000.
Download: Wholecell 2.1. Written and extensively tested in MATLAB R13 on a PC running Windows 2000.
Axon ABF analysis for MATLAB
pClamp is a popular software tool for data acquisition in intracellular experiments, but the analysis program is a bit limited, or at least it was back in 2001 when I was using it for slice physiology. I wrote a small set of routines and a GUI for analyzing the time course of synaptic responses in MATLAB. The functions for reading ABF files may be of particular interest, although they only support ABF files from pClamp versions 6 and 8. There are several other options for ABF I/O at MatlabCentral.
Download: MATLAB ABF Analyzer 1.0
Comedi driver for Measurement Computing PCI-DIO96
Comedi is a suite of device drivers and a programming interface for manipulating analog and digital acquisition cards. The Measurement Computing PCI-DIO96 is a 96-channel digital I/O card that is substantially cheaper than the 96-channel digital I/O card made by National Instruments. I wrote a device driver for the MC device, which I'm making available here, licensed under the GPL. This is NOT maintained, so if you need to get it to work with a more recent version of comedi (my version was written for comedi 0.7.70), contact the maintainers of the comedi project.