Software for Objective Coupled Planar Illumination (OCPI) microscopy:

See the OCPI paper in Publications for information about the technique. This software package handles image acquisition, z-scanning (repositioning of the objective), and laser shuttering to rapidly acquire a time series of three-dimensional stacks.

Imagine (85K)
This program was written in C++ and runs under Windows XP. Please see the readme.txt inside the zip package for more details.


Software for recording and analyzing mouse song:

Acquisition code (2.5M)
This acquistion code runs under the Linux version of Matlab. To do data acquisition, you need to first install comedi. Comedi is an unusually nice environment for data acquisition, but (unlike most Linux software) it is challenging for someone new to Linux to install. We recommend that you seek help from an experienced user.

You also need to install our Matlab wrappers for comedi. These were tested for release 13 of Matlab, they may need some updating for more recent versions.

Of course, there are other (e.g., commercial) ways of recording ultrasounds, and you should be able to use one of those and then import the results into our analysis software.


Analysis code (94K)
You need Matlab for this. This contains functions to pitch shift the songs, work with sonograms, identify syllables, classify syllables, etc. This code should run on any platform supported by Matlab (including Linux, Windows, and Macs).

Updated files (New! 2008-06-12)
We have had many requests for support for reading .wav files. Rather than coach everyone through adding support themselves, we have finally decided to add that support ourselves and post it here for general use. Also included are a couple of missing dependencies. Two of the files in this archive (sound2sng and spsngplot) can safely replace the versions of the files in the original archive (above).

Sample data set: sparse sonogram format (5.6M)
Download this if you want to play with our analysis code before going to the effort to obtain your own data. It's in a format that we call a "sparse sonogram," basically the sonogram stored in a sparse matrix format (thresholded by intensity). Functions in the "analysis code" package know how to read this.

Sample data set: raw format (79M)
Download this if you really need a raw recording. It's the same trial as above in sparse sonogram format. Note that you can "recover" a full waveform recording from the sparse sonogram using sng2sound, so you may not need this file.


Please: report bugs to either
     Tim Holy (holy, followed by @, then "wustl", a dot, and then "edu")
or
     Zhongsheng Guo (zsguo, followed by @, then "pcg.wustl", a dot, and then "edu")
(Try to parse that, spammers!)