Behavioral Conditioning

For troubleshooting go here: https://github.com/theunissenlab/lab-documentation/wiki/Troubleshooting-(pecking-test)

Our lab has developed a set of conditioning protocols that work very well. Check out Julie's papers, such as this one.

The documentation was mostly stored on the Theunissen Lab google drive (+spa FET lab one), which can be accessed in the fet-lab google drive/Pecking_test in a series of docs, but we are in the process of moving everything to this wiki. The old basic how-to doc is this one.

We use operant conditioning boxes designed by which are housed in NAF 125. There are two linux boxes in the same room which each control two operant boxes, interfaced via arduinos (old notes from Tyler). Here's an old description of the hardware from Tyler, and here is a similar description in google doc format which may be slightly more current.

operating the pecking test chamber notebook

pecking test commands notebook

pecking test data structure notebook

Pecking Test Commands file

How To... connecting to webcams and other assorted things

Operating the Pecking Test Chamber

Here are some notes on the webcams.

Diagram of 125 devices

Pyoperant

The software running the operant condition is a forked version of pyoperant which Tyler Lee modified for our lab's use. Pyoperant was originally developed by the Gentner lab but doesn't appear to be maintained any longer.. This is the best description of how to set up and run an experiment. TODO Where is the pyoperant documentation? The odds ratio, for determining how well the bird is doing, is:

OR = log2(𝑂NoRe / 𝑂Re) = log2( (𝑝NoRe / (1−𝑝NoRe)) / (𝑝Re/(1−𝑝Re)) ).

Training

For the actual behavior, there are many tricks involved to get zebra finches to engage in operant conditioning. The primary one, of course, is making them hungry. Tyler and Julie developed a series of google docs to make this easier to keep track of, because it is crucial to be accurate here, both to get good data and for the health of the birds. The whole record-keeping system is stored in the FET google drive I think. Fasting birds is serious business and the records need to be impeccable!

Rules to Feed the Birds!

Start Session Data Form

This directory has additional docs : /home/fet/drive/Pecking_test/PythonConfig on pumkin

Preference Tests

We are set up to run preference testing while the pecking test is going. To do this, we play distance calls from 2 (or more) individuals occasionally during the test, and record audio to catch if the subject responds. Right now we only have 2 microphones and use the only available microphone input on the USB soundcards (one on each computer), so only 1 of boxes 2/3 and boxes 5/6 can run at a time.

To run the preference test:

• Make sure the microphones have batteries and are on (switched to red) in the boxes (e.g. 2 and 5)
• In the yaml file, make sure the preference test directory is set (conditions > playback > kwds: file_path should point to the directory with the wav files)
• Make sure the microphone is set up for the right box in code/pyoperant/pyoperant/tlab/local_tlab.py. it should initialize with a line like mic="ROCCAT Juke: USB Audio (hw:2,0)". If we figure out the webcam microphones, it could be simpler.
• When running the test, add --preference option; like pecking_test 2 run --preference

Viewing Data

The pecking_analysis repo has code that lets you view stats for pecking test sessions, including a notebook that generates plots for each day and subject.