1. Connect the module’s output and input to the appropriate DAQ output/input using the connector module.
   
2. Set the model cell to the bath setting.
3. Hit pulse to output the default step wave (10mV/10ms square voltage wave at a holding potential of 0mV)
4. Check to see if resistance output matches the model cell settings for bath
   1. If resistance measured is infinity, make sure the module is connected correctly using the Connector Panel, and the DAQ output/inputs are being used are set to active with the System Control Panel
   2. If the resistance measured is wrong, make sure the scaling factors are set correctly. Use the System Control Panel if this was done manually or any amplifier control module being used.
5. Next, switch the amplifier model cell to the whole cell configuration, and check to see if the resistance again matches specifications
6. While pulse is still toggled, switch to the membrane properties tab by clicking on the tab
7. Hit Acquire to run the membrane property calculation. By default, it should be a single test using an average of 5 steps.
8. Check to make sure the calculated parameters match the model cell specifications, if they do not, run the test again. During experimentation, it is wise to run the test multiple times, or use the continuous mode.

1.  Install Qwt 5.2
Follow this link to the tutorial on installing Qwt 5.2.

2. Download RTXI v1.4 that includes Comedi snapshot
First, navigate to the preferred directory where you want to install RTXI and use the following command:

$ sudo git clone -b 1.4 https://github.com/RTXI/rtxi.git

* Note: If git has yet to be installed, it can be installed through

$ sudo apt-get install git

3. Compile and install the Comedi sources

$ cd rtxi-1.4/comedilib
$ sudo sh autogen.sh
$ sudo ./configure –-with-udev-hotplug=/lib --sysconfdir=/etc
$ sudo make clean
$ sudo make install

$ cd ../comedi_calibrate
$ sudo autoreconf -i
$ sudo ./configure
$ sudo make clean
$ sudo make install

$ cd ../comedi
$ sudo sh autogen.sh
$ sudo ./configure
$ sudo make clean
$ sudo make install
$ sudo mkdir -p /usr/local/include/linux
$ sudo cp include/linux/comedi.h include/linux/comedilib.h /usr/local/include/linux

4. Compile and Install RTXI v1.4

$ cd ../
$ sudo sh autogen.sh
$ sudo ./configure
$ sudo make clean
$ sudo make install
$ sudo cp rtxi.conf /etc

5. Adjust permissions that might interfere with access to DAQ card and RTXI Qt Preferences

$ sudo chmod a+rw -R /home/*/.qt
$ sudo chmod a+rw /dev/comedi*
$ sudo gedit /etc/rc.local

By adding the following lines to /etc/rc.local,  the permissions will be changed upon computer reboot, allowing RTXI to access these files without being run with sudo privileges:

chmod a+rw -R /home/*/.qt
chmod a+rw /dev/comedi*

6. Run RTXI

$ rtxi

7. Recompile all custom modules
In order to load any custom modules, they must be recompiled AFTER installing RTXI v1.4.

(Updated 5/20/2013: Sources are now downloaded through RTXI’s git repository)

Studies of behavioral and neural responses to distorted auditory feedback (DAF) can help shed light on the neural mechanisms of animal vocalizations. We describe an apparatus for generating real-time acoustic feedback. The system can very rapidly detect acoustic features in a song and output acoustic signals if the detected features match the desired acoustic template. The system uses spectrogram-based detection of acoustic elements. It is low-cost and can be programmed for a variety of behavioral experiments requiring acoustic feedback or neural stimulation. We use the system to study the effects of acoustic feedback on birds’ vocalizations and demonstrate that such an acoustic feedback can cause both immediate and long-term changes to birds’ songs.

The membrane test module is used to measure important electrophysiological parameters, such as electrode resistance and cell properties, during whole cell patch clamp experiments. This module comes bundled with RTXI v1.4 (Utilities -> Patch Clamp -> Membrane Test). Used in voltage clamp mode, the primary use of the module is to calculate the membrane resistance when applying a voltage pulse. This provides the user vital information about the recording electrode during the experiment. The user is able to quickly change settings such as holding potential, size, and width of the voltage pulse. The second major use of the module is to calculate several membrane properties once the whole cell configuration is reached (calculation details). These parameters include membrane capacitance, access resistance, and membrane resistance. A brief tutorial is available on connecting and testing the Membrane Test module along with a patch clamp amplifier:

Membrane Test Tutorial

Input Channels

1. input(0) – “Voltage Output (V)” : Voltage output of module, to be connected to external input of amplifier

Output Channels

1. output(0) – “Current Input (A)” : Current input of the module, to be connected to the output of the amplifier

For the majority that has installed RTXI through the use of our Live CDs, the COMEDI and Qwt sources must be installed prior to compiling RTXI. The upgrade instructions can be found here.

For those who have installed RTXI manually will find the upgrade process relatively simple. It requires updating the source code through SVN in the RTXI directory

$ sudo svn update

and installing a new dependency, Qwt (installation instructions here).

--disable-clampprotocol

For those who wish to install Qwt (http://qwt.sourceforge.net/), please perform the following instructions:

$ cd /opt/
$ sudo wget http://www.rtxi.org/wp-content/uploads/2013/01/qwt-5.2.tar.gz
$ sudo tar xzf qwt-5.2.tar.gz
$ cd qwt-5.2
$ sudo qmake
$ sudo make clean
$ sudo make install

To install RTXI v1.4 from scratch, please see our installation guide.

For a list of changes from v1.3, see below.

New Modules:

• FIR Filter
• IIR Filter
• Signal generator
• Wavemaker
• Noise generator
• TTL pulse generator

Patch Clamp Electrophysiology Suite:

•  Amplifier control modules allows RTXI to interface with commonly used amplifiers, allowing for automatic scaling of inputs/outputs to counter gains. The capabilities of the modules are determined by the specific amplifier it was designed to control.
• The membrane test module is a utility used to monitor pipette resistance and calculate cellular parameters during patch clamping.
• The clamp protocol module is designed to run complex voltage clamp protocols and display acquired data in real time. Future iterations will include data analysis tools, and current clamp.

Data Acquisition:

• Data recorder buffer size can now be changed through user preferences.
• Data recorder now shows data file size and trial number
• Analogy drivers have been added for Xenomai configured RTXI systems
• Updated comedi drivers to correctly use calibration from comedi_calibrate. Previously, it was not using the calibration.
• Added calibrate button to system control to allow control over when calibration is used on a specific channel.
• Comedi_calibrate works in conjunction with analogy
• Comedi can now be used if RTXI is configured in POSIX mode.
• Added button to calibrate COMEDI for /dev/comedi0 and return a message box for success/failure.

Other Changes:

• Organization of the RTXI menu has been changed. All bundled modules (outside of system modules) will be placed under Utilities.
• Performance measurement module has been improved
• Due to the incorporation of Qwt in the Clamp Protocol module, Qwt is now considered a dependency that has to be installed

Bug Fixes:

• The MATLAB getTrial script has been updated to fix a bug that scrambled the order of data if trials were >= 10
• Fixed issues with the oscilloscope not updating its time period correctly in rare cases, causing the output to be on the incorrect time scale
• Fixed issue where the number of comments recorded was limited by the number of parameters of a module

Axon Multiclamp 700 Series Commander

The VClamp and IClamp settings of the module must match the amplifier settings set by the user through the Axon software. The mode must also correspond to Axon software, unless the module is being to control the mode. Mode control is done through the amplifier’s mode input located on the front of the amplifier.

output(0) – “Mode Telegraph” : Outputs an analog voltage signal to the amplifier through the mode telegraph, allowing the module to control the mode of the amplifier. The “Ext” box must be checked on the Axon software, located next to the mode.

 Axon Axopatch 1D Commander

The settings of the module must match the settings of the Output Gain, Headstage Config, Ext. Command Sensitivity, and mode set by the amplifier’s switches. The module is able to accept the amplifier’s Gain Telegraph, allowing it to sense changes to the gain knob of the amplifier. It is also able to sense the mode of the amplifier through its Mode Telegraph. These are both located on the back of the amplifier.

input(0) – “Mode Telegraph” : The analog voltage signal from the amplifier’s mode telegraph, allowing the module to determine the mode of the amplifier when the auto button is toggled

input(1) – “Gain Telegraph” : The analog voltage signal from the amplifier’s gain telegraph, allowing the module to determine the gain set when the auto button is toggled.

Axon 200 Series Amplifier Commander

Tested with the 200A and 200B, the Output Gain, Headstage Config, and Amp Mode must match the amplifier settings set by its switches. The module is able to sense the mode through the amplifier’s mode telegraph, located on the back of the amplifier.

input(0) – “Mode Telegraph” : The analog voltage signal from the amplifier corresponding to the mode of the amplifier

RTXI HDF5 Matlab Files