Before commencing experiments, it is necessary to set up the stimulus parameter files. The way in which the program deals with the scaling of the data depends on these files, and there are several factors which interact. The ultimate indicator is the displayed data, which corresponds exactly to the numeric values of the data stored in the file.
In the configuration block, there is an entry for the amplifier type. The program recognizes several amplifiers from Axon Instruments, including the AxoProbe 1A (discontinued), the Axopatch 200 series, and the Multiclamp 700A. To get correct scaling for these amplifiers, you must enter the name of the amplifier in the field: edit config; amplifier axopatch, and save the configuration file. Additional amplifiers can be supported by editing the acquire_one.m file in the appropriate section.
There is no independent control of the stimulus scaling; it is set automatically according to the amplifier type and data collection mode (voltage or current clamp) in the acquire_one.m routine.
The recording scaling is a function of three different factors: the intrinsic gains of the amplifier, the setting of the gain selector on the output of the amplifier (for Axopatch and Multiclamp amplifiers), and the data collection mode. Recording scaling is controlled by the sensor parameter in the acquisition parameter block (edit acquisition). Typically these sensor values are large, rounded positive numbers, and there is a separate value for each channel collected. For example, to set the multiclamp commander, with the output gain set for 2 (corresponding to 1V/nA), the command:
sensor[40, 2]
will produce the correct data scaling. Note that in voltage clamp, the current channel is collected first, so this corresponds to a channel list (for example) of:
channel[11]
where the current output of the amplifier is connected to A/D input 11, and the voltage output is connected to A/D input 3. The recording scaling is also affected by the amplifier gain. For the Axoprobe, this is fixed in the software (10x for voltage, 1nA/V for the current), but for the Axopatch, the gain is read from the telegraph inputs, and is dependent on the mode (voltage or current clamp). For the Multiclamp, telegraphs are available, but we cannot read them into MATLAB yet, so it is treated as a fixed gain system, for which you will have to write down any variations from the standard gain settings.
In practice, setting the channel sensor factors is fairly easy, assuming that you have an independent way to verify the different outputs of the system.
Once the sensor values are set, it is a good idea to write a short MATLAB script to update these values, based on the setcc and setvc scripts found in the source directory. In this way, you add a command to the system that sets the gains automatically whenever you wish to design a new stimulus or acquisition protocol. A smart script would read the current configuration (global CONFIG), to get the amplifier type (in CONFIG.Amplifier.v), and set the gains accordingly.