Supporting Files

Configuration

The configuration file describes the location of data, acquisition and stimulus files, the amplifier type in use, and the default stimulus files to be used when switching to current or voltage clamp. The configuration file is created by the command new config, and the named fields can be filed in. The configuration file is saved with the command sc (for save config). A different configuration file can be loaded with the command gc (for get config). If the configuration parameters are not current visible in the window, they can be brought forward either by selecting the config button, or by issuing the command e config (editconfig).

When the configuration parameters are displayed, the names of the parameters, listed on the left side of the window, can be used as the commands to set the values on the right. Most of the parameters are self explanatory. However there are a few rules: The BasePath is the path under which the various stimulus parameter, acquisition parameter and data files are stored. The stimulus, acquisition and data paths should be entered relative to this base path:

BasePath c:\mat_datac\acq
StmPath StmPar (Where the program expects to find the stimulus files.
Note that this can be modified through the protocol menu.)
AcqPath AcqPar (Where the program expects to find the acquisition
parameter files.)
DataPath Data (Where the program stores the data, and associated
temporary data files.)

The configuration parameter UserExt defines a text string that is prepended to the filename. This is to allow the files to have unique identifiers in case the program is used to collect data in an environment with more than one data collection occurring on a given day.

Stimulus files

Stimulus files are central to the data acquisition operation of the program. The stimulus files are really MATLAB structures that are polymorphic: each different kind of stimulus is generated by a different method, which is driven by the data from the associated structure. The stimulus files all have a common header region, and a variable tail. The header contains identification of the file type (stim), the name of the file, and, upon writing to the data file, the m-code for the method and a possibly a copy of the stimulus waveforms. The header region is not visible to the user, and cannot be changed except within the program. Thus, this structure contains everything about the stimulus that might be needed at a later point either to reconstruct the stimulus or to determine glitches in stimulus computation (which of course will never happen).

The variable region of the stimulus file contains the data that is used to drive the generation of the stimulus waveforms by the method routine. For example, the files for the steps method contains information about the step levels and durations, the stimulus sequence, scale factors, holding voltages/currents, which parameter types and which step elements are to be sequenced, the associated acquisition control structure/file, and an optional pointer to a stimulus file that can be superimposed on the primary file. Note that if the associated acquisition control file field is empty, then the current acquisition field will be stored along with the stimulus data. This is the preferred method.

The current stimulus waveform can be previewed with the pv command, and saved to disk with the s [name] command. If the name doesn’t match the filename field in the structure, then the program will ask if the name should be changed. Stimulus files are restored from disk with the g [name] command; if no name is given a GUI file browser interface is provided to access the files. The contents of the current stimulus structure can be listed with the ls command from the MATLAB command line; and the structure itself can be returned to the base workspace with a command such as s = ls; s will contain STIM (s.STIM), which is the stimulus structure data. It is useful to examine these structures and the new.m file when writing new stimulus methods and structures (Details of the specific default methods provided with the program are described below).

Stimulus files are stored on disk in the directory designated by the configuration. The files are stored as standard MATLAB .mat files, and contain a single structure corresponding to the stimulus. If no acquisition file is specified when the stimulus file is stored with s, then the presently loaded acquisition file is save along with the stimulus file; thus the file contains two structures, and retrieving the stimulus file then retrieves the acquisition information also.

Acquisition parameters

The control of data acquisition is separate from the generation of stimuli, in the sense that it is held in a different structure that can be reused or shared by different stimulus paradigms, or alternatively, stored with the stimulus paradigm. Acquisition structures are not polymorphic (there is only one kind of acquisition structure). Each acquisition structure consists of a fixed section, and a variable, user modifiable section. Acquisition parameters include the channels to be collected, the sample rate, the number of points, the acquisition mode (voltage or current clamp), parameters that control the refresh of the display and points displayed, amplifier gains, acquisition hardware range settings and scale factors, filter settings, and potentially a junction potential offset. If not currently visible, the acquisition structure can be brought forward with the command e acq. The current structure can be saved with sa [name], and retrieved with ga [name]. The data in the structure can be listed at the MATLAB command line with the ld command, or retrieved into the base workspace with the command d = ld. When the acquisition structure is currently displayed, the parameters can be edited using the same methods as described above for the stimulus parameters.