Using the Clampex 6.0 DAC File Feature (Playing Back Data Files as Command Waveforms)

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Harry Watts
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1 Using the Clampex 6.0 DAC File Feature (Playing Back Data Files as Command Waveforms) Clampex 6.0 has the ability to play back data files as command waveforms. Unlike the Parameters Waveform table, which allows for up to eight step or ramp transitions per episode, using a data file allows the command to be specified point-by-point. The data files may be either recorded binary pclamp data files or arbitrarily constructed text files. The sections below describe how to scale the command waveform data properly. The examples assume that we are recording voltage data, such as an action potential, to be played back as a voltage clamp command using an Axopatch. Using a Binary Data File Using an Axopatch, the external command scaling in voltage-clamp mode is normally fixed at 20 mv at the cell per 1 V at the External Command Input, which is connected to the DAC. When recording data to be used as a DAC File, the data may either be recorded with the equivalent scaling, or the data may be scaled when it is played back, using the Parameters DACFile form. The input scaling in pclamp is expressed as Volts at the ADC per Unit at the cell. In the case of recording an action potential, the units are in mv. The output scaling in pclamp is expressed in a reciprocal manner: Units at the cell per Volt at the DAC. To see the relationship, the output scaling should be expressed in the same way as the input scaling: Reciprocal of 20 mv 1V = 0.05 V at the DAC 1V 20 mv 1 mv at the cell If you are able to scale the output of your instrument to 0.05 volts (50 mv) output per 1 mv measured at the cell, the data will be recorded in the data file perfectly for an output scaling of 20 mv at the cell per 1 V at the DAC. See Figure 1. Application Note #2 December 1993 Page 1 of 5

2 Figure 1. Recording data at the same scaling as the output scaling for an Axopatch (20 mv at cell / 1V at DAC). When data meant for playback are not recorded at the same scale as the output scaling, the parameter Scale factor in the Parameters DACFile form scales the data before it is played back as the command. For example, if data were recorded with the scaling at 100 mv at the ADC per 1 mv at the cell (input scaling factor of 0.1 under Parameters Scaling), when the data file was played back the command would be twice as large as expected because the command is sent at 50 mv at the DAC per 1 mv at the cell (this is the same as 20 mv at cell per volt at DAC). See Figure 2. The required scaling factor for playback is: 50 mv at the DAC per mv at the cell (output scaling) = 0.5 (no units) 100 mv at the ADC per mv at the cell (input scaling) Application Note #2 December 1993 Page 2 of 5

3 Figure 2. The data file was recorded with an input scaling of 0.1 V at ADC per mv at cell (top). When played back as a DAC file (bottom), the signal at the cell is twice as large (note the Y-axis scaling) because the output scaling is 50 mv at the DAC per 1 mv at the cell. Application Note #2 December 1993 Page 3 of 5

4 Figure 3. Scaling the data file for playback. By placing a Scale factor of 0.5 in the Parameters DACFile form (Figure 3), the WaveformPreview screen in the Figure 2 example would show that the output waveform was now half the amplitude, corresponding to the ±100 mv of the original input signal. When using recorded data files as DAC files, the Scale factor is determined by dividing the output scaling by the input scaling. You must express these two values such that the division cancel the units out. Creating a Text DAC File The Clampex DAC File feature accepts text files, so any function or arbitrary data set may be used as a command waveform. The data must be arranged in columns. Multiple columns are treated as multiple episodes. The number of points in each column should be the same as the number of points in each episode of the experiment. After creating the text file, use the ASC2ATF utility to convert the file to an ATFformat text file. Clampex expects to read the DAC file values in D/A units, but there is also a way to use real units (such as mv) in the DAC file. The scaling factors are explained here. The examples assume that we are using an Axopatch, which has a scaling factor of 20 mv at the cell per 1 V at the External Command Input (which is connected to the DAC). The TL-1/LabMaster and Digidata 1200 systems must be considered separately. The TL-1/LabMaster system has a 12-bit D/A converter ( ±2048 D/A units) and a ±10.00 V DAC range, therefore the scaling in the text DAC file is: 1000 mv at DAC * 2048 D/A units = D/A units 20 mv at cell 10,000 mv at DAC 1 mv at cell The Digidata 1200 system has a 12-bit D/A converter ±2048 ( D/A units) and a ±10.24V DAC range: 1000 mv at DAC * 2048 D/A units = 10 D/A units (But see below!) 20 mv at cell 10,240 mv at DAC 1 mv at cell For the Digidata 1200 system, there is one more factor to consider. The Digidata 1200 system treats all data as if they are 16-bit. The DAC is 12-bit, however, so the D/A unit values are placed in the upper 12 bits of the 16-bit DAC I/O register. The four lower bits would comprise the finer resolution if a 16-bit DAC were used. Since the DAC on the Digidata 1200 is 12-bit, the lower four bits are ignored. When you send data using a DAC file, you must send the values so that the 12-bit data is in the upper 12 bits of the 16-bit register. The data values must be shifted up four bits, which is the equivalent of multiplying the values by 16. Therefore the actual scaling factor when creating a text DAC file for the Digidata 1200 is 16 times 10 D/A units per mv, or 160 D/A units per mv. To send a DAC command of -100 mv at the cell, the DAC file value for the TL-1 should be and for the Digidata 1200 it should be Application Note #2 December 1993 Page 4 of 5

5 An easier method is to place the actual mv values in the DAC file, such as -100 for -100 mv, and put the scaling factor in the Parameters DACFile form. At the parameter Scale factor, for the TL-1 put (D/A units per mv at the cell), and for the Digidata 1200, put 160 (D/A units per mv at the cell). See Figure 4. Figure 4. Scaling a text data file for playback. Additional Notes 1. The section Creating a Text DAC File explains that the Digidata 1200 treats data as 16-bit, so that 12- bit data are placed in the upper 12 bits of a 16-bit register. This creates a problem when a binary data file is recorded using a TL-1/LabMaster, but is later used on a Digidata 1200 as a DAC file. The LabMaster-produced data file has the data in the lower 12 bits, but the Digidata expects to see it in the upper 12 bits. The solution is to place a Scale factor of 16 in the Parameters DACFile form. Multiplying by 16 is the same as shifting the data up four bits. 2. In Figure 2, the top picture show s the recorded sine wave. The bottom picture shows the data file being played back as a DAC file. Note that the first few points and the last few points are held at a constant level. This is because Clampex holds the first few and the last few points at the specified holding level. The number of points held at the holding level at the beginning and the end of the episode depends on the length of the episode. The formula is one point for every multiple of 64 points in the episode. For example, in a 512-point episode, 512 / 64 = 8 points at the beginning and 8 points at the end of every episode are at the holding level. This means that if you create a DAC file for a 512- point episode, the file should contain 512 points, but the first 8 and the last 8 points will be ignored, so place your waveform in the middle 496 points. There is an exception to this rule. Under Parameters Waveform, if you set Interepisode holding level to "Use last epoch," the last 8 points of the DAC file will be used. After the first episode, the first 8 points of the subsequent episodes will be held at the same level as the last point in the previous episode. Application Note #2 December 1993 Page 5 of 5

Contents. 1 Using a Recorded Waveform as Stimulus Rules An Example... 2

Contents. 1 Using a Recorded Waveform as Stimulus Rules An Example... 2 Contents 1 Using a Recorded Waveform as Stimulus 1 1.1 Rules............................... 1 1.2 An Example........................... 2 1. Using a Recorded Waveform as Stimulus The DAC-stimulus template