Cell Censor
The top left corner of the window shows a graphic, in this case a photograph of a spiral ganglion cell. This picture can be any bitmap (.jpg) that you desire and can be loaded in the ini file. Movement of the mouse over the picture opens a window that allows you to choose voltage clamp or current clamp mode. The Cell Censor channels are either 0 for output / 0 for input or 1 for output / 1 for input. V0 for channels 0/0 voltage clamp, I0 for channels 0/0 current clamp, V1 for channels 1/1 voltage clamp, and I1 for channels 1/1 current clamp. The check boxes wc0 and wc1 control whether clamping polarity is in whole cell mode (checked) or inside out mode (unchecked) for channel 0 or 1. This is equivalent to but more accessible than inverting the polarity of input and output gains in the ini file. A math model can be toggled on/off. If a board is present and properly set up in the inifile, the name of the board will appear in the caption of the Cell Censor Window, otherwise model will be displayed. The display of telegraph inputs from a patch clamp amplifier is also toggled on or off, showing an additional, separate window. See Telegraphs. Enabling Dis_dual uncouples the default dual patch clamping setup (channels in/out: 0/0 and 1/1). If checked, you may deliver a separate command out of channel 1 by selecting chan 1 in the Vhold box (see below), while monitoring channel 0 in CC. When in effect pulse stimulation out of channel 0 is stopped and is replaced by channel 1. In this way you can stimulate the cell with a mechanical stimulus, for example, while monitoring the current response.
The Offset box allows one to zero amplifier offsets with the pipette in the bath prior to patch clamping. The voltage offset correction is added to the command potential, but is invisible to the user. It can be enabled/disabled with the check box, but will store the offset value when disabled. I prefer to use the offset knob on the amplifier, but this will do it in software automatically.
The CC window can be collapsed by clicking on the left arrow bar on the upper right. At the bottom of the window, the domain (time or frequency) can be selected for cell parameter tracking. See Cm Tracking for more info.
CC on - checking this box begins monitoring of cell/clamp characteristics. The text “Save” of the adjacent check box blinks, indicating that it should be enabled to save CC data (see below). Clamp time constant (tau), electrode series resistance (Rs), membrane resistance (Rm), cell capacitance (Cm), holding current (Ih), and series resistance-corrected holding potential (Vm) are displayed. If you place the cursor over these values, a popup appears which shows the corresponding RMS noise value over a short period of time.
CC save - if checked, CC data are saved to disk as an appendable ascii file readable by any spreadsheet or text editor. The file is saved to <UserIinitialsDate.cc> ; e.g., JS96115.cc; this file can be viewed graphically when the Analysis window is opened.
CC auto save (set in ini under CC+ tab to enable at startup; toggle on/off in CC, shift right click over CC Save) - turns on CC Save when CC is turned on. Green is on/ black off.
If the check box in the Ih display is checked then upon switching to current clamp from voltage clamp, the holding current is transferred to current clamp mode. This should allow the cell voltage to remain close to the same during the switch.
If the check box in the Vm display is checked then upon switching to voltage clamp from current clamp, the membrane voltage is transferred to voltage clamp mode. This should allow the cell current to remain close to the same during the switch.
CC inter - If checked then CC data collection is continued during protocol episodic and averaging intervals; also during trigger waiting periods.
Cmd hld - Enable the use of protocol holding potential in CC during interval data collection; returns to CC hold after protocol is finished.
Auto FileName - [This entry is now only in the INI file.] Enables auto file naming for collected data. Files are named with the last name initial, date and a number ranging from 1 to 999. For example, if the user name is Tom Jones, the first file of the day on 9/13/95 would be named <j5913001.abf>. For months Oct-Dec, the initial are used instead; e.g., <j5o13001.abf>. Note that automatic directories are made for each day, and are named with using first and last initials and the date. The directory name for the information given above would be C:\TJ95913. If auto file save is disabled the user is prompted for a filename.
Auto FileSave - [This entry is now only in the INI file.] file are saved after collection. If disabled the user is prompted to save file.
Disable File - if enabled, no data is saved after collections and no prompts are displayed. This is useful when equipment is being checked.
Chan Watch - if enabled, movement of mouse on this item will open a new window. Four channels (1-4) in addition to CC Censor input (Ch 0) are allowed at a sampling rate defined by the user. Labels and scales can be entered. These data are saved to disk with CC Censor data, and can be viewed with CC History.
Digital Out - mouse movement over the icon of the amplifier will open a window which can set or clear TTL level output on digital channels 0-7 (channel 7 is reserved for oscilloscope triggering). First select the desired channel or channels and then press the Set button. The On column will indicate which channels are on (high or 5V). The Clear button sets all channels off (low or 0V). The digital out set here is steady state. Digital out can also be set in the Command Utility to provide transient or synchronous output with the analog output signal. Following any parameter run, the digital channels are reset to the values set here in Cell Censor, if CC on is enabled.
Vpulse - size of voltage or current pulse delivered to cell. Steppable from -40 mV to +40 mV in 5 mV increments, or from -10 to +10 nA, in 0.1 nA increments. A value can be entered directly in the text box, as well.
nAvg - number of pulses averaged to determine CC Censor data. The number of points (multiples of 512) for the stimulus is set in the INI file. The maximum number of averages depends on the number of points (25 averages for 512 pt stimulus), since the stimulus is delivered as one array, and the maximum array is about 16k. It is important that the current or voltage response reaches steady state in order for Cell Censor to calculate the proper cell/clamp parameters. This is especially important when averaging since the stimuli are delivered as a sequential train of pulses.
CC inter - time between data collections. With a 90 MHz Pentium and Stealth graphics accelerator, data has been collected at 20 Hz with interval set to zero and no averaging. Most intervals set in jClamp are estimates, since in Windows multitasking will not permit precise time definitions. Data collection timing, however, is exact since DMA is used. If you place the cursor over the CC inter text box, a popup appears which show the actual interval.
RPD - opens the rapid parameter directory window. Pressing insert opens and closes the window as well.
Vhold or Ihold - sets the holding current or voltage for the CC channel or channel 1. Three predefined (in the INI file) levels can be instantly set by checking the corresponding selector. For example, before establishing whole cell mode, an appropriate holding potential can be set. The scroll bar can also be used to set the potential, or a value can be entered directed by overwriting the indicated potential (blue numbers). The holding potential is set for the selected channel, 0 being the Cell Censor channel, and 1 being analog channel 0. If PASS is enabled, then the CC holding potential is used for any subsequent data collection via parameter files; i.e., the parameter file holding potential is overridden.
Sbutton - Movement over the S button will open a window to allow setting of holding potential stepping information. Clicking on the S button will step the holding potential to the various potentials for the set time interval. Check T to enable saving CC trace at the end of each step, and V to enable saving a video clip at the end of each step. Executable in a user script -- see Script File.
Clk - sets the clock for the CC stimulus. Since the stimulus length is fixed, the clock is used to change the length of time of the stimulus. For proper CC evaluation, the response must reach steady state, and this can be achieved either by setting the clock manually in the text box, or by clicking on the transient trace icon (which sets the clock automatically so that the stimulus delivery time is 10 times the response time constant). Alternatively, AUTO can be enabled, which will periodically check for changes in response time constant (actually clamp tau) and adjust the clock appropriately. If PASS is enabled, then the CC clock value will be is used for any subsequent data collection via parameter files; i.e., the parameter file clock is overridden.
NB - notes can be written to disk in either text format [click pencil icon] or audio format [click speaker icon (if a sound card is present)]. This is most useful when CC Save is enabled, since links to the comments are available when viewing the CC data file under the Analysis section. In addition, if a video board is present with Video for Windows drivers clicking on the camera icon will open a window that allows viewing and saving camera output in a scaleable window (see Look! Section of Help).
TeleShow - Toggle telegraphs display for amplifier - program interaction.
Channel Selection – Only channel 0 and 1 are available in Frequency domain mode. Choosing 0 (channels 0/0) selects output channel 0 and input channel 0 (e.g., connected to patch clamp #1 ); choosing 1 (channels 1/1) selects output channel 1 and input channel 1 (e.g., connected to patch clamp #2 ); choosing B (both channels) alternates between channels 0/0 and 1/1 (pseudo-simultaneous recording); choosing C (both channels) also alternates between channels 0/0 and 1/1, but measures single cell information and responses in the adjacent cell – enabling estimates of junctional conductance. Gj0 is the conductance between the cell recorded with amplifier #1 and that recorded with amplifier #2; and visa versa. Series resistance and membrane capacitance are measured with the technique of Santos-Sacchi (J. Neuroscience 13: 3599 - 3611 ) by default, which is designed for simple, fairly small, single cells, and is robust despite filter settings. There are two check boxes in the Rs Frame. If the top check box is checked, the series resistance is and capacitance is obtained by Rs corrected - steady state command voltage divided by maximum instantaneous electrode current (estimated at zero time), and total integrated charge divided by Rs corrected - steady state command voltage. If the bottom box is chaeked, Rs is ignored and input resistance is only displayed. Under this condition Auto clock is disabled, since tau is not measured.
Check boxes in the plot window permit various options including automatic software selectable hardware gain (if supported by the board); if disabled clicking on the gain number can scroll through hardware gain; zero current trace; fix plot gain (normally it is automatically scaled to fit within the window) - if enabled a spin button is used to manually changed plot gain; store function to maintain previous traces; FFT to look at no-signal frequency response, clock initially set to observe 60 Hz noise - clock can be changed to change frequency range. Beware of aliasing!
