Starting Ephus for the first time

Here we describe how to get started with the simplest electrophysiology experiments.

Hardware

Make sure your electrophysiology amplifiers are turned on and configured. For the MultiCLamp this includes running MultiClamp Commander.

All other hardware should be configured using the initialization file (see ephusInit_model.m or sample files). Study this file carefully and make sure all configurations are correct.

Starting up

Start the program by running ephus.m and selecting your initialization file when prompted, or by passing the name of your initialization file to the ephus.m function at the command-line.

This brings up all Ephus program windows. When prompted for a configuration select 'cancel'; after all you don't have one yet. Make the Matlab command window visible. You should see a bunch of messages,  concluding with 'loading completed'.

Move the GUIs around to make them visible. Each GUI corresponds to a program. You can view a description of all programs Description of all programs. Or you can skip ahead and simply close all but the following GUIs:
Oscilloscope
scopeGUI:ephysScopeAccessory
xsg

ScopeGUI

The ScopeGUI is a specialized program for whole-cell recordings. It is primarily used to hunt for cells and to check cell parameters. With a model cell configured, run the scope to verify that Ephus communicates via the amplifier. Start and stop the scope. Change the gain and mode settings on your amplifier to test the connection between Ephus and the amplifer. Changing the mode settings in MultiClamp Commander should change the modes indicated in the scopeGUI.

Program GUIs

Have a look at the menu bar of the XSG GUI. This menubar is shared by most other GUIs except programs related to the Oscilloscope. You can always use the 'Programs' menu to reactivate programs by clicking them.

Here are screenshots of the Mapper GUI, showing the 'File' and 'Programs' menus.

In the 'File' menu, above the separator we use 'Open' to configure GUI-related files (e.g. pulse directory for the pulseEditor; see below)
Below the separator is the ProgramManager menu item - which is used to save and load Ephus configurations.

Running an electrophysiology data acquisition

In the next few steps we will configure a simple electrophysiology experiment and save it in a configuration.

The XSG controls the saving of data files. For now, set it up in the following way:
Browse for your data folder (e.g. ..\cells). Check concat and autosave. Enter your initials.

Bring up ephys and the pulseEditor from the Program menu. Use 'File\Open' to select your pulse directory. Do this for both programs. (The pulse directory is one of the standard Ephus directories; see Ephus Tutorials > Setting Up Hardware and Software > System Requirements > Other Settings.)

In the pulseEditor, under pulseSets hit 'New'. The program will prompt you for a pulse set name. Type in 'basicEphys'.
Then make your first pulse by hitting 'New' in the Pulses panel; choose Normal. Name it testStep and pick give it some parameters as shown in the Figure (Number=1; ISI=100; width=100; amp=-5; delay=100). To view the pulse, select 'Plot' (modify the Display Time if necessary).

Now we want to apply this pulse (a  -5mV voltage step) during a whole cell recording using a test cell. In the ephys window select Stim On and Acq On. Select the pulse set and pulse using the drop-down menus. Set the trace length in seconds (i.e. 1 second). (Remember to turn off the scopeGUI; see warning above). Press 'Start' to collect your first electrophysiology trace. (If multiple channels are listed in the Ephys GUI 'Amplifier' listbox, you may need to select a pulse set and pulse for all channels, even if Stim On and Acq On are unchecked.)

The following happens:
The trace is displayed in the acquisition window
The trace is saved (as indicated in the Matlab Command window)
In the XSG the acquisition number increments by one to ready itself for the next acquisition
Running a looped data acquisition

Now we want to acquire a bunch of traces at regular time-intervals. Bring up the loopGUI. Try to use File\Open on this GUI. You will get an error message because the loopGUI is not associated with any data files. Under Timing Control select 'CPU'. Enter Iterations=3; Interval=3.

Select 'External' on the ephys GUI. Now this program is waiting to be started by another program. To start, select Loop on the loopGUI. 

The following should have happened:
The traces are displayed sequentially in the acquisition window
The traces are saved (as indicated by three new 'saved data' messages in the Matlab Command window)
02-Dec-2007 17:42:43 - Saved data to 'C:\Data\Gordon\cells\gs0001\gs0001AAAA0018.xsg'.
02-Dec-2007 17:42:46 - Saved data to 'C:\Data\Gordon\cells\gs0001\gs0001AAAA0019.xsg'.
02-Dec-2007 17:42:49 - Saved data to 'C:\Data\Gordon\cells\gs0001\gs0001AAAA0020.xsg'.
>>
In the XSG the acquisition number increments by three to ready itself for the next acquisition

Now let's save the state of the program, including settings and window positions, by saving a configuration. Go to any of the programs and select 'File/ProgramManager/Save Configuration Set' and make a new subfolder in your configurations folder 'basicEphys'.

To convince yourself that these settings have been saved select File/ExitAll on any program. Restart 'startEphus'. At the prompt select the basicEphys configuration.

This is going to be one of your configurations.

The gain setting for 700B

channel 1:

voltage clamp:

feedback Resistor:500m ?;external command Sensitivity: 20mv/V

current clamp:

feedback Resistor:500m ?;external command Sensitivity: 400pA/V