Starting EPHUS - Anatomy of a Startup File

Background

To start EPHUS, one must invoke a startup file at the MATLAB command line. The file is a MATLAB function file (i.e., .m extension), located in the current directory or somewhere on the user's MATLAB path. Every user/rig requires a customized startup file.

The best way to create this file is to modify one of the supplied example files, which are constantly maintained on this site. Startup files contain both configuration and application information. The vast majority of users only need to adjust the configuration information, which resides in clearly demarcated sections of the startup file.

This guide steps through a typical startup file, which follows the most current conventions. For completeness, both the configuration and application sections are described. Only power-users, however, should modify the application sections, and limited support can be provided for such uses.

The 'Specimen'

The Ventral View (Configuration)

The Head

Here's the beginning of our startup file 'specimen':

function gephus

%% STARTUP BOILERPLATE 
%Set up a wait bar to show the progress.
wb = waitbarWithCancel(0, 'Starting ephus...', 'Name', 'Loading software...');
pos = get(wb, 'Position');
pos(2) = pos(2) - pos(4);
set(wb, 'Position', pos);

This section contains the function declaration, with the name of the startup file – in this case, 'gephus'.

The next section (%%Startup Boilerplate) should not be modified, as the name implies. This section contains the code that is common to all startup files.

The double-parenthesis(%%) signifies a MATLAB M-file cell. They are used throughout the startup file to help clearly demarcate the different file sections, when viewed in the MATLAB editor.

Device/Channel Configuration

This section contains the configuration information for each of the devices & channels connected to this installation of EPHUS:

%% DEVICE/CHANNEL CONFIGURATION

%Amplifier objects for ephys
patch{1} = multi_clamp('text_file_location', 'C:\MATLAB6p1\work\Physiology\MClamp700BChannel1.txt', 'scaledOutputBoardID', 1, 'scaledOutputChannelID', 0, ...
    'vComBoardID', 1, 'vComChannelID', 0, 'channel', 1, 'name', '700B-1');

patch{2} = multi_clamp('text_file_location', 'C:\MATLAB6p1\work\Physiology\MClamp700BChannel2.txt', 'scaledOutputBoardID', 1, 'scaledOutputChannelID', 4, ...
    'vComBoardID', 1, 'vComChannelID', 1, 'channel', 2, 'name', '700B-2');

%Acquirer channels 
acqChannelNames = {'photodiode1'};
acqBoardIDs =   [2];
acqChanIDs =    [0];

%Stimulator channels 
stimChannelNames = {'pockelsCell' 'shutter0' 'xMirror' 'yMirror' 'shutter1' 'ao5' 'ao6' 'ao7'};
stimBoardIDs = [3 3 3 3 3 3 3 3];
stimChanIDs =  [0 1 2 3 4 5 6 7];

EPHUS programs sometimes employ specialized devices, which are implemented as MATLAB objects. In this case, for instance, the ephys program employs amplifier objects. All objects require a constructor in order to be created – this is a function which must be called and typically consists of several arguments initializing the particular object's properties. In EPHUS, all devices must be 'constructed' upon startup, and presumed to exist 'forever' (until EPHUS is closed).

In this case, the multi_clamp function calls create a particular type of amplifier – this refers to the MultiClamp 700B patch-clamp amplifier from Axon Instruments. The multi_clamp object definition is a 'class' (or, technically, a 'subclass') of amplifier. Another amplifier class that could be (but isn't) constructed here, is an axopatch200B, referring to the Axopatch 200B instrument, also from Axon Instruments.

The Device Constructors page documents the syntax for the various devices presently supported by EPHUS, such as the MultiClamp 700B and Axopatch 200B.

In addition to devices, EPHUS contains two programs – acquirer and stimulator – which are included in virtually every EPHUS deployment. These programs allow a number of National Instruments A/D, D/A, and buffered digital output channels to be user-defined and controlled. As with devices, the channels must be configured on EPHUS startup, and persist until EPHUS is closed (it is presumed that users are not re-connecting signals during an experiment!).

For A/D channels, handled by the acquirer, three variables must be entered: acqChannelNames, acqBoardIDs, acqChanIDs. The variable acqChannelNames is a MATLAB cell array, while acqBoardIDs and acqChanIDs are numeric arrays of integers. Each of the arrays is a 'row vector' of the same length.

• acqChannelNames: A cell array of strings specifying descriptive names for each of the A/D channels.
• acqBoardIDs: An array of integers specifying the numeric indices of the National Instruments (NI) boards associated with each of the named channels in acqChannelNames. The Board IDs are defined in the NI Measurement and Automation Explorer program included with the DAQmx driver. The NI convention is that boards are named 'Dev#', i.e. 'Dev1', 'Dev2', etc. EPHUS presumes this convention is followed, and the BoardID refers to the number following 'Dev'.
• acqChanIDs: An array of integers specifying the A/D channel indices corresponding to each of the named channels in acqChannelNames. Different boards have differing numbers of supported A/D indices. Channel indices for NI begin with 0.

The D/A channels are specified to initialize the stimulator in a similar fashion, with the variables stimChannelNames, stimBoardIDs, and stimChanIDs.

Configuration Variables

The next section contains configuration variables that can/should be modified by the user. In our sample file, we see:

%% CONFIGURATION VARIABLES
triggerOrigin = '/dev1/port0/line0'; %Specifies the digital line terminal on which the trigger pulse is output at the start of each acquisition
triggerDest = 'PFI0'; %Specifies the digital line terminal on which the trigger pulse is received. On /every/ board, this must be connected to the triggerOriginal terminal

xsgStartDirectory = 'C:\Data\'; %Default directory in which to save data files

pockelsOn=1; %Logical value specifying whether Pockels Cell is in fact attached/active on 

%Size, in microns, of the camera FOV (a camera application is required by the mapper program)
xVideoScaleFactor =  2625;
yVideoScaleFactor = 1980;

%% *************************END OF CONFIGURATION***************************************

The number and names of the configuration variables in a startup file will depend on the particular application (as determined by the application sections below). Generally, they should be well-documented via MATLAB comments as seen here.

Some variables appear in virtually all EPHUS deployments. For instance, triggerOrigin and triggerDest are used in all cases to specify, respectively, the digital line on which the trigger pulse for each acquisition is output and the terminal on which each board expects to receive this trigger signal, ensuring all boards begin acquisition at the same moment.

The end of this section is marked as the 'END OF CONFIGURATION'. The following sections represent the application areas of the startup file, and are only intended for modification by developers and power-users.

The Dorsal View (Application)

Timing/Clock Setup

This section initializes daqjob objects used by the various programs and handles the configuration of trigger and clock functions on the DAQ boards. This section makes use of daqjob, and in some cases nimex, class method calls.

For this file, we can see that the only task required is to configure the start trigger input and output lines:

%% TIMING/CLOCK SETUP 
%Set up the triggering.   
acqJob = daqjob('acquisition');
scopeJob = daqjob('scope');
setTriggerOrigin(acqJob, triggerOrigin);
setTriggerOrigin(scopeJob, triggerOrigin);
setTriggerDestination(acqJob, triggerDest);
setTriggerDestination(scopeJob, triggerDest);

Program Startup

This section starts each of the EPHUS programs needed for this particular application. In addition, the programs are sometimes configured further following their initialization.

Here, we can see the programs which are opened by this startup file:

%% PROGRAM STARTUP 
if waitbarUpdate(0.0, wb, 'Starting experimentSavingGui...'); return; end
xsg = openprogram(progmanager,{'xsg', 'experimentSavingGui'});
setLocalBatch(progmanager, xsg, 'directory',xsgStartDirectory);

if waitbarUpdate(0.1, wb, 'Starting ephys...'); return; end
ep = openprogram(progmanager,'ephys',patch);

if waitbarUpdate(0.16, wb,  'Starting ephysScopeAccessory...'); return; end
openprogram(progmanager,'ephysScopeAccessory',patch);

if waitbarUpdate(0.24, wb,  'Starting stimulator...'); return; end
stim = openprogram(progmanager, 'stimulator');
stim_addChannels(stim,stimChannelNames,stimBoardIDs,stimChanIDs);

if waitbarUpdate(0.32, wb, 'Starting acquirer...');return;end
acq = openprogram(progmanager,'acquirer');
acq_addChannels(acq,acqChannelNames,acqBoardIDs,acqChanIDs);

if waitbarUpdate(0.48, wb, 'Starting pulseJacker...');return;end
openprogram(progmanager, 'pulseJacker',{ep,stim});

if waitbarUpdate(0.52, wb, 'Starting userFcns...');return;end
openprogram(progmanager, 'userFcns');

if waitbarUpdate(0.56, wb, 'Starting autonotes...');return;end
openprogram(progmanager, 'autonotes');

if waitbarUpdate(0.60, wb, 'Starting headerGui...');return;end
openprogram(progmanager, 'headerGUI');

if waitbarUpdate(0.64, wb, 'Starting HotSwitch...');return;end
openprogram(progmanager,{'hotswitch', 'hotswitch', 'hotswitch', 'hs_config', 'hs_config'});

if waitbarUpdate(.68, wb, 'Starting photodiode configuration...');return;end
    pdiodeConfig = openprogram(progmanager, {'photodiode' 'photodiodeConfiguration'},'photodiode1');
end

if waitbarUpdate(0.76, wb, 'Starting mapper...');return;end
if pockelsOn
    mapper = openprogram(progmanager, 'mapper','xMirror','yMirror','pockelsCell','shutter0',pdiodeConfig);
else %Don't associate either Pockels or Photodiode channel with mapper, if Pockels is not used
    mapper = openprogram(progmanager, 'mapper','xMirror','yMirror','','shutter0');
end    
setLocalBatch(progmanager, mapper, 'xVideoScaleFactor', xVideoScaleFactor, 'yVideoScaleFactor', xVideoScaleFactor);

Each of the programs is opened by invoking openprogram(), which is a method of the Program Manager (@progmanager) class that is central to EPHUS.

The syntax for openprogram is:

Let's step through the arguments:

• hProg: An instance of a program object, which can be treated as a 'handle' to the program.
• progmanager: The (singleton) @progmanager object, which can be obtained by simply calling 'progmanager'
• programName: For typical programs, this argument is used, specifying the name of the program to start. The program names are those in the <EPHUS>\Programs directory of the installation. The program's figure will have the same title as the name.
• programInfo: A cell array can be supplied instead of a simple string. This can be used for two purposes.
  1. A two-element cell array can be used to display the program GUI with a different title than the program name. Note that the alias 'xsg' is supplied before the actual program in the array.
  2. For programs which contain multiple GUIs (noted as such in EPHUS Programs), the cell array programInfo option must be used. For legacy reasons, both the first and second elements should be the program's alias, while the third element should be the actual program name (i.e. the M-file in <EPHUS>\Programs). Thereafter, elements are added in pairs; the first is the sub-gui's alias and the second is the sub-gui's actual name (M filename).

• constructorArg#:

For our current example, most calls to openprogram() employ the simpl

UserFcn Bindings

The Tail

Final Comments

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