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Background
To start EPHUS, one must invoke a startup file at the MATLAB command line. The file is a MATLAB function file
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(i.e.,
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.m
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extension),
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located
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in
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the
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current
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directory
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or
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somewhere
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on
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the
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user's
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MATLAB
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path.
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Every
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user/rig
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requires
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a
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customized
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startup
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file.
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The
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best
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way
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to
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create
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this
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file
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is
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to
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modify
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one
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of
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the
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supplied
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...
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,
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which
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are
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constantly
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maintained
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on
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this
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site.
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The
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startup
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files
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contain
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both
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configuration
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and
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application
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information.
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The
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vast
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majority
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of
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users
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only
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need
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to
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adjust
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the
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configuration
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information,
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which
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resides
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in
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clearly
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demarcated
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sections
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of
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the
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startup
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file.
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This
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guide
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steps
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through
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a
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typical
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startup
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file
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(
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), following the most current conventions.
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For
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completeness,
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both
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the
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configuration
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and
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application
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sections
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are
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described.
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Only
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power-users,
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however,
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should
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modify
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the
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application
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sections,
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and
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limited
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support
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can
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be
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provided
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in
...
this
...
case.
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The
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'Specimen'
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The Head
Here's
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the
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beginning
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of
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our
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startup
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file
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'specimen':
| Code Block |
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} 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); {code} The h3. Device/Channel _Configuration_ h3. _Configuration_ Variables h3. Program Startup (_Application_) h3. User Fcns (_Application_) h3. The End h2. Final Comments |
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 is common to all startup files.
The double-parenthesis(%%) signifies a MATLAB M-file cell. It helps to 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:
| Code Block |
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%% 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];
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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 specifying the particular object's properties. The Device Constructor page documents the syntax for the various devices presently supported by EPHUS. In this case, the multi_clamp function calls create a particular type of amplifier ( multi_clamp is a subclass of amplifier; an axopatch200B amplifier class is also defined, for instance).
In addition to devices, EPHUS contains two programs – acquirer and stimulator – which are employed in virtually every EPHUS deployment.