SYSTEM REQUIREMENTS
Matlab
(a) Version issues. Official support is for use with Matlab6p5; the software has been ported over to MatlabR2006a and it should run on both. However, there may be significant board timing errors with R2006a under certain conditions mainly having to do with fast scanning, due to bugs in recent versions of the Matlab Daq Toolbox.
(b) Required toolboxes:
MATLAB Version 6.5.2 , release 13 with patches
Data Acquisition Toolbox Version 2.2
Image Acquisition Toolbox Version Beta
(b) Recommended additional toolboxes:
Curve Fitting Toolbox Version 1.1
Image Processing Toolbox Version 4.1
Signal Processing Toolbox Version 6.1 - only the addmenu.m function is required
Statistics Toolbox Version 4.1
Data acquisition boards
Currently only National Instruments (NI) data acquisition boards are supported.
NIDAQ version issues -
currently the traditional NI drivers are supported (Use Nidaq 6.9, patch 1 & 2)
The mx drivers are not supported. If you have both drivers loaded Matlab will default to traditional automatically.
Recommended are three DAQ boards
2x MIO 16-4
1x 6713
Amplifier
The software supports the following amplifiers:
Multiclamp 700A
Multiclamp 700B
Axopatch 200B
Installing the software
Current version is located at the SVN repository
Best to use Tortoise SVN
http://tortoisesvn.tigris.org/
Then go to the SVN repository (login required):
https://svn.janelia.org/svobodalab/software/distribution/trunk
Grab the entire 'svobodalab' directory into a directory work/svobodalab on your local machine
If you are planning to make changes and check these back in use
SVN checkout (in your windows file menu, after installing tortoise)
Otherwise (recommended) use
SVN export
Typically it's good to rename the previous svobodalab folder to something like svobodalab_<current date> so that it's easy to go back.
Set the Matlab Path as follows:
Folders with subfolders:
MATLAB6p5p2\work\svobodalab\library
MATLAB6p5p2\work\svobodalab\Programs
MATLAB6p5p2\work\svobodalab\UserFcns
Folders without subfolders:
MATLAB6p5p2\work\svobodalab
MATLAB6p5p2\work\svobodalab\USERCLASSES
Setting up the triggering
All data acquisitions (DA, AD) are externally triggered. All boards are slaved to one DIO event. See BoardWiring_200B.pdf for one example.
Modifying settings in startEphys.m
startEphys is a startup file which configures the hardware (boards etc) and also starts the programs.
This file essentially establishes the correspondence between hardware channels and data and takes care of a few additional rig-specific paramters. It needs to be modified in multiple places. Study the example here startEphysMapper200B.m.
Look for places marked by
% <<<<<<<<<<---------- CONFIG
These need to be set by the user.
setLocalBatch(progmanager, mapper, 'xVideoScaleFactor', 2667, 'yVideoScaleFactor', 2000);%<<<<<<<<<<---------- CONFIG
Sample rate is currently hardcoded to 10K and is not user-settable in either testEphys or via a gui in Ephus.
Other settings
Typically it is convenient to create the following directories on your hard drive:
C:\DATA
C:\DATA\username1, etc - where primary data goes
C:\DATA\ephus
C:\DATA\ephus\configs
C:\DATA\ephus\cycles
C:\DATA\ephus\mapPatterns
C:\DATA\ephus\pulses
C:\DATA\ephus\userFunctions
These directories will hold a variety of settings related to experiments.
configs - contain configurations of various programs (i.e. GUIs)
cycles - contain cycles --experiments in which configurations are changed from one cycle position to the next.
mapPatterns - contain files that control the positions of the laser beam during maps
pulses - waveforms used to generate DA objects
userFuctions - .m files that are executed at particular places in the code to allow user-defined on-line analysis and other functionality
Where does one place the Multiclamp files?