Any other software needed for your hardware, e.g. MultiClamp Commander
Download and run installer for desired release (from table above)
The installer places each release in a new subfolder, which does not conflict with previous releases
Set the Matlab path
Remove any older Ephus versions from your path
Add the new folder (e.g. C:\Program Files\Ephus\R210\Ephus) to your path, along with its subfolders
Add the startfiles folder (e.g. C:\Program Files\Ephus\startfiles) to your path
Edit the initialization file
The installer created a model initialization file, e.g. startfiles\initialize-R210.m. Alternatively, sample files can be downloaded.
Edit this file to reflect your hardware configuration, according to the instructions found therein
To run, first ensure any required programs (such as MultiClamp Commander) are running, then start Ephus in Matlab by passing the name of the initialization file to the ephus command, e.g. ephus('initialize-R210.m')
Alternatively, instead of using the installer program, you may download a ZIP file for the release (from table above), unzip it to your desired location, add this folder to the Matlab path, and use the Ephus\ephusInit_model.m file as a template for your rig-specific initialization.
Ephus is named for the fabled baseball pitch, and pronounced as "EFF-ess". As with the pitch, it may trick you at first, but eventually you're sure to hit a home run. Of course, the name also evokes electrophysiology, which is the fundamental orientation of the project, be it optical or electrical.
How to Analyze Data
Analysis is most easily performed using Matlab
For analysis using other programs, you must be able to load/read Matlab .mat files, or else first convert to your preferred file format
XSG data file format
.xsg data files are binary Matlab (.mat) files and can be loaded using load('somefile.xsg', '-mat')
each file contains a data and a header structure
In a typical patch-clamp single-amplifier experiment, the membrane potential/current recording is found in the following field: data.ephys.trace_1
Meta-data are stored in the header structure; for example, the sampling rate is stored in the following field: header.ephys.ephys.sampleRate
The header structure contains fields for all the individual ephys programs, while the data structure contains fields for only those programs that acquired data (typically ephys for patch-clamp amplifier channels and acquirer for everything else)
Autonotes data file: For each experiment (typically for each neuron), Ephus saves a .txt file containing timestamped notes, which (a) are automatically added for every new data acquisition or hotswitch, and (b) can be added manually (e.g. "added 10 uM NBQX").
The LSPS program stores map data in a special manner
Each map is stored as an .xsg file in a sub-directory named e.g. "map01"
mapAnalysis is a Matlab GUI program for rapidly analyzing and averaging multiple maps, typically recorded from a single neuron
mapAnalysis will generate an .m file containing meta-data and processed map data (e.g. mean current per map pixel, peak current per map pixel)
If you wish to use *mapAnalysis", you may download it here: Analysis Tools
mapAverager is a Matlab GUI program for averaging maps across multiple experiments/neurons, and can also compare two groups of experiments/neurons (optionally restricted to a region-of-interest, ROI)
If you wish to use mapAverager, you may download it here: Analysis Tools