gphys-package: Analyse electrophysiology data acquired by Neuromatic / Igor...

In jefferis/gphys: Analyse Electrophysiology Data Acquired by 'Neuromatic' / 'Igor Pro'

Description

gphys = Greg's ephys (and perhaps gee whiz)

Details

You can use functions such as PlotRasterFromSweeps to view spike data. This function and others depend on spike times stored in Igor Pro text files. For details of how to make these files in Igor see:

http://flybrain.mrc-lmb.cam.ac.uk/dokuwiki/doku.php?id=protocols:analysing_spikes

Spike times read in from Igor Pro text files by CollectSpikesFromSweeps are stored in R a modified list of S3 class spiketimes. You can add, subset and split these lists - see spiketimes and links therein for details.

You can also add continuous traces such as membrane voltage, PID signals etc to your raster plots. See AddLinesToRasterPlot.

If you have a mistake in the assignments of your ODD channels (e.g. you were opening channel 27 when you thought you were opening 29) you will likely need to use the function fix.odd to make the correct assignments. If you simply want to relabel a channel you can use the relabelfun argument of PlotRasterFromSweeps - see function documentation for examples.

Note that you may find it useful to set e.g. options(gphys.datadir='/Volumes/JData/JPeople/Jonny/physiology/data') appropriately at the start of a session or in your .Rprofile file. You can then use relative paths to your Igor data folders in the plot functions.

Finally as.repeatedTrain provides a bridge to the STAR package which includes many spike analysis functions including (smoothed) peristimulus time histograms.

See Also

options, spiketimes, PlotRasterFromSweeps, CollectSpikesFromSweeps and STAR package for further analysis.

jefferis/gphys documentation built on June 5, 2019, 9:45 p.m.