Installing Spikoscope or SpikoRT on Windows

Installing program without source code: Download and run Spikoscope or SpikoRT installer (setup.exe). Launch Spikoscope.exe or SpikoRT.exe.

Installing program with source code: a)install labview 8.2.1 from National Instruments, b)download Spikoscope or SpikoRT source code, c)run labview, d)from labview open Spikoscope.vi or SpikoRT.vi, e)press the "run" button located in the upper left corner of the screen. Access the source code through menu "Window/Show Block Diagram". Double click any "vi" (virtual instrument) to access its content.

Spikoscope and SpikoRT are independant packages. They can be installed and run on the same computer, however source codes cannot be edited simultaneously.

SpikoRT analog input

SpikoRT requires a Labview compatible analog input board. Most National Instruments analog input board will work fine (the PCI-6034E is a common choice, connect inputs as differential using AI0-AI8 as first channel, then AI1-AI9, AI2-AI10...). Other board manufacturers provide labview drivers and replacement for standard acquisition VIs.

SpikoRT requires Traditional (Legacy) NI-DAQ driver (version 7.4.1) that can be downloaded from National Instruments (http://www.ni.com). SpikoRT works best with a screen resolution of 1280 x 1024 or higher.

Running Spikoscope or SpikoRT on other systems (linux, Mac)

Use method 2 with Labview 8.2.1 for that operating system. Labview will take some time at first launch to recompile Spikoscope/SpikoRT source code for the new system. There is one specific difficulty here. Labview cannot automatically recompile/relink SpikeOMatic (a spike sorting C code by C. Pouzat and M. Delescluse that is included in Spikoscope) on the new system. However a labview implementation of the same algorithm is provided, so you can remove SpikeOMatic without loosing major functionality. To remove SpikeOMatic, go to vi "FTWSortWhitenedEventsEM.vi" and remove the case condition SpikeOMatic_EM in the block diagram (right click the mouse and select "Delete this case"). SpikoRT does not include SpikeOMatic. The current (2007) development version of Spikoscope includes binaries for Windows and Mac (PPC and MacIntel native versions for OS X). Email if you need help or want to try the latest development version.

First contact

First, click Spikoscope "File" button to open recording data. The program supports several formats: the recording can be either a single file with multiplexed channels, or a directory containing one file per channel. Big and little endians, as well as 32 bits floating point or 16 bits integers are supported. The upper left buttons in the "File" screen give access to common formats: Axon binary file (abf) from Molecular Devices' Axoscope, multiplexed [all channels in one file] integer file (bdf), directory [one file per channel] float or directory integer. At this time Axon file format support is limited to continuous recording. Click one of those buttons and select your data file or directory (for example click "DIRfl" and select Spikoscope/SpikeOMaticInterface/SpikeOMatic_em/inst/doc/DemoRecord/DemoRecord, this is a tetrode recording by C Pouzat in locust). Verify/edit the descriptor of the recording data structure to suit your needs in terms of amplifier gain, offset, etc. Click “OK & get settings” to exit.

Back to Spikoscope main screen select "Extra_Plots", select channel 0 (control is right to the selector menu) , check "source" trace and set some display color/thickness/gain/offset. Last: go to Time Selection (in the selector menu) and set start at 0 and length of 1000ms for example. Important: set N to 1, and mode to "each trace". You should see your signal. If the signal looks strange, reverse big/little endian or integer/float in the "File" screen/descriptor editor.

Then try filtering, detection, computation of spike rate curves, spikes sorting, correlation histograms, etc. For each of these processings, set your parameters and call the corresponding functions with buttons located above the main display. Note that filtered trace "Filtered4EAPDetection" has to be generated before detection of extracellular action potential can be performed. EAP detection is based on the formula presented in Cohen and Miles 2000. It is quite fast/reliable and doesn't require a high signal/noise, but filtering has to be tuned for good result (typically bandpass 50Hz-3kHz, order 4 Bessel filter, file sampling at 15-20KHz, invert signal if polarity is opposite to that used in the 2000 paper).  Spike sorting is based on "Filtered4SpikeSorting" trace, typically through a 300Hz high pass, order 4 filter. So for spike sorting you'll need both "Filtered4EAPDetection" and "Filtered4SpikeSorting".

To estimate synchrony at the level of a local population or between two distinct sites, based on multi-unit activity, proceed through successive steps. 1-filter traces for extracellular action potential (EAP) detection, 2-detect EAPs, 3-compute single channel frequencies, both short term variations and trends (time constants are set in Extra_parameters as Tau and Tau2, typically 20-100ms and 10-30s, click button EAPFreq), 4-compute single channel variance and channel pair covariance by setting the Var&Cov_parameter time constant Tau (typicllay 10-30s) then clicking EAPVar&Cov button, 5-Plot selection and legends can be set from Extra_plots and ExtraPair_plots.

Generating figures

To make figures select the figure model in the upper screen selector, then click the figure button next to the selector. A new window appears with the figure.

Printing is controlled from each figure screen. The main display in Spikoscope is set for a maximum of 2048 points per trace, while figure screens are set at 8192. This is adapted for the better resolution of printer output and graphic editors used to generate publication quality figures, while it preserves a reasonnable data memory size. For example, without compression a single 15 minutes trace sampled at 20kHz would be composed of 18 million points, taking 72Mbytes of memory. The same trace compressed to 8192 samples takes 32kbytes and can be easily manipulated with a graphic editor.

There are 2 ways to export a figure from Spikoscope to editors such as Powerpoint or Illustrator:

1) From Spikoscope main figure or any preset figure, right click the mouse on the display and select Copy or Import Simplified Image, then paste into or open with a graphic editor. This method is quick and good for traces of 100-1000ms, but quality is degraded for longer traces due to the poor screen resolution.

2) From Windows control panel, set the default printer to print to postscript file (add printer, port FILE: Print to File, select a postscript printer such as HP Color LaserJet PS, set as default printer). From Spikoscope click the figure button and check the Print option control. Enter filename, open file from Illustrator. Figures genarated in this way are high, print quality, resolution.

Help and more

Look for tip strips when the mouse cursor passes over buttons. Questions and suggestions are welcome! Send mail and/or go to Spikoscope Forum on Sourceforge.net. For advanced spike sorting check the latest SpikeOMatic algorithms by Christophe Pouzat. For advanced analysis of intracellular synaptic potentials look for DETECTiVENT by Norbert Ankri.

Spikoscope - Browse and analyze electrophysiology recordings