Analysis of Head Direction Cells

This analysis estimates the frequency of neuronal firing as a function of a head direction of an animal. The head direction should be described by two pairs of continuously recorded variables (head base X and Y and nose X and Y).

Parameters

Parameter

Description

Head Base X Position

Continuous variable that describes X position of the head base of the animal.

Head Base Y Position

Continuous variable that describes Y position of the head base of the animal.

Nose X Position

Continuous variable that describes X position of the nose of the animal.

Nose Y Position

Continuous variable that describes Y position of the nose of the animal.

Bad Position Value

When LED is obscured by the wires, both position variables may suddenly jump to 0 and then jump back to the previous position. All the data points where BaseX, BaseY, NoseX or NoseY is equal to Bad Bad Position Value are ignored.

Min Distance between LEDs

All the data points where the distance between base and nose LEDs is smaller than this value are ignored.

Direction Bin (degrees)

The bin for head directions. Head direction is measured in degrees (from 0 to 360). This parameter represents the size of the head direction bin in degrees.

Select Data

If Select Data is From Time Range, only the data from the specified (by Select Data From and Select Data To parameters) time range will be used in analysis. See also Data Selection Options.

Select Data From

Start of the time range in seconds.

Select Data To

End of the time range in seconds.

Interval filter

Specifies the interval filter that will be used to preselect data before analysis. See also Data Selection Options.

Send to Matlab

An option to send the matrix of numerical results to Matlab. See also Matlab Options.

Matrix Name

Specifies the name of the results matrix in Matlab workspace.

Matlab command

Specifies a Matlab command that is executed after the numerical results are sent to Matlab.

Send to Excel

An option to send numerical results or summary of numerical results to Excel. See also Excel Options.

Sheet Name

The name of the worksheet in Excel where to copy the numerical results.

TopLeft

Specifies the Excel cell where the results are copied. Should be in the form CR where C is Excel column name, R is the row number. For example, A1 is the top-left cell in the worksheet.

Summary of Numerical Results

The following information is available in the Summary of Numerical Results

Column

Description

Variable

Variable name.

YMin

Histogram minimum.

YMax

Histogram maximum.

Mean Hist.

The mean of the histogram bin values.

St. Dev. Hist.

The standard deviation of the histogram bin values

Algorithm

  • Position points that have coordinates that are within 0.001 of the specified ‘bad’ X and X values are removed

  • Head direction is calculated for each position

  • Direction bins are [0, b), [b, 2*b), [2*b, 3*b), etc., where b is Direction Bin

  • The intervals in time are calculated where head direction is in one of the direction bins

  • The number of of spikes in all the intervals where head direction was in a specific bin (for example, the head direction was from 0 to 10 degrees) is calculated

  • The number of spikes is then divided by the duration of the intervals for this bin to get the firing rate at the bin’s head direction