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., whereb
is Direction BinThe 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