Place Cell Analysis

This analysis estimates the frequency of neuronal firing as a function of position of an animal. The animal position should be described by two continuously recorded variables.

Parameters

Parameter

Description

X Position

Continuous variable that describes X position of the animal.

Y Position

Continuous variable that describes Y position of the animal.

Fix Positions

This option specifies whether NeuroExplorer needs to fix problems that often occur in recording of position variables. For example, when LED is obscured by the wires, both position variables suddenly jump to 0 and then jump back to the previous position.

Fix Threshold

Fix Positions parameter. See Algorithm section below for details.

Fix Bad X

Fix Positions parameter. The ‘bad’ value of X variable. See Algorithm section below for details.

Fix Bad Y

Fix Positions parameter. The ‘bad’ value of Y variable. See Algorithm section below for details.

X Min

X axis minimum in X Position units.

X Max

X axis maximum in X Position units.

Y Min

Y axis minimum in Y Position units.

Y Max

Y axis maximum in Y Position units.

Number of Bins (X)

Number of bins along X axis.

Number of Bins (Y)

Number of bins along Y axis.

Display

This parameter determines what kind of Place Cell Analysis display is shown (Path, Firing Positions, Time Spent (in each cell), Number of Visits (to each cell), Spike Counts (for each cell), Firing Rates (for each cell), Firing Fields).

Min. Time Spent

Minimum time spent. This parameter is used only with Firing Rates display. If the animal spent less time in the cell than Min Time Spent, the firing rate for the cell is set to zero.

Min Visits

Minimum number of visits. This parameter is used only with Firing Rates display. If the animal visited the cell less than Min Visits number of times, the firing rate for the cell is set to zero.

Firing Rate Bin

Bin size (in seconds) to calculate firing rates.

Min Std. Dev. in Field

Minimum standard deviation in the field. See Algorithm section below for details.

Min. Pixels in Field

Minimum number of pixels in the field. See Algorithm section below for details.

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.

Int. filter type

Specifies if the analysis will use a single or multiple interval filters.

Interval filter

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

Create filter on-the-fly

Specifies if a temporary interval filter needs to be created (and used to preselect data).

Create filter around

Specifies an event that will be used to create a temporary filter.

Start offset

Offset (in seconds, relative to the event specified in Create filter around parameter) for the start of interval for the temporary filter.

End offset

Offset (in seconds, relative to the event specified in Create filter around parameter) for the end of interval for the temporary filter.

Fix overlaps

An option to automatically merge the overlapping intervals in the temporary filter.

Smooth Matrix

An option to smooth the matrix after the calculation. See Post-Processing Options for details.

Smooth Radius

The radius of the smoothing filter (in cells) See Post-Processing Options for details.

Smooth Colors

An option to smooth colors (blend colors across cells to make smooth color transitions). This option may require considerable computation time.

Bins with Num Visits Less than Min

An option on how to display cells where the number of visits is less than the specified minimum (Min Visits parameter).

Bins with Time Spent Less than Min

An option on how to display cells where the time spent is less than the specified minimum (Min. Time Spent parameter).

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.

Spikes

The number of spikes used in calculation.

Filter Length

The length of all the intervals of the interval filter (if a filter was used) or the length or the recording session (in seconds).

Position ISI mode

Average interval between two consecutive position data points (in seconds).

Mean Firing Rate

Mean firing rate (mean of all the firing rates for all the cells).

St. Dev. Firing Rate

Standard deviation of the firing rate (st. dev. of all the firing rates for all the cells).

Firing Fields

The number of firing fields.

Field N Num Cells

The number of cells in the firing field N.

Field N Centroid X

X coordinate of the field N centroid.

Field N Centroid Y

Y coordinate of the field N centroid.

Field N Peak Rate

Maximum firing rate among the cells inside the firing field N.

Field N Spikes

Number of spikes in field N.

Field N Time Spent

Total time spend in the field N.

Field N Rate

Average firing rate in field N (Field N Spikes divided by Field N Time Spent).

Field N Coherence

Coherence measures the local smoothness of the firing rate distribution in the field. It is the Pearson correlation of the firing rate in each cell (pixel) with the firing rate averaged over the pixel and its 8 nearest neighbors.

Algorithm

If Fix Positions is set to Use 4 Neighbors, NeuroExplorer will analyze X and Y position variables and do the following:

for each point x[t], calculate the average of its 4 neighbors:

aver = (x[t-2]+x[t-1]+x[t+1]+x[t+2])/4

if abs(x[t] - aver) > FixThreshold, then assign x[t] the average of its neighbors:

x[t] = aver

If Fix Positions is set to Ignore Bad, NeuroExplorer will ignore position points that have coordinates that are within 0.001 of the specified ‘bad’ X and X values.

If Fix Positions is set to Interpolate, for each position point that has coordinates that are within 0.001 of the specified ‘bad’ X and X values, the X and Y values are interpolated using the closest previous valid position and the closest next valid position.

The following steps are then performed:

The position space is divided into cells with width (XMax - XMin)/Number of Bins (X) and height (YMax - YMin)/Number of Bins (Y).

For each cell, the number of visits to this cell and the time spent in the cell are calculated.

For each of the neuron firing times, the position of the animal is calculated using linear interpolation of animal positions before and after the spike.

For each cell, the number of times the neuron fired in this cell is calculated.

With Firing Rates display, if the animal spent less time in the cell than Min Time Spent or visited the cell less than Min Visits number of times, the firing rate for the cell is set to zero. Otherwise the number of times the neuron fired in this cell is divided by the time the animal spent in the cell producing the firing rate for the cell.

Firing Field a set of at least Min. Pixels in Field contiguous cells where each cell in the field shared at least one side with another cell in the field and each cell had a firing rate greater than (Session_mean + Min Std. Dev. in Field * Session_st_dev), where Session_mean is the firing rate of the complete recording session, Session_st_dev is the standard deviation of the mean firing rate. Session_mean and Session_st_dev are calculated the following way: the recording session is divided into time bins of size Firing Rate Bin. For each bin i, neuron firing rate R[i] is calculated. Session_mean is the mean of array R[i], Session_st_dev is the standard deviation of array R[i].

Centroid of field location is the arithmetic mean center of a firing field’s spatial firing rate distribution determined after the coordinates of each cell in the field was multiplied by the firing rate in the cell.

Coherence measures the local smoothness of the firing rate distribution in the field. It is the Pearson correlation of the firing rate in each cell with the firing rate averaged over the cell and its 8 nearest neighbors.

Reference

  1. Fentona, Gyorgy Csizmadiab, and Robert U. Muller. Conjoint Control of Hippocampal Place Cell Firing by Two Visual Stimuli I. The Effects of Moving the Stimuli on Firing Field Positions. The Journal of General Physiology, Volume 116, Number 2, August 1, 2000 191-210.