Use to get firing rate maps of neurons in an open field. It can get information scores, sparsity, etc. You can use it to analyze the firing properties of grid cells or border cells. Can do some shuffling to get the spatial properties that you would get by chance.
session
Name of the recording session
cmPerBin
Number of cm in each bin of a firing rate map, 2 by default
smoothOccupancySd
Standard deviation in cm of the gaussian kernel used to smooth the occupancy map, 3 by default
smoothRateMapSd
Standard deviation in cm of the gaussian kernel used to smooth the firing rate histograms, 3 by default
nColMap
Number of columns in the firing rate maps
nRowMap
Number of rows in the firing rate maps
nColAuto
Number of columns in the spatial autocorrelation
nRowAuto
Number of rows in the spatial autocorrelation
nColCross
Number of columns in the spatial crosscorrelation
nRowCross
Number of rows in the spatial crosscorrelation
xSpikes
x position of the animal for each spike time
ySpikes
y position of the animal for each spike time
maps
Array containing the firing rate maps of the neurons
ccMaps
Array containing the crosscorrelation of firing rate maps
occupancy
Matrix containing the occupancy map
occupancy3D
Array containing the occupancy for x and y positions and head-direction.
autos
Array containing the spatial autocorrelation of the firing rate maps
autosDetect
Array with the spatial autocorrelation once the firing fields have been removed
autosDoughnut
Array with the spatial autocorrelation containing only the ring of the 6 closest fields (excluding central field)
autosDoughnutRotate
Array with the rotated spatial autocorrelations
cellList
List of cells
cellPairList
List of cell pairs
reduceSize
Logical indicating if the size of map should be minimized by setting smallest x and y to 0
minValidBinsAuto
Number of valid bins to calculate a r value in the spatial autocorrelation maps
minValidBinsCross
Number of valid bins to calculate a r value in the spatial crosscorrelation maps
peakRate
Peak firing rates in the maps
infoScore
Information score of the firing rate maps
sparsity
Sparsity of the firing rate maps
borderScore
Border score for each firing rate maps
borderCM
Value of CM when calculating the border score
borderDM
Value of DM when calculating the border score
borderNumFieldsDetected
Number of detected fields when calculating the border score
borderPercentageThresholdField
Threshold for a bin being part of a field, expressed as percentage of peak
borderMinBinsInField
Minimum number of bins to be considered a field
mapPolarity
How polarized is the firing rate of the cell in the map. Each bin of the map is given an angle and firing rate. mapPolarity is the resultant mean vector length
gridScore
Grid score calculated form the spatial autocorrelation
gridOrientation
Grid orientation
gridSpacing
Grid spacing in cm
gridScoreNumberFieldsToDetect
Maximal number of fields that will be detected
gridScoreMinNumBinsPerField
Minimum number of bins to be considered a field
gridScoreFieldThreshold
Minimum value of firing fields in the spatial autocorrelation map
nAutoRotations
Number of rotations when rotating the spatial autocorrelation map
AutoRotationDegree
Angle of rotation of the spatial autocorrelation map
speedScore
Speed score of the neurons
speedRateSlope
Slope of the linear regression line between speed and rate
speedRateIntercept
Rate intercept of the linear regression line between speed and rate
nShufflings
Number of shufflings to get chance levels, by default 100
minShiftMs
Minimum time shift of the position data when doing shuffling
peakRateShuffle
peak firing rate in the shuffling analysis
infoScoreShuffle
Information score from the shuffling analysis
sparsityShuffle
Sparsity from the shuffling analysis
borderScoreShuffle
Border score form the shuffling analysis
borderCMShuffle
Border CM from the shuffling analysis
borderDMShuffle
Border DM from the shuffling analysis
borderNumFieldsDetectedShuffle
Number of detected fields when calculating shufflings of the border score
mapPolarityShuffle
Map polarity from the shuffling analysis
gridScoreShuffle
Grid score from the shuffling analysis
speedScoreShuffle
Speed score from the shuffling analysis
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