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2.29. 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.
Page 99
- NeuroExplorer Manual 1
- Table of Contents 3
- 1. Getting Started 9
- NeuroExplorer Updates 10
- Files Panel 14
- Multi Channel Systems Files 20
- Neuralynx Files 20
- File Import Options 20
- 1.10. 1D Data Viewer 26
- 1.11. Analyzing Data 27
- 1.16. Analysis Templates 33
- 1.17. Numerical Results 34
- 1.18. Post-processing 35
- 1.20. Working with Matlab 37
- 1.21. Working with Excel 38
- 1.22. Saving Graphics 39
- 2. Analysis Reference 40
- 2.1. Data Types 41
- 2.1.2. Events 42
- 2.1.3. Intervals 42
- 2.1.4. Markers 44
- 2.1.5. Population Vectors 45
- 2.1.6. Waveforms 46
- Limitations 47
- 2.2. Data Selection Options 48
- 2.3. Post-Processing Options 49
- 2.4. Matlab Options 50
- 2.5. Excel Options 50
- 2.7. Cumulative Sum Graphs 52
- 2.8. Rate Histograms 53
- 2.10. Autocorrelograms 58
- 2.11. Perievent Histograms 61
- Peak and Trough Statistics 64
- 2.12. Crosscorrelograms 66
- Shift-Predictor Algorithm 71
- More on Time Intervals 72
- 2.14. Rasters 73
- 2.15. Perievent Rasters 74
- 2.16. Joint PSTH 77
- 2.18. Instant Frequency 80
- (t[i], t[i] - t[i-1]) 81
- 2.21. Synchrony vs. Time 83
- 2.22. Trial Bin Counts 85
- 2.24. Burst Analysis 90
- 2.26. PSTH Versus Time 95
- 2.28. Regularity Analysis 99
- Algorithm 100
- Reference 100
- 2.29. Place Cell Analysis 101
- Summary of Numerical Results 102
- 2.30. Reverse Correlation 105
- 2.31. Epoch Counts 108
- 2.32. Coherence Analysis 110
- 2.33. Spectrogram Analysis 113
- 2.34. Perievent Spectrograms 115
- 2.35. Joint ISI Distribution 117
- Parameters 119
- 3. Working with Graphics 121
- 3.4. Text Labels 124
- 3.5. Lines 125
- 3.6. Rectangles 126
- 4. Working with 3D Graphics 127
- 4.2. 3D Graphics Parameters 129
- 5. Programming with NexScript 133
- 5.1. Script Variables 135
- 5.2. File Variables 136
- 5.3. Expressions 138
- 5.4. Flow Control 139
- Conditional operators 140
- 5.5. Functions 141
- See Also 142
- 5.5.1.2. GetFileName Function 144
- 5.5.1.3. OpenFile Function 145
- 5.5.1.4. CloseFile Function 146
- 5.5.1.5. ReadLine Function 147
- 5.5.1.6. WriteLine Function 148
- 5.5.1.8. NewDocument Function 150
- CloseDocument(doc) 151
- 5.5.1.15. MergeFiles Function 157
- 5.5.1.16. ReadBinary Function 158
- 5.5.1.17. FileSeek Function 159
- 5.5.1.18. SelectFile Function 160
- 5.5.2.1. GetDocPath Function 162
- 5.5.2.2. GetDocTitle Function 163
- SetDocEndTime(doc, 1200.3) 166
- 5.5.3.1. GetVarCount Function 169
- 5.5.3.2. GetVarName Function 170
- 5.5.3.4. GetVar Function 172
- 5.5.3.5. DeleteVar Function 173
- 5.5.3.6. Delete Function 174
- 5.5.3.8. NewEvent Function 176
- 5.5.3.9. NewIntEvent Function 177
- 5.5.3.12. NewContVar Function 180
- 5.5.4.1. IsSelected Function 183
- 5.5.4.2. Select Function 184
- 5.5.4.3. Deselect Function 185
- 5.5.4.4. SelectVar Function 186
- 5.5.4.5. DeselectVar Function 187
- 5.5.4.6. Select Function 188
- 5.5.4.7. Deselect Function 189
- 5.5.4.8. SelectAll Function 190
- 5.5.4.9. DeselectAll Function 191
- SelectAllNeurons(doc) 192
- EnableRecalcOnSelChange () 194
- 5.5.5.1. GetName Function 197
- AddTimestamp(eventVar, 1.5) 199
- 5.5.5.6. AddInterval Function 202
- 5.5.6. Analysis Functions 203
- PrintGraphics(doc) 206
- 5.5.7.1. GetNumRes Function 217
- 5.5.8.1. Rename Function 231
- 5.5.8.2. Join Function 232
- 5.5.8.3. Sync Function 233
- 5.5.8.4. NotSync Function 234
- 5.5.8.5. FirstAfter Function 235
- 5.5.8.6. FirstNAfter Function 236
- 5.5.8.7. LastBefore Function 237
- "Trials")) 238
- 5.5.8.11. SelectEven Function 241
- 5.5.8.12. SelectOdd Function 242
- 5.5.8.13. ISIFilter Function 243
- 5.5.8.22. IntOr Function 252
- 5.5.8.23. IntAnd Function 253
- 5.5.8.24. IntSize Function 254
- 5.5.8.25. IntFind Function 255
- 5.5.8.27. Shift Function 257
- 5.5.8.28. NthAfter Function 258
- 5.5.9. Matlab Functions 263
- SendSelectedVarsToMatlab(doc) 264
- 5.5.10. Excel Functions 270
- CloseExcelFile(excelFilePath) 272
- 5.5.12.1. RunScript Function 277
- 5.5.12.2. Sleep Function 278
- 5.5.13. Math Functions 279
- 5.5.13.1. seed Function 281
- 5.5.13.2. expo Function 282
- 5.5.13.3. floor Function 283
- 5.5.13.4. ceil Function 284
- 5.5.13.5. round Function 285
- 5.5.13.6. abs Function 286
- 5.5.13.7. sqrt Function 287
- 5.5.13.8. pow Function 288
- 5.5.13.9. exp Function 289
- 5.5.13.10. min Function 290
- 5.5.13.11. max Function 291
- 5.5.13.12. log Function 292
- 5.5.13.13. sin Function 293
- 5.5.13.14. cos Function 294
- 5.5.13.15. tan Function 295
- 5.5.13.16. acos Function 296
- 5.5.13.17. asin Function 297
- 5.5.13.18. atan Function 298
- 5.5.13.19. RoundToTS Function 299
- % x now equals to 1 303
- 5.5.13.25. GetBit Function 305
- 5.5.14. String Functions 306
- 5.5.14.1. Left Function 307
- 5.5.14.2. Mid Function 308
- 5.5.14.3. Right Function 309
- 5.5.14.4. Find Function 310
- 5.5.14.5. StrLength Function 311
- 5.5.14.6. NumToStr Function 312
- 5.5.14.7. StrToNum Function 313
- % numFields is now equal to 4 314
- 5.5.14.10. CharToNum Function 316
- 5.5.14.11. NumToChar Function 317
- 5.5.15. Debug Functions 318
- 5.5.15.1. Trace Function 319
- 5.5.15.2. MsgBox Function 320
- 6. COM/ActiveX Interfaces 321
- 6.1. Application 322
- 6.1.2. DocumentCount Property 324
- 6.1.3. Version Property 325
- 6.1.4. Visible Property 326
- 6.1.5. OpenDocument Method 327
- 6.1.6. Document Medhod 328
- 6.1.7. Sleep Method 329
- 6.1.8. RunNexScript Method 330
- 6.2. Document 332
- 6.2.1. Path Property 334
- 6.2.2. FileName Property 335
- 6.2.3. Comment Property 336
- 6.2.5. StartTime Property 338
- 6.2.6. EndTime Property 339
- 6.2.7. VariableCount Property 340
- 6.2.8. NeuronCount Property 341
- 6.2.9. EventCount Property 342
- 6.2.11. MarkerCount Property 344
- 6.2.12. WaveCount Property 345
- 6.2.14. Variable Method 347
- 6.2.15. Neuron Method 348
- 6.2.16. Event Method 349
- 6.2.17. Interval Method 350
- 6.2.18. Marker Method 351
- 6.2.19. Wave Method 352
- 6.2.20. Continuous Method 353
- 6.2.21. DeselectAll Method 354
- 6.2.24. ApplyTemplate Method 357
- 6.2.26. Close Method 359
- 6.3. Variable 360
- 6.3.1. Name Property 361
- 6.3.3. Timestamps Method 363
- 6.3.4. IntervalStarts Method 364
- 6.3.5. IntervalEnds Method 365
- 6.3.7. FragmentCounts Method 367
- 6.3.9. MarkerValues Method 369
- 6.3.10. WaveformValues Method 370
- 6.3.11. Select Method 371
- 6.3.12. Deselect Method 372
- Page 371 373
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