Examples for using NeuroXidence
Three example data sets with spiking activity from 3, 8, and 70 neurons are included in a zip package you can download (Toy_data_1: 8 Neurons, Toy_data_2: 3 Neurons, Toy_data_3: 70 Neurons ). For each of the toy data sets a matlab script, Example_call_NX_Restricted_Dataset_1.m, Example_call_NX_Restricted_Dataset_2.m, and Example_call_NX_Restricted_Dataset_3.m is included.
Toy data set 3:
Toy data set 2 contains 40 trials of 1s spiking activity from 70 Neurons. Please use Example_call_NX_Restricted_Dataset_3.m to run the demo. The spike rate is 5 ap/s. During the periods 0-0.4s and 0.8-2s the spike activity of all 70 neurons is mutually independent. Periods between 0.4s and 0.8s contain correlated spiking activity based on a single interaction process (see publication). The computation time for analyzing each period amounts on ~10 min on average (Notebook with 1.6 GHz, 2 GB Ram). It holds for the following periods:
- Period 2 (0.4-0.8s): 7 sets of each 4 neurons are correlated and share 1 JSE/s
(set 1: Neuron 7,8,9,10 / set 2: Neuron 17,18,19,20 / set 3: Neuron 27,28,29,30 / set 4: Neuron 37,38,39,40 / 5: Neuron 47,48,49,50 / set 6: Neuron 57,58,59,50 / set 7: Neuron 67,68,69,70)
- Period 3 (0.4-0.8s): 2 sets of each 8 neurons are correlated and share 1 JSE/s
(set 1: Neuron 7,8,9,10,11,12,13,14 / set 2: Neuron 42,43,44,45,46,47,48,49)
Toy data set 2:
Toy data set 2 contains 50 trials of 9s spiking activity from 3 Neurons. The spike rate in the first 3s and the last 1s is 30 ap/s. During the periods 0-2s and 8-9s the spike activity of all three neurons is mutually independent. Periods between 3s and 8s are correlated based on a single Interaction process (see publication). It holds for the following periods:
- 2-3s: Neuron 1 and 2 are correlated and share 5 JSE/s.
- 3-4s: Neuron 1 and 2 are correlated and share 2 JSE/s.
- 4-5s: Neuron 1 and 2 are correlated and share 5 JSE/s.
- 5-6s: Neuron 1,2 and 3 are correlated and share 2 JSE/s.
- 6-7s: Neuron 1,2 and 3 are correlated and share 5 JSE/s.
To explore the data set you can call the function Example_call_NX_Restricted_Dataset_2.m that is contained in the zip file that can be downloaded. Do not forget to include all provided function files *.p as well as the license file into the matlab path. If you use NeuroXidence without a license file it will switch into an restricted mode if you are analysing any other data set than one of the three toy demo data sets contained in the demo package. However, if you apply NeuroXidence without an lisence file on one of the three data sets that are included in the the demo package NeuroXidence turns temporally in an unrestricted version.
After the computation finished you should find 4 folders that contain .fig, .eps , .pdf, and .jpg files. Besides the PSTH you will find Raster plots for all Joint-spike events that show all spikes and all Joint-spike patterns in red irrespective if individual patterns are significant or not (e.g. Raster_Pattern_Plot_C2_C3Raster_plot_with_Joint_spike_Events_window1.jpg).
In addition you will find raster plots that contain only those patterns that are significantly more often than expected by chance (e.g. Raster_Pattern_Plot_C2_C3Raster_plot_with_significant_Joint_spike_Events_window1.jpg).
Example for using NeuroXidence (Toy_Dataset_1):
Toy data set 1 contains 50 trials from 8 Neurons. Only the second half from 1.5-3s contains correlated activity.
To explore the data set you can call the function Example_call_NX_Restricted_Dataset_1.m that is contained in the zip or rar file that can be downloaded. Do not forget to include all provided function files *.p into the matlab path.