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README.md

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+## Package for analyzing multi-electrode data with a Markov-Ising model. 
+
+This package corresponds to the paper: 
+
+Prediction of spatio-temporal patterns of neural activity from  
+pairwise correlations.
+
+Olivier Marre, Sami El Boustani, Yves Frégnac and Alain Destexhe
+
+*Physical Review Letters*, 2009.  
+
+[http://arxiv.org/abs/0903.0127](http://arxiv.org/abs/0903.0127)
+
+
+The code here allows to reproduce easily the fig 1, analyze your own  
+multi-electrode data, and generate surrogate data with the same  
+statistics than the ones captured by the Markov model. The approach is  
+the following:
+
+- load or generate a raster  
+- compute the mean activity of each neuron (m), the instantaneous  
+  pairwise correlations (C), and the pairwise correlations between time  
+  t and time t+1.  
+- estimate the h, J and J1 parameters of the model corresponding to the  
+  m, C and C1: by an analytical approximation followed by a gradient  
+  descent. This might not be enough for a large number of neurons.  
+- Estimating the performance of the fit by comparing the prediction,  
+  and the empirical estimation, of the ocurrence rate of different  
+  spatio-temporal spiking patterns. This is done for different temporal  
+  sizes of these patterns.
+
+The program "BatchOctestGlauber" is performing all these steps. 
+
+## 1) How to use this program:
+
+- The best is probably to first have a look on the code which  
+  reproduces the figure 1. First launch "i2mPath" to set all the  
+  sub-directories. Then "BatchOctestGlauber" will do all the analysis  
+  (it takes several minutes), and stores the results in the WorkSpace  
+  directory. Then launch "Fig1" to draw the figure.  
+- To analyze your data, construct a file "spikes.txt" which contain the  
+  spike times, with the format explained in /LoadRaster/LoadRaster.m  
+- The directory InfoTools contains some simple methods to measure the  
+  Kullback-Leibler (KL) and the Jensen Shannon (Djs) divergences.  
+- /Surrogate/Surrogate.m will generate some surrogate data having the  
+  same statistics than the ones captured by the model.
+
+## 2) The code is organized in different directories:
+
+- Common: The core of the program. Contains all the functions needed to  
+  fit the model to mean and correlations measured from the data.  
+- FigurePlot: routines to plot the Figure 1 of the paper  
+- Figures: directory where automatically generated figures will be  
+  stored.  
+- Glauber: to simulate the Glauber model  
+- InfoTools: contains some simple methods to measure the  
+  Kullback-Leibler (KL) and the Jensen Shannon (Djs) divergences.  
+- LoadRaster: to load and bin a raster  
+- surrogate: Surrogate.m will generate some surrogate data having the  
+  same statistics than the ones captured by the model.  
+- Workspace: where the workspace is stored after running one of the  
+  batchs.
+
+---
+
+2025-06-02: Converted README to Markdown.