Xsembles

Neuronal ensembles extraction tool

Xsembles

Xsembles is a tool for identifying neuronal ensembles and their associated offsembles from a recording of population neuronal activity. The MATLAB function to use it is Get_Xsembles.m.

Demo to run Xsembles method

You will need a raster variable representing the population neuronal activity, which should be a binary matrix (0 = inactivity; 1 = activity) where each column represents a time point and each row represents the activity of a neuron. As an example, you can load our raster obtained from experimental data from the file raster_example.mat into the MATLAB worskpace:

load raster_example.mat

Next, run the function Get_Xsembles(raster) and get a structure variable analysis as an output:

analysis = Get_Xsembles(raster);

Then, you can plot the results of the neuronal activity found:

Plot_Raster_Ensemble_Activity(analysis)

The Demo_Xsembles.m file includes the demo code to test this method.

How to get ensemble and offsemble neurons

Having the structure variable analysis, you can get the ensemble neurons from analysis.Ensembles.EnsembleNeurons and the offsemble neurons from analysis.Ensembles.OffsembleNeurons. For example, if you want to get the neurons of the ensemble 1 and their associated neurons of the offsemble 1 you can run the following code:

% Get neurons from ensemble 1
ensemble_neurons = analysis.Ensembles.EnsembleNeurons{1};

% Get neurons from offsemble 1 (associated with ensemble 1)
offsemble_neurons = analysis.Ensembles.OffsembleNeurons{1};

All variables inside the structure variable analysis

• analysis.Options
  • analysis.Options.Network
    • analysis.Options.Network.Bin
    • analysis.Options.Network.Iterations
    • analysis.Options.Network.Alpha
    • analysis.Options.Network.NetworkMethod
    • analysis.Options.Network.ShuffleMethod
    • analysis.Options.Network.SingleThreshold
  • analysis.Options.Vectors
    • analysis.Options.Vectors.Method
    • analysis.Options.Vectors.CoactivityThreshold
  • analysis.Options.Clustering
    • analysis.Options.Clustering.SimilarityMeasure
    • analysis.Options.Clustering.LinkageMethod
    • analysis.Options.Clustering.EvaluationIndex
    • analysis.Options.Clustering.EvaluationClustering
    • analysis.Options.Clustering.Range
  • analysis.Options.Ensemble
    • analysis.Options.Ensemble.Iterations
    • analysis.Options.Ensemble.Alpha
• analysis.Raster
• analysis.Neurons
• analysis.Frames
• analysis.Network
• analysis.Filter
  • analysis.Filter.RasterFiltered
  • analysis.Filter.SpikesFractionRemoved
  • analysis.Filter.RasterVectors
  • analysis.Filter.VectorID
• analysis.Clustering
  • analysis.Clustering.Similarity
  • analysis.Clustering.Tree
  • analysis.Clustering.RecommendedClusters
  • analysis.Clustering.ClusteringIndex
  • analysis.Clustering.EvaluationClustering
  • analysis.Clustering.ClusteringRange
  • analysis.Clustering.ClusteringIndices
  • analysis.Clustering.TreeID
• analysis.Ensembles
  • analysis.Ensembles.Count
  • analysis.Ensembles.ActivationSequence
  • analysis.Ensembles.Activity
  • analysis.Ensembles.ActivityBinary
  • analysis.Ensembles.Networks
  • analysis.Ensembles.OffsembleNetworks
  • analysis.Ensembles.AllEnsembleNetwork
  • analysis.Ensembles.AllOffsembleNetwork
  • analysis.Ensembles.Vectors
  • analysis.Ensembles.Indices
  • analysis.Ensembles.Similarity
  • analysis.Ensembles.VectorCount
  • analysis.Ensembles.Structure
  • analysis.Ensembles.StructureSilenced
  • analysis.Ensembles.StructureBelongingness
  • analysis.Ensembles.EB
  • analysis.Ensembles.StructureP
  • analysis.Ensembles.StructureWeights
  • analysis.Ensembles.StructureWeightsSignificant
  • analysis.Ensembles.StructureSorted
  • analysis.Ensembles.Weights
  • analysis.Ensembles.EnsembleNeurons
  • analysis.Ensembles.OffsembleNeurons
  • analysis.Ensembles.NeuronID
  • analysis.Ensembles.VectorID
  • analysis.Ensembles.Durations
  • analysis.Ensembles.PeaksCount
  • analysis.Ensembles.Probability
  • analysis.Ensembles.Iterations
  • analysis.Ensembles.AlphaEnsemble
• analysis.NonEnsembles
  • analysis.NonEnsembles.Count
  • analysis.NonEnsembles.Activity
  • analysis.NonEnsembles.ActivityBinary
  • analysis.NonEnsembles.Networks
  • analysis.NonEnsembles.OffsembleNetworks
  • analysis.NonEnsembles.Vectors
  • analysis.NonEnsembles.Indices
  • analysis.NonEnsembles.Similarity
  • analysis.NonEnsembles.VectorCount
  • analysis.NonEnsembles.Structure
  • analysis.NonEnsembles.StructureSilenced
  • analysis.NonEnsembles.StructureBelongingness
  • analysis.NonEnsembles.EB
  • analysis.NonEnsembles.StructureP
  • analysis.NonEnsembles.StructureWeights
  • analysis.NonEnsembles.StructureWeightsSignificant
  • analysis.NonEnsembles.EnsembleNeurons
  • analysis.NonEnsembles.OffsembleNeurons
  • analysis.NonEnsembles.Durations
  • analysis.NonEnsembles.PeaksCount
  • analysis.NonEnsembles.Probability
• analysis.Log