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
.
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.
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};
- 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.Options.Network
- 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
Cite As
Jesus Perez (2024). Xsembles (https://github.com/PerezOrtegaJ/Xsembles), GitHub. Retrieved .
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Version | Published | Release Notes | |
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1.0.0 |
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