List of CARMEN Services

Retinal Spike Services

  • Fourplot Service – plots graphs based on MEA retinal data.
  • MEA Movie Calculator Service – Creates an animated .gif file showing bursting over time on a MEA grid.
  • MEA Burst and IBI Cumulative Distribution Calculator Service – calculates the cumulative distribution functions for burst lengths and inter-burst intervals of spike time series, returning pdfs of the burst length distribution versus burst length, the inter-burst interval distribution versus the interval length, and also returns comma separated variable files for x-y coordinates of the above plots.
  • Episode Detection of MEA data – performs episode detection from all MEA retinal data formats currently on CARMEN.
  • Network Analysis of MEA data: CC, APL, and CD – performs Network Analysis on detected episodes from all MEA retinal data formats currently on CARMEN.
  • Burst Detection – Finds bursts of activity from spike times, for each channel in an MEA recording.
  • NDF Burst Detection – Finds bursts of activity from spike times, for each channel in an MEA recording.  NDF Version
  • Analyse Waves APS2 – takes the output from NDF burst detection service and classifies the bursts into waves.
  • APS HDF5 to NDF Convertor – converts APS HDF5 data into NDF.
  • Plot burst duration – Plot burst duration for spontaneous activity recorded. The curve shows the cumulative distribution (CDF) of burst durations

Spike Detection & Sorting Services

  • High Pass Filter Service
  • Waveclus High Pass Filter Service
  • Spike Detector – NEO
  • Spike Detector – Plain
  • Spike Detector – COB
  • Spike Detector – Wave
  • Spike Detector – Morphological
  • Waveclus Spike Detector
  • Spike Sorter
  • Waveclus Spike Sorter
  • Waveclus Spike Feature Extractor

NDF Spike Detection & Sorting Services

  • NDF High Pass Filter Service
  • Waveclus NDF High-Pass Filter
  • NDF Spike Detector – NEO
  • NDF Spike Detector – plain
  • NDF Spike Detector – COB
  • Waveclus NDF Spike Detector
  • NDF Spike Sorter Service
  • KlustaKwik NDF Spike Sorter
  • Waveclus NDF Spike Sorter
  • Waveclus NDF Spike Feature Extractor
 Other Services
  • Read and sort UTAH array files.
  • Power Spectrum for UTAH Array – creates an array of power spectrum plots for each channel of the UTAH MEA.
  • EEG Stage Identification – This service identifies Awake, Non-REM and REM stages in EEG data
  • EEG stage ground truth comparison.
  • Fitcell Service – models the cell by a simple electrical circuit of capacitors and resistors
  • Hiergraph – Creates hierarchical graphs depending on the model desired
  • Graphviz SFDB visualisation tool – uses Graphviz SFDB layout engine for undirected graphs
  • Plots relative link-strength matrix as image – creates an image from a relative link-strength matrix
  • Sets score value of self-excitatory parent-configurations to zero – This service filters for parent-configurations in which self-excitatory connections occur.
  • Sets score value of exclusive self-excitatory parent-configurations to zero – This service filters for exclusive self-excitatory parent-configurations by setting the score value of the corresponding child to zero.
  • Small World Inverse Service – Takes a matrix of a given size (number of nodes and edges) and turns it into a small world network.
  • Clustering Coefficient Service – Takes a small world network adjacency matrix and calculates the average cluster coefficient, locally and globally.
  • Disconnectedness Service – Takes a small world adjacency matrix and calculates the average disconnectedness, locally and globally.
  • Weight Matrix to DOT convertor – thresholds and converts weight matrices to the DOT format.
  • LASER FILTER TIF Service –  read in and clean a series of .tif stack images. The processed data is used to generate a movie and give plots of power spectra, raw data traces, filtered data traces, and a Matlab .mat file containing the data.
  • LASER Data Plot Service – Takes the input matlab file from the LASER Filter TIF Service, and plots the raw, filtered and power spectra graphs for a specified pixel.
  • Finding Cells – Finding extra-cellular single units in brief periods of recording. The algorithm detects the number of different single units (ncells) and how well seperated they are (quality).
  • Generate all parent-configurations up to a given number of parents – generates all possible parent-configurations of a node.
  • Calculate relative link-strength from config-score list
  • Extract best scoring parent-configurations of each node
  • Set score values below link-acceptance-threshold to zero
  • Basal Ganglia Service
  • Generate DOT description to plot a relative link-strength matrix
  • FBA Metabolic Modelling
  • Cell Response Service – Produces Peri-stimulus time interval histogram (PSTH) normalised to give firing rate, raster plot and interspike interval histogram (INTH). It also computes an irregularity (IR) measure (displayed in INTH title).
  • Wave Average Service – Waveform average of a wave relative to an event
  • Cross Correlation of Single Unit Activity – Computes the cross correlation histogram using spikes from two single units.
  • Spike Synchrony – Calculate Event Synchrony by Quiroga et al., 2002; Code: T. Kreuz
  • Extract Spike APS – designed to convert Oliver Muthmann’s spike detection algorithm output to spikes times based on one optional parameter of the threshold.
  • Brain ripple algorithm – This algorithm bandpass filters the data, detecting ripple events and determining peak frequency for each event.
  • Calculate LSA – Calculates spreading across columns of activation
  • Spike time to spike train convertor – Mostly, lists of spike-times can encode neural data efficiently, but situations exist where spike-train representation is advantageous. This converter transforms a spike-time file to a spike-train one.
  • Calculate Snap Shot score for all parent-configurations
  • Coherence Waveform Service – Detects whether each file is a .sp or .spt, and calculates the power spectra and coherence plus phase appropriately for a waveform or event.
  • Spike-LFP Crosstalk Free Estimator Service – This service is based on Waldert et al., 2013 (JPysiol), and estimates the extent of spike contamination in intra-cortical LFPs.
  • Dopamine-modulated medium spiny neuron, reduced model service – extends Izhikevich’s reduced model of the striatal medium spiny neuron (MSN) to account for dopaminergic modulation of its intrinsic ion channels and synaptic inputs.
 DATA Conversion Services
  • Raw data to NDF Convertor – Converts raw data files (mcd, nev, nex, plx, map, abf, abf2, edf, edf+, bdf, bdf+ and smr) into NDF format
  • Extract NDF Neural Event data from NDF Segment data – Extract NDF Neural Event data from NDF Segment data
  • APS HDF5 to NDF Convertor – converts APS project data in HDF5 file format into NDF neural event data
  • Neuralynx NCS to NDF Convertor – for single channel data.
  • APS mat to NDF convertor – takes an exported matlab file from brainwave (3brain.com software) and converts it to NDF
  • NCS to NDF convertor with timestamps – converts NCS continuous data with gaps, and outputs NDF segment and event data.
  • Adjacency matrix to DOT convertor
  • Dot to PDF service
  • PDF to Postscript convertor
  • Postscript to PDF convertor
  • Text file format conversion – converts text between DOS, UNIX and MAC format
  • MAT to NDF convertor for signgle channel timeseries data
  • Grainger Causality Service – Quantifies the influence of one time-series to another.