burst_detection
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cancellation
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Cooperative cancellation for pipeline runs. |
channel_layout
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Electrode channel-ID -> spatial coordinate lookup, port of getCoordsFromLayout.m. |
example_data
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Download the shared example dataset used by the MATLAB and Python test pipelines. |
firing_rates
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io
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I/O helpers for MEA-NAP pipeline files. |
louvain
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Louvain modularity optimization, port of community_louvain.m (BCT). |
modularity
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Consensus-clustering modularity, port of mod_consensus_cluster_iterate.m. |
network_metrics
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Network metrics, ported from the Brain Connectivity Toolbox (Functions/2019_03_03_BCT/*.m) as called by ExtractNetMet.m. |
nmf
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Non-negative matrix factorization dimensionality metrics, port of calNMF.m (called from ExtractNetMet.m for the num_nnmf_components /nComponentsRelNS/nnmf_residuals/nnmf_var_explained fields). |
null_models
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Degree/strength-preserving network randomization, ports of randmio_und_signed.m, null_model_und_sign.m, randmio_und_v2.m and latmio_und_v2.m (BCT / Functions/CC_PL_SW/). |
output_folders
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Create the MEA-NAP output folder tree, mirroring CreateOutputFolders.m. |
parula
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plotting
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plotting_step2
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plotting_step4
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Step 4 check plots: plotConnectivityProperties.m, StandardisedNetworkPlot.m (base + betweenness-centrality-colored variants), NodeCartography.m, StandardisedNetworkPlotNodeColourMap.m (circular/module variant), electrodeSpecificMetrics.m (half-violin panel of all node metrics), and StandardisedNetworkPlotNodeCartography.m (circular/cartography variant). |
probabilistic_threshold
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Probabilistic edge thresholding, port of adjM_thr_parallel.m. |
report
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Self-contained HTML output viewer for a MEA-NAP pipeline run. |
runner
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Top-level pipeline runner, orchestrating steps to mirror MEApipeline.m. |
spike_detection
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MEA spike detection algorithms — Python port of MATLAB WATERS. |
spreadsheet
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Read the recording list spreadsheet, mirroring pipelineReadCSV.m. |
step2
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step3
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Step 3: functional connectivity (adjacency matrices), port of the generateAdjMs.m / adjM_thr_parallel.m portion of MEApipeline.m. |
step4
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Step 4: network activity metrics, port of ExtractNetMet.m (see network_metrics.py for exactly which metrics are and aren't in scope, and which are deterministic vs. |
sttc
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Spike Time Tiling Coefficient (STTC), port of get_sttc.m / sttc_m.m. |