Network Viewer

The Network Viewer tab interactively explores the functional connectivity network from a completed MEA-NAP run, including optional cell-type overlays. It’s the Python equivalent of MATLAB’s runMEANAPviewer.m.

Using the Network Viewer tab

  1. Click Browse… and select a MEA-NAP output .mat file from the ExperimentMatFiles/ subfolder of an output directory, e.g. OutputData.../ExperimentMatFiles/<recording>_OutputData....mat.

  2. The network renders immediately. Recording metadata (name, DIV, group, active node count) appears in the left panel.

  3. Adjust settings to update the plot in real time:

    • Lag — which functional connectivity lag value to view (e.g. 1000 ms, 2500 ms, 5000 ms).

    • Edge threshold — minimum correlation weight required to draw an edge.

    • Node color metric — color nodes by any node-level metric present in the file (betweenness centrality, node strength, z-score, …), or leave as None for flat cyan nodes.

  4. (Optional) Click Load cell types from file… to overlay cell-type information — see below.

Node size is always proportional to node degree (ND). Node color uses the viridis colormap, with a colorbar legend on the right.

Cell-type overlay

Cell types are rendered as concentric rings on each node, one line style per type, mirroring the MATLAB viewer.

Loading cell types:

  1. Prepare (or locate) a cell-type spreadsheet: each column is one cell type, each cell contains the 1-indexed channel number of a cell belonging to that type. Columns with no cells for a given type should be left blank. The PutativeCellType_*.xlsx files produced alongside MEA-NAP runs use this format.

    NeuN+

    PV+

    SST+

    68

    25

    110

    78

    42

    216

    117

  2. In the Cell types group, click Load cell types from file… and select the .xlsx or .csv file.

  3. A listbox appears with every cell type found — select one or more to filter the displayed network.

Filtering by cell type:

  • Selecting one type shows only nodes of that type.

  • Selecting multiple types shows only nodes belonging to all selected types (intersection — consistent with the MATLAB viewer).

  • Deselecting everything returns to showing all active nodes.

The concentric-circle legend at the bottom of the plot identifies which ring style corresponds to which cell type.

Note on .mat cell-type data

MEA-NAP stores Info.CellTypes inside output .mat files as a MATLAB MCOS table object, which scipy.io can’t decode. When the viewer detects this, it logs a message and prompts you to load the cell-type spreadsheet directly — the same .xlsx file originally supplied to the MATLAB pipeline.

Using the network plotting API from Python

The plotting code underneath this tab is a standalone module, meanap.network_plot, usable independently of the GUI. See the network-plotting notebook tutorial for a runnable, end-to-end walkthrough with real output baked in, or the API reference for the full function/class list.