Software for offline analysis of data recorded with CMOS-MEA-Control.
Navigate and filter the data, detect and sort spikes, and extract STA.

Analyzing the Data Offline

To explore the vast amount of data gathered with the CMOS-MEA5000-System, a one-click activity summary generates temporal and spatial overviews. This allows easy navigation to interesting times and areas in your sample. Various filters can be used to optimize the signal quality prior to additional processing.

Spike detection, spike sorting based on independent component analysis (ICA), and extracting STA are fully automated. To further speed things up, you can process one or multiple files in batch mode or even use distributed network processing with clients for Windows or Linux.

Outcomes are stored in HDF5 file format with compatibility to Matlab, Python, R, and others or can be exported to ASCII CSV. We also supply sample code for how to access the raw data in C#, Matlab, and Python.

Activity Summary

With one click, an activity summary is generated with an overview of the temporal and spatial distribution of detected spikes. This helps to find the times and regions with important activity.

Spike activity based on time and position

Filter Pipeline

Assemble a filter pipeline from different spatial, temporal, or artifact filters with a preview while adjusting filter settings. Optimizing the signal quality by proper filtering can greatly improve spike detection and sorting.

Drag and drop filter pipeline

Spike Detection

The Spike Explorer tool can detect spikes and create cutouts of spike overlays. Sensors can automatically or manually be selected for further processing.

Detect spikes with cutouts and raster plot

Spike Sorting

Featuring fully automated spike sorting, the spike sorting algorithm implemented in the software is based on the work published in Leibig et al., J.Neurosci. Meth., 2016. It allows unsupervised identification of neuronal units with a single mouse click.

Client software allows you to run performance intensive sorting tasks on several computers in a network simultaneously.

Spike sorter
Automated spike sorting based on independent component analysis (ICA)

Spike Triggered Averages, STA

Spike triggered averages allow to detect repetitive events correlated to each spike on a specific electrode, like axonal signals, which are usually hidden in the noise. The travelling axonal signals can be visualized and saved as movie files.

Network Explorer

The Network Explorer is an imaging tool designed to reveal the location and shape of active neurons combined with the temporal characteristics of the action potential and its associated axonal signal conduction. The analysis can be based either on the spikes detected on a given sensor (Spike Explorer) or on the units extracted by the Spike Sorter.

The main features of the Network Explorer are:

  1. Create the neuron’s footprint and watch its spatiotemporal characteristics.
  2. Extract the path of the neuron’s axon from the electrical signal.
  3. Calculate the conduction velocity of action potentials of each neuron’s axon.
1. Spatiotemporal characteristic of the axonal action potential
2. Footprint with somas and axons of all neurons
3. Conduction velocity histogram
Want To Do a Test Drive?

CMOS-MEA-Tools is free to use. Check out the demo mode or use our demo data.