Multi-Electrode Arrays Processing

Backgorund

#TODO

Multi-Electrode Arrays System utilies an array of electrodes mounted on a small plate as a grid electrodes (e.g. 60) evenly spaced (700mm apart). It is used to analyse the eletrophysiology of cells/tissues under different clinical conditions by stimulating with certain voltage on a regular intervals. As shown in figure below, a plate of MEA system of 60 electrodes (source: https://www.multichannelsystems.com/products/meas-60-electrodes). One of the commonly used research field is the cardiac electrophysiology.

This python library analyse the recorded signal file, by extracting the electrograms (EGMs) from signal recoding of each eletrodes, and extracting the features of each EGM.

#TODO

Complete Analysis of a recording

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One of the simple function to provide complete analysis of recorded file is to use `spkit.mea.analyse_mea_file` function. This uses the default settings of all the paramters for extracting electrograms, identifying bad eletrodes, extracting features and plotting figures.

`spkit.mea.analyse_mea_file` needs two essential inputs, `files_name` : a full path of recoding file in ‘.h5’ format and `stim_fhz` frequency of stimulus in Hz.

import spkit as sp
sp.mea.analyse_mea_file(files_name,stim_fhz=1)

Step-wise Analysis

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There are 13 steps to analyse a recording file, which are as follow

1. Read HDF File

2. Stim loc

3. Align Cycles

4. Average Cycles/Select one

5. Activation Time

6. Activation & Repolarisation Time

7. APD

8. Extract EGM

9. EGM Feature Extraction

10. BAD Channels

11. Feature Matrix

12. Interpolation

13. Conduction Velocity

1. Read HDF File

#TODO

sp.io.read_hdf

2. Stim Localisation

#TODO

sp.mea.get_stim_loc

3. Alignment of Stim Cycles

#TODO

sp.mea.align_cycles

4. Averaging Cycles or Selecting one

#TODO

5. Activation Time

#TODO

sp.mea.activation_time_loc

6. Repolarisation Time (optional)

#TODO

sp.mea.activation_repol_time_loc

7. APD (if RT is computed)

#TODO

apd_ms = rt_loc_ms-at_loc_ms

8. Extracting EGM

#TODO

sp.mea.extract_egm

9. EGM Feature Extraction

#TODO

sp.mea.egm_features

10. Identifying BAD Channels/electrodes

#TODO

sp.mea.find_bad_channels_idx

11. Creating Feature Matrix

#TODO

sp.mea.feature_mat

12. Interpolation

#TODO

sp.fill_nans_2d

13. Conduction Velocity

#TODO

sp.mea.compute_cv

Plots and Figures

#TODO

sp.mea.plot_mea_grid
sp.mea.mea_feature_map
sp.mea.mat_list_show
sp.direction_flow_map

Extracting EGM

EGM Processing & Feature Extractions

Conduction and Activation Map

#TODO