Multi-Electrode Arrays Processing
================================

.. image:: https://raw.githubusercontent.com/spkit/spkit.github.io/master/assets/images/docs_fig/mea_proce_2.png
   :width: 800
   :align: center
   
 

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.

.. image:: https://raw.githubusercontent.com/spkit/spkit.github.io/master/assets/images/docs_fig/mea_plate_source.png
   :width: 400
   :align: center


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

.. image:: https://raw.githubusercontent.com/spkit/spkit.github.io/master/assets/images/docs_fig/mea_proce_3.png
   :width: 800
   :align: center






Complete Analysis of a recording
---------------------------------

#TODO

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)




.. image:: https://raw.githubusercontent.com/spkit/spkit.github.io/master/assets/images/docs_fig/mea_proce_3.png
   :width: 800
   :align: center



Step-wise Analysis
------------------

#TODO

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
--------------

.. image:: https://raw.githubusercontent.com/spkit/spkit.github.io/master/assets/images/docs_fig/mea_grid_egm_1.png
   :width: 800
   :align: center


EGM Processing & Feature Extractions
------------------------------------

.. image:: https://raw.githubusercontent.com/spkit/spkit.github.io/master/assets/images/docs_fig/egm_processing_1.png
   :width: 800
   :align: center



Conduction and Activation Map
------------------------------------

.. image:: https://raw.githubusercontent.com/spkit/spkit.github.io/master/assets/images/docs_fig/mea_act_cv_map_2.png
   :width: 800
   :align: center



.. image:: https://raw.githubusercontent.com/spkit/spkit.github.io/master/assets/images/docs_fig/mea_act_cv_map_1.png
   :width: 1000
   :align: center




#TODO