Note
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MEA: Minimal Setting: Example¶
In this example code, we demonstrate analysis of MEA Recording, with minimal settings, using signle line that includes all the 13 steps
Read HDF File
Stim loc
Align Cycles
Average Cycles/Select one
Activation Time
Activation & Repolarisation Time
APD computation
Extract EGM
EGM Feature Extraction
BAD Channels
Feature Matrix
Interpolation
Conduction Velocity
#sp.mea
import numpy as np
import matplotlib.pyplot as plt
import os, requests
import spkit as sp
print('spkit-version: ',sp.__version__)
# Download Sample file if not done already
file_name= 'MEA_Sample_North_1000mV_1Hz.h5'
if not(os.path.exists(file_name)):
path = 'https://spkit.github.io/data_samples/files/MEA_Sample_North_1000mV_1Hz.h5'
req = requests.get(path)
with open(file_name, 'wb') as f:
f.write(req.content)
spkit-version: 0.0.9.7
Features_df,Features_ch,Features_mat, Data = sp.mea.analyse_mea_file(file_name,stim_fhz=1)
----------------------------------------------------------------------------------------------------
file name
MEA_Sample_North_1000mV_1Hz.h5
----------------------------------------------------------------------------------------------------
500 ms of duration after stimulus is selected, to change it set 'dur_after_spike'
Reading File...
base key(s) found in file <KeysViewHDF5 ['Data']>
Shape of Signals: (60, 250000)
- #Channels = 60
- Duration (s) = 10.0
Shape: (60, 12450, 9)
Number of EGMs/Cycles per channel = 9
-- Averaged All EGM
EGM Shape : (60, 12450)
----------------------------------------------------------------------------------------------------
Following EGM Features are etracted: ['peak_to_peak', 'egm_duration', 'f_index', 'new_duration', 'energy_mean', 'energy_sd', 'noise_var']
EGM_Feat shape : (60, 7)
Shapes: XE = (60, 250) , AT = (60,) , EGM_F= (60, 7)
----------------------------------------------------------------------------------------------------
BAD CHANNELS
- BASED ON STIM thr = 2
- ch: [21, 31, 43, 41, 51, 61, 71]
- BASED ON Peak-to-Peak volt thr: 5
- ch: [15, 21, 31, 43, 41, 52, 51, 61, 71]
- BASED ON Activation time (ms) range thr: [0, 50]
- ch: [27, 15, 21, 31, 43, 41, 52, 51, 61, 71, 73, 85]
- Manually passed:
- ch: []
GOOD CHANNELS passed:
- ch: []
--------------------------------------------------
Final list of Bad Channels:
- ch: [15, 21, 27, 31, 41, 43, 51, 52, 61, 71, 73, 85]
Final list of Good Channels:
- ch: [47 48 46 45 38 37 28 36 17 26 16 35 25 14 24 34 13 23 12 22 33 32 44 42
53 54 62 63 72 82 83 64 74 84 75 65 86 76 87 77 66 78 67 68 55 56 58 57]
----------------------------------------------------------------------------------------------------
Interpolated Original
CV_mean 26.817 24.965
CV_median 24.969 24.292
CV_sd 5.987 2.459
inv_speed 0.004 0.004
avg_angle -1.693 -1.685
Smooth Plot
With upsampling by 2
Results¶
print(Features_df)
print(Features_ch)
Original Interpolated
at_ms_mean 11.484167 67.361333
at_ms_median 11.06 13.94
at_ms_sd 5.393794 116.845063
peak_to_peak_mean 194.296019 156.026815
peak_to_peak_median 198.877604 170.335079
peak_to_peak_sd 80.811005 105.284933
egm_duration_mean 37.043771 35.840246
egm_duration_median 31.205426 30.812905
egm_duration_sd 20.499696 24.769817
f_index_mean 1.020833 1.266667
f_index_median 1.0 1.0
f_index_sd 0.142826 1.424391
new_duration_mean 38.886978 39.366179
new_duration_median 31.396708 31.099283
new_duration_sd 22.934721 31.052041
energy_mean_mean 634.703597 508.018861
energy_mean_median 528.960827 429.291967
energy_mean_sd 440.939276 468.763144
energy_sd_mean 2331.557953 1865.581011
energy_sd_median 1981.04279 1463.436099
energy_sd_sd 1702.987816 1785.685722
noise_var_mean 4.483589 3.748528
noise_var_median 4.398441 4.078418
noise_var_sd 1.679903 2.1329
cv_cm_s_mean 24.964751 26.143832
cv_cm_s_median 24.292091 24.923668
cv_cm_s_sd 2.458801 4.490185
inv_speed 0.004041 0.003854
avg_angle -1.685121 -1.692971
n_bad_ch 12 0
n_good_ch 48 60
file_name MEA_Sample_North_1000mV_1Hz.h5 MEA_Sample_North_1000mV_1Hz.h5
at_ms peak_to_peak egm_duration f_index new_duration energy_mean energy_sd noise_var cv_cm_s CH_Label Bad_CH
0 16.64 185.024967 32.888097 1.0 32.888097 484.839536 1738.891824 4.806276 24.994262 47 False
1 19.56 207.645492 29.078587 1.0 29.078587 564.528219 1965.390988 4.757493 23.972602 48 False
2 13.96 137.696900 45.199420 1.0 45.199420 346.427159 1313.511807 5.826316 24.300282 46 False
3 10.88 110.208074 37.244166 1.0 37.244166 188.060420 589.373654 2.835411 23.614175 45 False
4 19.52 194.957333 28.186365 1.0 28.186365 461.934628 1633.030667 3.361641 26.406259 38 False
5 16.88 146.507319 31.930925 1.0 31.930925 291.667150 1035.150207 3.791908 25.158138 37 False
6 20.04 284.495890 26.216436 1.0 26.216436 963.708430 3611.331072 3.189918 28.737474 28 False
7 14.04 220.728300 29.077200 1.0 29.077200 602.182147 2302.812305 3.838855 25.588377 36 False
8 323.44 9.426356 19.029424 1.0 19.029424 5.987956 8.203725 2.408528 25.561067 27 True
9 18.60 163.620594 27.617619 1.0 27.617619 339.587586 1234.744236 2.870040 33.872723 17 False
10 14.84 236.031266 28.412209 1.0 28.412209 742.615567 2896.596687 4.079189 24.898835 26 False
11 16.16 108.990994 115.117881 1.0 115.117881 184.759779 807.893237 3.395177 22.627833 16 False
12 11.48 101.917566 22.773716 1.0 22.773716 128.956645 513.439767 2.768145 23.349423 35 False
13 12.40 46.874862 22.418585 2.0 110.892525 30.794201 143.344650 1.137642 25.123060 25 False
14 284.08 0.695701 23.789267 2.0 35.323118 0.031301 0.040085 0.187772 24.775147 15 True
15 10.64 26.462483 33.079279 1.0 33.079279 22.501121 63.254152 0.801556 30.250936 14 False
16 9.48 105.900375 28.313894 1.0 28.313894 155.303754 663.290624 1.506374 23.691410 24 False
17 8.24 183.043845 27.251336 1.0 27.251336 489.891978 2187.811774 4.457476 22.689037 34 False
18 9.00 135.499567 22.598340 1.0 22.598340 255.465681 1225.741769 4.232107 29.345526 13 False
19 7.00 208.095476 30.768363 1.0 30.768363 592.269185 1996.694592 5.713667 24.572447 23 False
20 8.04 174.705308 29.125530 1.0 29.125530 423.162994 1794.933818 2.115191 20.856701 12 False
21 5.00 197.765137 31.110845 1.0 31.110845 448.354167 1605.567895 2.933420 22.889576 22 False
22 5.48 199.990070 37.185192 1.0 37.185192 592.492698 2428.124139 4.159148 23.929110 33 False
23 174.48 0.672183 147.479525 12.0 204.713549 0.088024 0.119499 0.305310 27.257815 21 True
24 2.72 234.087601 30.857447 1.0 30.857447 1134.540542 3941.533424 8.792507 27.295478 32 False
25 176.40 1.220167 21.325327 1.0 21.325327 0.089396 0.130375 0.271223 29.789960 31 True
26 8.04 267.936098 32.318821 1.0 32.318821 1015.256365 4205.093145 5.288281 24.013662 44 False
27 357.00 1.085440 22.911071 1.0 22.911071 0.071337 0.123967 0.217650 22.412884 43 True
28 394.88 0.475323 11.002538 1.0 11.002538 0.274187 0.299669 0.597950 36.126649 41 True
29 1.84 28.585665 92.324811 1.0 92.324811 24.792306 68.006625 2.563891 27.265852 42 False
30 349.76 2.784590 26.700329 1.0 26.700329 0.224369 0.403634 0.427144 29.575117 52 True
31 345.48 0.949954 17.314854 1.0 17.314854 0.099146 0.136271 0.300426 42.650681 51 True
32 4.72 85.242921 42.173367 1.0 42.173367 121.738626 416.599180 2.618208 22.388949 53 False
33 7.88 154.565858 38.989405 1.0 38.989405 424.997858 1319.499289 3.854213 21.678996 54 False
34 209.08 0.020953 1.206467 1.0 1.206467 0.167395 0.198213 0.467681 45.108018 61 True
35 1.48 249.095678 34.198601 1.0 34.198601 1342.348732 3865.931980 5.747313 29.443430 62 False
36 201.60 0.818095 22.494695 2.0 31.005287 0.125530 0.164918 0.365871 34.893927 71 True
37 4.64 301.713155 31.300006 1.0 31.300006 1185.619945 4548.332537 5.208267 22.831155 63 False
38 2.68 262.489993 35.555927 1.0 35.555927 1259.552318 3845.349801 7.809549 26.468601 72 False
39 4.12 165.964851 37.289210 1.0 37.289210 433.586076 1321.304302 4.306614 25.849839 82 False
40 330.32 9.289875 9.507392 2.0 31.100453 3.686527 4.543717 1.983761 25.086544 73 True
41 6.56 286.334120 30.977130 1.0 30.977130 1075.300290 3690.857045 4.709205 25.321557 83 False
42 7.56 247.082172 31.098113 1.0 31.098113 917.583124 3972.649231 7.058398 23.808972 64 False
43 7.92 354.963382 28.989166 1.0 28.989166 1744.744082 7221.839931 6.985230 24.575674 74 False
44 9.24 48.073097 129.149889 1.0 129.149889 84.932773 150.594577 6.105692 25.241695 84 False
45 343.92 7.961333 49.552862 2.0 73.763354 4.513844 5.714858 2.166059 27.084073 85 True
46 10.96 270.760250 29.885907 1.0 29.885907 999.765942 3957.074664 5.452439 23.681946 75 False
47 10.52 366.615413 28.754012 1.0 28.754012 1886.732748 7866.874997 7.662611 23.166111 65 False
48 14.32 235.104306 35.903772 1.0 35.903772 922.811550 3289.930349 6.583009 24.173149 86 False
49 13.76 221.883263 34.859990 1.0 34.859990 694.105695 2237.905717 5.284190 24.283899 76 False
50 17.12 246.211356 30.157142 1.0 30.157142 841.472934 2985.265406 4.497298 30.173894 87 False
51 16.68 285.388401 26.533913 1.0 26.533913 972.235101 3509.150114 4.464566 23.511653 77 False
52 13.60 149.778181 36.610816 1.0 36.610816 326.930537 1060.727601 4.077647 23.481472 66 False
53 19.68 195.988603 30.106471 1.0 30.106471 493.393435 1688.048984 4.306425 23.215825 78 False
54 16.48 275.228959 31.493410 1.0 31.493410 1024.767000 3944.379419 5.551180 23.807320 67 False
55 19.48 316.971262 28.380379 1.0 28.380379 1215.230557 4342.037972 4.339405 23.325041 68 False
56 11.16 216.102190 32.922939 1.0 32.922939 646.841359 2337.948079 4.871648 23.137746 55 False
57 13.92 106.317816 52.826650 1.0 52.826650 232.242177 790.835827 5.137693 24.948501 56 False
58 19.52 143.025948 34.196825 1.0 34.196825 289.011529 945.021764 3.442592 25.359655 58 False
59 16.76 234.536550 34.652898 1.0 34.652898 845.736027 2641.059900 5.917260 24.989802 57 False
Total running time of the script: (0 minutes 6.922 seconds)
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