ASPP/2024-heraklion-data
8
1
Fork 20
Code Issues 7 Pull requests 2 Actions Packages Projects Releases Wiki Activity
2024-heraklion-data/exercises/tabular_split_apply_combine/split_apply_combine.ipynb
Pietro Berkes 1f6bc07c51 ASPP 2024 material
2024-08-27 15:27:53 +03:00

14 KiB
Raw Blame History

Exercise: Compute summary statistics for the neural data

In [2]:
%matplotlib inline

import matplotlib.pyplot as plt
import pandas as pd

# Set some Pandas options: maximum number of rows/columns it's going to display
pd.set_option('display.max_rows', 1000)
pd.set_option('display.max_columns', 100)

Load the processed neural data

In [3]:
df = pd.read_csv('processed_QC_passed_2024-07-04_collected_v1.csv')
In [4]:
df.shape
Out[4]:
(659, 35)
In [5]:
df.head()
Out[5]:
OP filename slice cell_ch cell_ID day treatment hrs_incubation repatch hrs_after_OP Rs Rin resting_potential max_spikes Rheobase AP_heigth TH max_depol max_repol membra_time_constant_tau capacitance comments rheo_ramp AP_halfwidth Rheobse_ramp Unnamed: 27 rheos_ramp comment high K concentration RMP_from_char tissue_source area patient_age patcher
0 OP230420 23420003.abf S1 1 23420S1c1 D1 TTX 0.0 no 10.416389 6.675643 39.025301 -74.285889 24 200.0 80.749512 -35.278320 336.181641 -60.791016 19.40 510.601767 0 753.380113 1.151009 NaN NaN NaN NaN NaN 8 mM -61.828554 Bielefeld temporal 13.0 Verji
1 OP230420 23420003.abf S1 3 23420S1c3 D1 TTX 0.0 no 10.416389 7.867174 48.728367 -69.573975 26 300.0 78.448486 -32.043457 350.097656 -67.138672 17.30 393.397918 1 585.102837 1.006321 NaN NaN NaN NaN NaN 8 mM -60.460298 Bielefeld temporal 13.0 Verji
2 OP230420 23420003.abf S1 6 23420S1c6 D1 TTX 0.0 no 10.416389 8.820134 35.971082 -54.956055 22 300.0 76.660156 -29.827881 270.629883 -52.246094 14.85 426.098774 3 173.915797 1.266335 NaN NaN NaN NaN NaN 8 mM -59.615979 Bielefeld temporal 13.0 Verji
3 OP230420 23420003.abf S1 8 23420S1c8 D1 TTX 0.0 yes 10.416389 6.000400 31.599917 -70.550537 22 350.0 81.011963 -33.068848 309.448242 -61.401367 16.65 575.513924 5 786.927898 1.182830 NaN NaN NaN NaN NaN 8 mM -60.956350 Bielefeld temporal 13.0 Verji
4 OP230420 23420061.abf S1_D2 8 23420S1c8 D2 TTX 19.0 yes 29.633333 8.271614 30.607259 -70.745850 1 1300.0 48.883057 -20.855713 100.952148 -27.465820 13.25 864.892430 29 565.938865 1.504127 NaN NaN NaN NaN NaN 8 mM -61.283967 Bielefeld temporal 13.0 Verji

1. Does capacitance change with age?

  • Compute the capacitance by patient age, and plot it
  • Does it change with age? (eyeballing is enough)
In [ ]:

2. Spiking threshold after potassium incubation

  1. Does the spiking threshold (TH) change between Day 1 and Day 2?
  2. Does this result depend on the treatment?
In [ ]: