447 lines
14 KiB
Plaintext
447 lines
14 KiB
Plaintext
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{
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"cells": [
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{
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"cell_type": "markdown",
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"id": "6f634238",
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"metadata": {},
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"source": [
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"# Exercise: Compute summary statistics for the neural data"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 2,
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"id": "8f9bc8b1",
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"metadata": {},
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"outputs": [],
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"source": [
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"%matplotlib inline\n",
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"\n",
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"import matplotlib.pyplot as plt\n",
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"import pandas as pd\n",
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"\n",
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"# Set some Pandas options: maximum number of rows/columns it's going to display\n",
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"pd.set_option('display.max_rows', 1000)\n",
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"pd.set_option('display.max_columns', 100)"
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]
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},
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{
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"cell_type": "markdown",
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"id": "141ca000",
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"metadata": {},
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"source": [
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"# Load the processed neural data"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 3,
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"id": "d2dfebd3",
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"metadata": {},
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"outputs": [],
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"source": [
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"df = pd.read_csv('processed_QC_passed_2024-07-04_collected_v1.csv')"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 4,
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"id": "09554c84",
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"metadata": {},
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"outputs": [
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{
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"data": {
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"text/plain": [
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"(659, 35)"
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]
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},
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"execution_count": 4,
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"metadata": {},
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"output_type": "execute_result"
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}
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],
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"source": [
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"df.shape"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 5,
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"id": "df95a10b",
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"metadata": {},
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"outputs": [
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{
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"data": {
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"text/html": [
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"<div>\n",
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"<style scoped>\n",
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" .dataframe tbody tr th:only-of-type {\n",
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" vertical-align: middle;\n",
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" }\n",
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"\n",
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" .dataframe tbody tr th {\n",
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" vertical-align: top;\n",
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" }\n",
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"\n",
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" .dataframe thead th {\n",
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" text-align: right;\n",
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" }\n",
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"</style>\n",
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"<table border=\"1\" class=\"dataframe\">\n",
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" <thead>\n",
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" <tr style=\"text-align: right;\">\n",
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" <th></th>\n",
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" <th>OP</th>\n",
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" <th>filename</th>\n",
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" <th>slice</th>\n",
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" <th>cell_ch</th>\n",
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" <th>cell_ID</th>\n",
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" <th>day</th>\n",
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" <th>treatment</th>\n",
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" <th>hrs_incubation</th>\n",
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" <th>repatch</th>\n",
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" <th>hrs_after_OP</th>\n",
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" <th>Rs</th>\n",
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" <th>Rin</th>\n",
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" <th>resting_potential</th>\n",
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" <th>max_spikes</th>\n",
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" <th>Rheobase</th>\n",
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" <th>AP_heigth</th>\n",
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" <th>TH</th>\n",
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" <th>max_depol</th>\n",
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" <th>max_repol</th>\n",
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" <th>membra_time_constant_tau</th>\n",
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" <th>capacitance</th>\n",
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" <th>comments</th>\n",
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" <th>rheo_ramp</th>\n",
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" <th>AP_halfwidth</th>\n",
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" <th>Rheobse_ramp</th>\n",
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" <th>Unnamed: 27</th>\n",
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" <th>rheos_ramp</th>\n",
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" <th>comment</th>\n",
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" <th></th>\n",
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" <th>high K concentration</th>\n",
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" <th>RMP_from_char</th>\n",
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" <th>tissue_source</th>\n",
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" <th>area</th>\n",
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" <th>patient_age</th>\n",
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" <th>patcher</th>\n",
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" </tr>\n",
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" </thead>\n",
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" <tbody>\n",
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" <tr>\n",
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" <th>0</th>\n",
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" <td>OP230420</td>\n",
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" <td>23420003.abf</td>\n",
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" <td>S1</td>\n",
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" <td>1</td>\n",
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" <td>23420S1c1</td>\n",
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" <td>D1</td>\n",
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" <td>TTX</td>\n",
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" <td>0.0</td>\n",
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" <td>no</td>\n",
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" <td>10.416389</td>\n",
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" <td>6.675643</td>\n",
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" <td>39.025301</td>\n",
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" <td>-74.285889</td>\n",
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" <td>24</td>\n",
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" <td>200.0</td>\n",
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" <td>80.749512</td>\n",
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" <td>-35.278320</td>\n",
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" <td>336.181641</td>\n",
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" <td>-60.791016</td>\n",
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" <td>19.40</td>\n",
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" <td>510.601767</td>\n",
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" <td>0</td>\n",
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" <td>753.380113</td>\n",
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" <td>1.151009</td>\n",
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" <td>NaN</td>\n",
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" <td>NaN</td>\n",
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" <td>NaN</td>\n",
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" <td>NaN</td>\n",
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" <td>NaN</td>\n",
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" <td>8 mM</td>\n",
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" <td>-61.828554</td>\n",
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" <td>Bielefeld</td>\n",
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" <td>temporal</td>\n",
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" <td>13.0</td>\n",
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" <td>Verji</td>\n",
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" </tr>\n",
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" <tr>\n",
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" <th>1</th>\n",
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" <td>OP230420</td>\n",
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" <td>23420003.abf</td>\n",
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" <td>S1</td>\n",
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" <td>3</td>\n",
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" <td>23420S1c3</td>\n",
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" <td>D1</td>\n",
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" <td>TTX</td>\n",
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" <td>0.0</td>\n",
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" <td>no</td>\n",
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" <td>10.416389</td>\n",
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" <td>7.867174</td>\n",
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" <td>48.728367</td>\n",
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" <td>-69.573975</td>\n",
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" <td>26</td>\n",
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" <td>300.0</td>\n",
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" <td>78.448486</td>\n",
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" <td>-32.043457</td>\n",
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" <td>350.097656</td>\n",
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" <td>-67.138672</td>\n",
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" <td>17.30</td>\n",
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" <td>393.397918</td>\n",
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" <td>1</td>\n",
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" <td>585.102837</td>\n",
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" <td>1.006321</td>\n",
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" <td>NaN</td>\n",
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" <td>NaN</td>\n",
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" <td>NaN</td>\n",
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" <td>NaN</td>\n",
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" <td>NaN</td>\n",
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" <td>8 mM</td>\n",
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" <td>-60.460298</td>\n",
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" <td>Bielefeld</td>\n",
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" <td>temporal</td>\n",
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" <td>13.0</td>\n",
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" <td>Verji</td>\n",
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" </tr>\n",
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" <tr>\n",
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" <th>2</th>\n",
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" <td>OP230420</td>\n",
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" <td>23420003.abf</td>\n",
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" <td>S1</td>\n",
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" <td>6</td>\n",
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" <td>23420S1c6</td>\n",
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" <td>D1</td>\n",
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" <td>TTX</td>\n",
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" <td>0.0</td>\n",
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" <td>no</td>\n",
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" <td>10.416389</td>\n",
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" <td>8.820134</td>\n",
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" <td>35.971082</td>\n",
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" <td>-54.956055</td>\n",
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" <td>22</td>\n",
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" <td>300.0</td>\n",
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" <td>76.660156</td>\n",
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" <td>-29.827881</td>\n",
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" <td>270.629883</td>\n",
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" <td>-52.246094</td>\n",
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" <td>14.85</td>\n",
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" <td>426.098774</td>\n",
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" <td>3</td>\n",
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" <td>173.915797</td>\n",
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" <td>1.266335</td>\n",
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" <td>NaN</td>\n",
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" <td>NaN</td>\n",
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" <td>NaN</td>\n",
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" <td>NaN</td>\n",
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" <td>NaN</td>\n",
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" <td>8 mM</td>\n",
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" <td>-59.615979</td>\n",
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" <td>Bielefeld</td>\n",
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" <td>temporal</td>\n",
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" <td>13.0</td>\n",
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" <td>Verji</td>\n",
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" </tr>\n",
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" <tr>\n",
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" <th>3</th>\n",
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" <td>OP230420</td>\n",
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" <td>23420003.abf</td>\n",
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" <td>S1</td>\n",
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" <td>8</td>\n",
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" <td>23420S1c8</td>\n",
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" <td>D1</td>\n",
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" <td>TTX</td>\n",
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" <td>0.0</td>\n",
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" <td>yes</td>\n",
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" <td>10.416389</td>\n",
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" <td>6.000400</td>\n",
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" <td>31.599917</td>\n",
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" <td>-70.550537</td>\n",
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" <td>22</td>\n",
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" <td>350.0</td>\n",
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" <td>81.011963</td>\n",
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" <td>-33.068848</td>\n",
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" <td>309.448242</td>\n",
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" <td>-61.401367</td>\n",
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" <td>16.65</td>\n",
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" <td>575.513924</td>\n",
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" <td>5</td>\n",
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" <td>786.927898</td>\n",
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" <td>1.182830</td>\n",
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" <td>NaN</td>\n",
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" <td>NaN</td>\n",
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" <td>NaN</td>\n",
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" <td>NaN</td>\n",
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" <td>NaN</td>\n",
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" <td>8 mM</td>\n",
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" <td>-60.956350</td>\n",
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" <td>Bielefeld</td>\n",
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" <td>temporal</td>\n",
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" <td>13.0</td>\n",
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" <td>Verji</td>\n",
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" </tr>\n",
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" <tr>\n",
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" <th>4</th>\n",
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" <td>OP230420</td>\n",
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" <td>23420061.abf</td>\n",
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" <td>S1_D2</td>\n",
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" <td>8</td>\n",
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" <td>23420S1c8</td>\n",
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" <td>D2</td>\n",
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" <td>TTX</td>\n",
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" <td>19.0</td>\n",
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" <td>yes</td>\n",
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" <td>29.633333</td>\n",
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" <td>8.271614</td>\n",
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" <td>30.607259</td>\n",
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" <td>-70.745850</td>\n",
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" <td>1</td>\n",
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" <td>1300.0</td>\n",
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" <td>48.883057</td>\n",
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" <td>-20.855713</td>\n",
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" <td>100.952148</td>\n",
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" <td>-27.465820</td>\n",
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" <td>13.25</td>\n",
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" <td>864.892430</td>\n",
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" <td>29</td>\n",
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" <td>565.938865</td>\n",
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" <td>1.504127</td>\n",
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" <td>NaN</td>\n",
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" <td>NaN</td>\n",
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" <td>NaN</td>\n",
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" <td>NaN</td>\n",
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" <td>NaN</td>\n",
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" <td>8 mM</td>\n",
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" <td>-61.283967</td>\n",
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" <td>Bielefeld</td>\n",
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" <td>temporal</td>\n",
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" <td>13.0</td>\n",
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" <td>Verji</td>\n",
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" </tr>\n",
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" </tbody>\n",
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||
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"</table>\n",
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||
|
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"</div>"
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||
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],
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||
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"text/plain": [
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||
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" OP filename slice cell_ch cell_ID day treatment \\\n",
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"0 OP230420 23420003.abf S1 1 23420S1c1 D1 TTX \n",
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"1 OP230420 23420003.abf S1 3 23420S1c3 D1 TTX \n",
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"2 OP230420 23420003.abf S1 6 23420S1c6 D1 TTX \n",
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"3 OP230420 23420003.abf S1 8 23420S1c8 D1 TTX \n",
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"4 OP230420 23420061.abf S1_D2 8 23420S1c8 D2 TTX \n",
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"\n",
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" hrs_incubation repatch hrs_after_OP Rs Rin \\\n",
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"0 0.0 no 10.416389 6.675643 39.025301 \n",
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"1 0.0 no 10.416389 7.867174 48.728367 \n",
|
||
|
|
"2 0.0 no 10.416389 8.820134 35.971082 \n",
|
||
|
|
"3 0.0 yes 10.416389 6.000400 31.599917 \n",
|
||
|
|
"4 19.0 yes 29.633333 8.271614 30.607259 \n",
|
||
|
|
"\n",
|
||
|
|
" resting_potential max_spikes Rheobase AP_heigth TH max_depol \\\n",
|
||
|
|
"0 -74.285889 24 200.0 80.749512 -35.278320 336.181641 \n",
|
||
|
|
"1 -69.573975 26 300.0 78.448486 -32.043457 350.097656 \n",
|
||
|
|
"2 -54.956055 22 300.0 76.660156 -29.827881 270.629883 \n",
|
||
|
|
"3 -70.550537 22 350.0 81.011963 -33.068848 309.448242 \n",
|
||
|
|
"4 -70.745850 1 1300.0 48.883057 -20.855713 100.952148 \n",
|
||
|
|
"\n",
|
||
|
|
" max_repol membra_time_constant_tau capacitance comments rheo_ramp \\\n",
|
||
|
|
"0 -60.791016 19.40 510.601767 0 753.380113 \n",
|
||
|
|
"1 -67.138672 17.30 393.397918 1 585.102837 \n",
|
||
|
|
"2 -52.246094 14.85 426.098774 3 173.915797 \n",
|
||
|
|
"3 -61.401367 16.65 575.513924 5 786.927898 \n",
|
||
|
|
"4 -27.465820 13.25 864.892430 29 565.938865 \n",
|
||
|
|
"\n",
|
||
|
|
" AP_halfwidth Rheobse_ramp Unnamed: 27 rheos_ramp comment \\\n",
|
||
|
|
"0 1.151009 NaN NaN NaN NaN NaN \n",
|
||
|
|
"1 1.006321 NaN NaN NaN NaN NaN \n",
|
||
|
|
"2 1.266335 NaN NaN NaN NaN NaN \n",
|
||
|
|
"3 1.182830 NaN NaN NaN NaN NaN \n",
|
||
|
|
"4 1.504127 NaN NaN NaN NaN NaN \n",
|
||
|
|
"\n",
|
||
|
|
" high K concentration RMP_from_char tissue_source area patient_age \\\n",
|
||
|
|
"0 8 mM -61.828554 Bielefeld temporal 13.0 \n",
|
||
|
|
"1 8 mM -60.460298 Bielefeld temporal 13.0 \n",
|
||
|
|
"2 8 mM -59.615979 Bielefeld temporal 13.0 \n",
|
||
|
|
"3 8 mM -60.956350 Bielefeld temporal 13.0 \n",
|
||
|
|
"4 8 mM -61.283967 Bielefeld temporal 13.0 \n",
|
||
|
|
"\n",
|
||
|
|
" patcher \n",
|
||
|
|
"0 Verji \n",
|
||
|
|
"1 Verji \n",
|
||
|
|
"2 Verji \n",
|
||
|
|
"3 Verji \n",
|
||
|
|
"4 Verji "
|
||
|
|
]
|
||
|
|
},
|
||
|
|
"execution_count": 5,
|
||
|
|
"metadata": {},
|
||
|
|
"output_type": "execute_result"
|
||
|
|
}
|
||
|
|
],
|
||
|
|
"source": [
|
||
|
|
"df.head()"
|
||
|
|
]
|
||
|
|
},
|
||
|
|
{
|
||
|
|
"cell_type": "markdown",
|
||
|
|
"id": "0b4f6091",
|
||
|
|
"metadata": {},
|
||
|
|
"source": [
|
||
|
|
"# 1. Does capacitance change with age?\n",
|
||
|
|
"\n",
|
||
|
|
"* Compute the capacitance by patient age, and plot it\n",
|
||
|
|
"* Does it change with age? (eyeballing is enough)"
|
||
|
|
]
|
||
|
|
},
|
||
|
|
{
|
||
|
|
"cell_type": "code",
|
||
|
|
"execution_count": null,
|
||
|
|
"id": "bb796266",
|
||
|
|
"metadata": {},
|
||
|
|
"outputs": [],
|
||
|
|
"source": []
|
||
|
|
},
|
||
|
|
{
|
||
|
|
"cell_type": "markdown",
|
||
|
|
"id": "1940d3fe",
|
||
|
|
"metadata": {},
|
||
|
|
"source": [
|
||
|
|
"# 2. Spiking threshold after potassium incubation\n",
|
||
|
|
"\n",
|
||
|
|
"1. Does the spiking threshold (TH) change between Day 1 and Day 2?\n",
|
||
|
|
"2. Does this result depend on the treatment?"
|
||
|
|
]
|
||
|
|
},
|
||
|
|
{
|
||
|
|
"cell_type": "code",
|
||
|
|
"execution_count": null,
|
||
|
|
"id": "dd5023cd",
|
||
|
|
"metadata": {},
|
||
|
|
"outputs": [],
|
||
|
|
"source": []
|
||
|
|
}
|
||
|
|
],
|
||
|
|
"metadata": {
|
||
|
|
"kernelspec": {
|
||
|
|
"display_name": "Python 3 (ipykernel)",
|
||
|
|
"language": "python",
|
||
|
|
"name": "python3"
|
||
|
|
},
|
||
|
|
"language_info": {
|
||
|
|
"codemirror_mode": {
|
||
|
|
"name": "ipython",
|
||
|
|
"version": 3
|
||
|
|
},
|
||
|
|
"file_extension": ".py",
|
||
|
|
"mimetype": "text/x-python",
|
||
|
|
"name": "python",
|
||
|
|
"nbconvert_exporter": "python",
|
||
|
|
"pygments_lexer": "ipython3",
|
||
|
|
"version": "3.11.3"
|
||
|
|
}
|
||
|
|
},
|
||
|
|
"nbformat": 4,
|
||
|
|
"nbformat_minor": 5
|
||
|
|
}
|