Data_prep/allen_data_download_2018FEB.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Clustering neuron data\n",
    "## electrophysiology and morpology data from allen brain data portal\n",
    "\n",
    "### Purpose of this notebook\n",
    "1. download fresh data from allen data portal.\n",
    "1. extract necessary feature(deleting columns)\n",
    "1. cre reporter status tagging to binary(E vs I)\n",
    "1. saving csv file.\n",
    "\n",
    "## This note was created 2018-FEB. If you rerun the cells, you'll get different results due allen database updated.\n",
    "## New notebook can be checked [here](./allen_data_download_2018JUL.ipynb)\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Requirements for this notebook\n",
    "* __allensdk__ for python2.7\n",
    "* [Reference notebook](http://alleninstitute.github.io/AllenSDK/_static/examples/nb/cell_types.html)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "from allensdk.core.cell_types_cache import CellTypesCache\n",
    "from allensdk.api.queries.cell_types_api import CellTypesApi\n",
    "from allensdk.core.cell_types_cache import ReporterStatus as RS\n",
    "import pandas as pd"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "ctc = CellTypesCache(manifest_file='cell_types/manifest.json')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "All cells: 1337\n"
     ]
    }
   ],
   "source": [
    "# all cells\n",
    "cells = ctc.get_cells()\n",
    "print(\"All cells: %d\" % len(cells))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "1337\n"
     ]
    },
    {
     "data": {
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       "\n",
       "    .dataframe tbody tr th {\n",
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       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>adaptation</th>\n",
       "      <th>avg_isi</th>\n",
       "      <th>electrode_0_pa</th>\n",
       "      <th>f_i_curve_slope</th>\n",
       "      <th>fast_trough_t_long_square</th>\n",
       "      <th>fast_trough_t_ramp</th>\n",
       "      <th>fast_trough_t_short_square</th>\n",
       "      <th>fast_trough_v_long_square</th>\n",
       "      <th>fast_trough_v_ramp</th>\n",
       "      <th>fast_trough_v_short_square</th>\n",
       "      <th>...</th>\n",
       "      <th>trough_t_ramp</th>\n",
       "      <th>trough_t_short_square</th>\n",
       "      <th>trough_v_long_square</th>\n",
       "      <th>trough_v_ramp</th>\n",
       "      <th>trough_v_short_square</th>\n",
       "      <th>upstroke_downstroke_ratio_long_square</th>\n",
       "      <th>upstroke_downstroke_ratio_ramp</th>\n",
       "      <th>upstroke_downstroke_ratio_short_square</th>\n",
       "      <th>vm_for_sag</th>\n",
       "      <th>vrest</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>0.093021</td>\n",
       "      <td>81.498750</td>\n",
       "      <td>-6.184375</td>\n",
       "      <td>0.205899</td>\n",
       "      <td>1.126905</td>\n",
       "      <td>2.768700</td>\n",
       "      <td>1.025464</td>\n",
       "      <td>-51.187504</td>\n",
       "      <td>-50.328125</td>\n",
       "      <td>-55.312504</td>\n",
       "      <td>...</td>\n",
       "      <td>2.804613</td>\n",
       "      <td>1.333809</td>\n",
       "      <td>-56.531254</td>\n",
       "      <td>-56.812502</td>\n",
       "      <td>-69.306253</td>\n",
       "      <td>3.904747</td>\n",
       "      <td>4.131130</td>\n",
       "      <td>3.899439</td>\n",
       "      <td>-85.156258</td>\n",
       "      <td>-68.233376</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>0.064384</td>\n",
       "      <td>76.283333</td>\n",
       "      <td>26.135000</td>\n",
       "      <td>0.195247</td>\n",
       "      <td>1.102660</td>\n",
       "      <td>4.005247</td>\n",
       "      <td>1.024873</td>\n",
       "      <td>-48.718750</td>\n",
       "      <td>-49.875001</td>\n",
       "      <td>-51.500004</td>\n",
       "      <td>...</td>\n",
       "      <td>4.005453</td>\n",
       "      <td>1.344913</td>\n",
       "      <td>-48.843754</td>\n",
       "      <td>-50.093753</td>\n",
       "      <td>-67.416669</td>\n",
       "      <td>4.231335</td>\n",
       "      <td>4.299535</td>\n",
       "      <td>3.939083</td>\n",
       "      <td>-78.593750</td>\n",
       "      <td>-66.085068</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>-4.600001</td>\n",
       "      <td>0.055443</td>\n",
       "      <td>1.104820</td>\n",
       "      <td>9.092507</td>\n",
       "      <td>1.025024</td>\n",
       "      <td>-48.093750</td>\n",
       "      <td>-49.541669</td>\n",
       "      <td>-50.312503</td>\n",
       "      <td>...</td>\n",
       "      <td>9.103360</td>\n",
       "      <td>1.197772</td>\n",
       "      <td>-49.531250</td>\n",
       "      <td>-49.968753</td>\n",
       "      <td>-75.656255</td>\n",
       "      <td>2.154281</td>\n",
       "      <td>1.486651</td>\n",
       "      <td>2.400687</td>\n",
       "      <td>-87.156250</td>\n",
       "      <td>-75.141449</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>0.048709</td>\n",
       "      <td>118.397143</td>\n",
       "      <td>-90.575616</td>\n",
       "      <td>0.307589</td>\n",
       "      <td>1.069770</td>\n",
       "      <td>7.203945</td>\n",
       "      <td>1.024593</td>\n",
       "      <td>-45.968754</td>\n",
       "      <td>-49.093754</td>\n",
       "      <td>-53.800002</td>\n",
       "      <td>...</td>\n",
       "      <td>7.204045</td>\n",
       "      <td>1.233473</td>\n",
       "      <td>-46.156254</td>\n",
       "      <td>-49.218753</td>\n",
       "      <td>-66.318753</td>\n",
       "      <td>2.026000</td>\n",
       "      <td>1.827572</td>\n",
       "      <td>1.818158</td>\n",
       "      <td>-82.406250</td>\n",
       "      <td>-65.503044</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>0.042215</td>\n",
       "      <td>81.394545</td>\n",
       "      <td>13.653750</td>\n",
       "      <td>0.162729</td>\n",
       "      <td>1.089750</td>\n",
       "      <td>2.336427</td>\n",
       "      <td>1.027302</td>\n",
       "      <td>-48.906250</td>\n",
       "      <td>-51.083335</td>\n",
       "      <td>-55.800002</td>\n",
       "      <td>...</td>\n",
       "      <td>2.361778</td>\n",
       "      <td>1.691744</td>\n",
       "      <td>-52.093750</td>\n",
       "      <td>-57.614586</td>\n",
       "      <td>-73.337500</td>\n",
       "      <td>4.208485</td>\n",
       "      <td>4.274151</td>\n",
       "      <td>4.096372</td>\n",
       "      <td>-99.093758</td>\n",
       "      <td>-72.174675</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>5 rows × 55 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "   adaptation     avg_isi  electrode_0_pa  f_i_curve_slope  \\\n",
       "0    0.093021   81.498750       -6.184375         0.205899   \n",
       "1    0.064384   76.283333       26.135000         0.195247   \n",
       "2         NaN         NaN       -4.600001         0.055443   \n",
       "3    0.048709  118.397143      -90.575616         0.307589   \n",
       "4    0.042215   81.394545       13.653750         0.162729   \n",
       "\n",
       "   fast_trough_t_long_square  fast_trough_t_ramp  fast_trough_t_short_square  \\\n",
       "0                   1.126905            2.768700                    1.025464   \n",
       "1                   1.102660            4.005247                    1.024873   \n",
       "2                   1.104820            9.092507                    1.025024   \n",
       "3                   1.069770            7.203945                    1.024593   \n",
       "4                   1.089750            2.336427                    1.027302   \n",
       "\n",
       "   fast_trough_v_long_square  fast_trough_v_ramp  fast_trough_v_short_square  \\\n",
       "0                 -51.187504          -50.328125                  -55.312504   \n",
       "1                 -48.718750          -49.875001                  -51.500004   \n",
       "2                 -48.093750          -49.541669                  -50.312503   \n",
       "3                 -45.968754          -49.093754                  -53.800002   \n",
       "4                 -48.906250          -51.083335                  -55.800002   \n",
       "\n",
       "     ...      trough_t_ramp  trough_t_short_square  trough_v_long_square  \\\n",
       "0    ...           2.804613               1.333809            -56.531254   \n",
       "1    ...           4.005453               1.344913            -48.843754   \n",
       "2    ...           9.103360               1.197772            -49.531250   \n",
       "3    ...           7.204045               1.233473            -46.156254   \n",
       "4    ...           2.361778               1.691744            -52.093750   \n",
       "\n",
       "   trough_v_ramp  trough_v_short_square  \\\n",
       "0     -56.812502             -69.306253   \n",
       "1     -50.093753             -67.416669   \n",
       "2     -49.968753             -75.656255   \n",
       "3     -49.218753             -66.318753   \n",
       "4     -57.614586             -73.337500   \n",
       "\n",
       "   upstroke_downstroke_ratio_long_square  upstroke_downstroke_ratio_ramp  \\\n",
       "0                               3.904747                        4.131130   \n",
       "1                               4.231335                        4.299535   \n",
       "2                               2.154281                        1.486651   \n",
       "3                               2.026000                        1.827572   \n",
       "4                               4.208485                        4.274151   \n",
       "\n",
       "   upstroke_downstroke_ratio_short_square  vm_for_sag      vrest  \n",
       "0                                3.899439  -85.156258 -68.233376  \n",
       "1                                3.939083  -78.593750 -66.085068  \n",
       "2                                2.400687  -87.156250 -75.141449  \n",
       "3                                1.818158  -82.406250 -65.503044  \n",
       "4                                4.096372  -99.093758 -72.174675  \n",
       "\n",
       "[5 rows x 55 columns]"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "ephys_features = ctc.get_ephys_features()\n",
    "ef_df = pd.DataFrame(ephys_features)\n",
    "print(len(ef_df))\n",
    "ef_df.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "cell_index = { c['id']: c for c in cells }"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "reporter_status = [cell_index[cid]['reporter_status'] for cid in ef_df['specimen_id']]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "tg_line = [cell_index[cid]['transgenic_line'] for cid in ef_df['specimen_id']]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "hemisphere = [cell_index[cid]['hemisphere'] for cid in ef_df['specimen_id']]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>adaptation</th>\n",
       "      <th>avg_isi</th>\n",
       "      <th>electrode_0_pa</th>\n",
       "      <th>f_i_curve_slope</th>\n",
       "      <th>fast_trough_t_long_square</th>\n",
       "      <th>fast_trough_t_ramp</th>\n",
       "      <th>fast_trough_t_short_square</th>\n",
       "      <th>fast_trough_v_long_square</th>\n",
       "      <th>fast_trough_v_ramp</th>\n",
       "      <th>fast_trough_v_short_square</th>\n",
       "      <th>...</th>\n",
       "      <th>trough_t_short_square</th>\n",
       "      <th>trough_v_long_square</th>\n",
       "      <th>trough_v_ramp</th>\n",
       "      <th>trough_v_short_square</th>\n",
       "      <th>upstroke_downstroke_ratio_long_square</th>\n",
       "      <th>upstroke_downstroke_ratio_ramp</th>\n",
       "      <th>upstroke_downstroke_ratio_short_square</th>\n",
       "      <th>vm_for_sag</th>\n",
       "      <th>vrest</th>\n",
       "      <th>transgenic_line</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>0.093021</td>\n",
       "      <td>81.498750</td>\n",
       "      <td>-6.184375</td>\n",
       "      <td>0.205899</td>\n",
       "      <td>1.126905</td>\n",
       "      <td>2.768700</td>\n",
       "      <td>1.025464</td>\n",
       "      <td>-51.187504</td>\n",
       "      <td>-50.328125</td>\n",
       "      <td>-55.312504</td>\n",
       "      <td>...</td>\n",
       "      <td>1.333809</td>\n",
       "      <td>-56.531254</td>\n",
       "      <td>-56.812502</td>\n",
       "      <td>-69.306253</td>\n",
       "      <td>3.904747</td>\n",
       "      <td>4.131130</td>\n",
       "      <td>3.899439</td>\n",
       "      <td>-85.156258</td>\n",
       "      <td>-68.233376</td>\n",
       "      <td>Cux2-CreERT2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>0.064384</td>\n",
       "      <td>76.283333</td>\n",
       "      <td>26.135000</td>\n",
       "      <td>0.195247</td>\n",
       "      <td>1.102660</td>\n",
       "      <td>4.005247</td>\n",
       "      <td>1.024873</td>\n",
       "      <td>-48.718750</td>\n",
       "      <td>-49.875001</td>\n",
       "      <td>-51.500004</td>\n",
       "      <td>...</td>\n",
       "      <td>1.344913</td>\n",
       "      <td>-48.843754</td>\n",
       "      <td>-50.093753</td>\n",
       "      <td>-67.416669</td>\n",
       "      <td>4.231335</td>\n",
       "      <td>4.299535</td>\n",
       "      <td>3.939083</td>\n",
       "      <td>-78.593750</td>\n",
       "      <td>-66.085068</td>\n",
       "      <td>Chrna2-Cre_OE25</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>-4.600001</td>\n",
       "      <td>0.055443</td>\n",
       "      <td>1.104820</td>\n",
       "      <td>9.092507</td>\n",
       "      <td>1.025024</td>\n",
       "      <td>-48.093750</td>\n",
       "      <td>-49.541669</td>\n",
       "      <td>-50.312503</td>\n",
       "      <td>...</td>\n",
       "      <td>1.197772</td>\n",
       "      <td>-49.531250</td>\n",
       "      <td>-49.968753</td>\n",
       "      <td>-75.656255</td>\n",
       "      <td>2.154281</td>\n",
       "      <td>1.486651</td>\n",
       "      <td>2.400687</td>\n",
       "      <td>-87.156250</td>\n",
       "      <td>-75.141449</td>\n",
       "      <td>None</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>0.048709</td>\n",
       "      <td>118.397143</td>\n",
       "      <td>-90.575616</td>\n",
       "      <td>0.307589</td>\n",
       "      <td>1.069770</td>\n",
       "      <td>7.203945</td>\n",
       "      <td>1.024593</td>\n",
       "      <td>-45.968754</td>\n",
       "      <td>-49.093754</td>\n",
       "      <td>-53.800002</td>\n",
       "      <td>...</td>\n",
       "      <td>1.233473</td>\n",
       "      <td>-46.156254</td>\n",
       "      <td>-49.218753</td>\n",
       "      <td>-66.318753</td>\n",
       "      <td>2.026000</td>\n",
       "      <td>1.827572</td>\n",
       "      <td>1.818158</td>\n",
       "      <td>-82.406250</td>\n",
       "      <td>-65.503044</td>\n",
       "      <td>Sst-IRES-Cre</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>0.042215</td>\n",
       "      <td>81.394545</td>\n",
       "      <td>13.653750</td>\n",
       "      <td>0.162729</td>\n",
       "      <td>1.089750</td>\n",
       "      <td>2.336427</td>\n",
       "      <td>1.027302</td>\n",
       "      <td>-48.906250</td>\n",
       "      <td>-51.083335</td>\n",
       "      <td>-55.800002</td>\n",
       "      <td>...</td>\n",
       "      <td>1.691744</td>\n",
       "      <td>-52.093750</td>\n",
       "      <td>-57.614586</td>\n",
       "      <td>-73.337500</td>\n",
       "      <td>4.208485</td>\n",
       "      <td>4.274151</td>\n",
       "      <td>4.096372</td>\n",
       "      <td>-99.093758</td>\n",
       "      <td>-72.174675</td>\n",
       "      <td>Cux2-CreERT2</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>5 rows × 56 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "   adaptation     avg_isi  electrode_0_pa  f_i_curve_slope  \\\n",
       "0    0.093021   81.498750       -6.184375         0.205899   \n",
       "1    0.064384   76.283333       26.135000         0.195247   \n",
       "2         NaN         NaN       -4.600001         0.055443   \n",
       "3    0.048709  118.397143      -90.575616         0.307589   \n",
       "4    0.042215   81.394545       13.653750         0.162729   \n",
       "\n",
       "   fast_trough_t_long_square  fast_trough_t_ramp  fast_trough_t_short_square  \\\n",
       "0                   1.126905            2.768700                    1.025464   \n",
       "1                   1.102660            4.005247                    1.024873   \n",
       "2                   1.104820            9.092507                    1.025024   \n",
       "3                   1.069770            7.203945                    1.024593   \n",
       "4                   1.089750            2.336427                    1.027302   \n",
       "\n",
       "   fast_trough_v_long_square  fast_trough_v_ramp  fast_trough_v_short_square  \\\n",
       "0                 -51.187504          -50.328125                  -55.312504   \n",
       "1                 -48.718750          -49.875001                  -51.500004   \n",
       "2                 -48.093750          -49.541669                  -50.312503   \n",
       "3                 -45.968754          -49.093754                  -53.800002   \n",
       "4                 -48.906250          -51.083335                  -55.800002   \n",
       "\n",
       "        ...         trough_t_short_square  trough_v_long_square  \\\n",
       "0       ...                      1.333809            -56.531254   \n",
       "1       ...                      1.344913            -48.843754   \n",
       "2       ...                      1.197772            -49.531250   \n",
       "3       ...                      1.233473            -46.156254   \n",
       "4       ...                      1.691744            -52.093750   \n",
       "\n",
       "   trough_v_ramp  trough_v_short_square  \\\n",
       "0     -56.812502             -69.306253   \n",
       "1     -50.093753             -67.416669   \n",
       "2     -49.968753             -75.656255   \n",
       "3     -49.218753             -66.318753   \n",
       "4     -57.614586             -73.337500   \n",
       "\n",
       "   upstroke_downstroke_ratio_long_square  upstroke_downstroke_ratio_ramp  \\\n",
       "0                               3.904747                        4.131130   \n",
       "1                               4.231335                        4.299535   \n",
       "2                               2.154281                        1.486651   \n",
       "3                               2.026000                        1.827572   \n",
       "4                               4.208485                        4.274151   \n",
       "\n",
       "   upstroke_downstroke_ratio_short_square  vm_for_sag      vrest  \\\n",
       "0                                3.899439  -85.156258 -68.233376   \n",
       "1                                3.939083  -78.593750 -66.085068   \n",
       "2                                2.400687  -87.156250 -75.141449   \n",
       "3                                1.818158  -82.406250 -65.503044   \n",
       "4                                4.096372  -99.093758 -72.174675   \n",
       "\n",
       "   transgenic_line  \n",
       "0     Cux2-CreERT2  \n",
       "1  Chrna2-Cre_OE25  \n",
       "2             None  \n",
       "3     Sst-IRES-Cre  \n",
       "4     Cux2-CreERT2  \n",
       "\n",
       "[5 rows x 56 columns]"
      ]
     },
     "execution_count": 9,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "ef_df['transgenic_line'] = pd.Series(tg_line, index=ef_df.index)\n",
    "ef_df.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "\n",
       "    .dataframe tbody tr th {\n",
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       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>adaptation</th>\n",
       "      <th>avg_isi</th>\n",
       "      <th>electrode_0_pa</th>\n",
       "      <th>f_i_curve_slope</th>\n",
       "      <th>fast_trough_t_long_square</th>\n",
       "      <th>fast_trough_t_ramp</th>\n",
       "      <th>fast_trough_t_short_square</th>\n",
       "      <th>fast_trough_v_long_square</th>\n",
       "      <th>fast_trough_v_ramp</th>\n",
       "      <th>fast_trough_v_short_square</th>\n",
       "      <th>...</th>\n",
       "      <th>trough_v_long_square</th>\n",
       "      <th>trough_v_ramp</th>\n",
       "      <th>trough_v_short_square</th>\n",
       "      <th>upstroke_downstroke_ratio_long_square</th>\n",
       "      <th>upstroke_downstroke_ratio_ramp</th>\n",
       "      <th>upstroke_downstroke_ratio_short_square</th>\n",
       "      <th>vm_for_sag</th>\n",
       "      <th>vrest</th>\n",
       "      <th>transgenic_line</th>\n",
       "      <th>reporter_status</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>0.093021</td>\n",
       "      <td>81.498750</td>\n",
       "      <td>-6.184375</td>\n",
       "      <td>0.205899</td>\n",
       "      <td>1.126905</td>\n",
       "      <td>2.768700</td>\n",
       "      <td>1.025464</td>\n",
       "      <td>-51.187504</td>\n",
       "      <td>-50.328125</td>\n",
       "      <td>-55.312504</td>\n",
       "      <td>...</td>\n",
       "      <td>-56.531254</td>\n",
       "      <td>-56.812502</td>\n",
       "      <td>-69.306253</td>\n",
       "      <td>3.904747</td>\n",
       "      <td>4.131130</td>\n",
       "      <td>3.899439</td>\n",
       "      <td>-85.156258</td>\n",
       "      <td>-68.233376</td>\n",
       "      <td>Cux2-CreERT2</td>\n",
       "      <td>cre reporter negative</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>0.064384</td>\n",
       "      <td>76.283333</td>\n",
       "      <td>26.135000</td>\n",
       "      <td>0.195247</td>\n",
       "      <td>1.102660</td>\n",
       "      <td>4.005247</td>\n",
       "      <td>1.024873</td>\n",
       "      <td>-48.718750</td>\n",
       "      <td>-49.875001</td>\n",
       "      <td>-51.500004</td>\n",
       "      <td>...</td>\n",
       "      <td>-48.843754</td>\n",
       "      <td>-50.093753</td>\n",
       "      <td>-67.416669</td>\n",
       "      <td>4.231335</td>\n",
       "      <td>4.299535</td>\n",
       "      <td>3.939083</td>\n",
       "      <td>-78.593750</td>\n",
       "      <td>-66.085068</td>\n",
       "      <td>Chrna2-Cre_OE25</td>\n",
       "      <td>cre reporter positive</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>-4.600001</td>\n",
       "      <td>0.055443</td>\n",
       "      <td>1.104820</td>\n",
       "      <td>9.092507</td>\n",
       "      <td>1.025024</td>\n",
       "      <td>-48.093750</td>\n",
       "      <td>-49.541669</td>\n",
       "      <td>-50.312503</td>\n",
       "      <td>...</td>\n",
       "      <td>-49.531250</td>\n",
       "      <td>-49.968753</td>\n",
       "      <td>-75.656255</td>\n",
       "      <td>2.154281</td>\n",
       "      <td>1.486651</td>\n",
       "      <td>2.400687</td>\n",
       "      <td>-87.156250</td>\n",
       "      <td>-75.141449</td>\n",
       "      <td>None</td>\n",
       "      <td>not applicable</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>0.048709</td>\n",
       "      <td>118.397143</td>\n",
       "      <td>-90.575616</td>\n",
       "      <td>0.307589</td>\n",
       "      <td>1.069770</td>\n",
       "      <td>7.203945</td>\n",
       "      <td>1.024593</td>\n",
       "      <td>-45.968754</td>\n",
       "      <td>-49.093754</td>\n",
       "      <td>-53.800002</td>\n",
       "      <td>...</td>\n",
       "      <td>-46.156254</td>\n",
       "      <td>-49.218753</td>\n",
       "      <td>-66.318753</td>\n",
       "      <td>2.026000</td>\n",
       "      <td>1.827572</td>\n",
       "      <td>1.818158</td>\n",
       "      <td>-82.406250</td>\n",
       "      <td>-65.503044</td>\n",
       "      <td>Sst-IRES-Cre</td>\n",
       "      <td>cre reporter positive</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>0.042215</td>\n",
       "      <td>81.394545</td>\n",
       "      <td>13.653750</td>\n",
       "      <td>0.162729</td>\n",
       "      <td>1.089750</td>\n",
       "      <td>2.336427</td>\n",
       "      <td>1.027302</td>\n",
       "      <td>-48.906250</td>\n",
       "      <td>-51.083335</td>\n",
       "      <td>-55.800002</td>\n",
       "      <td>...</td>\n",
       "      <td>-52.093750</td>\n",
       "      <td>-57.614586</td>\n",
       "      <td>-73.337500</td>\n",
       "      <td>4.208485</td>\n",
       "      <td>4.274151</td>\n",
       "      <td>4.096372</td>\n",
       "      <td>-99.093758</td>\n",
       "      <td>-72.174675</td>\n",
       "      <td>Cux2-CreERT2</td>\n",
       "      <td>cre reporter positive</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>5 rows × 57 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "   adaptation     avg_isi  electrode_0_pa  f_i_curve_slope  \\\n",
       "0    0.093021   81.498750       -6.184375         0.205899   \n",
       "1    0.064384   76.283333       26.135000         0.195247   \n",
       "2         NaN         NaN       -4.600001         0.055443   \n",
       "3    0.048709  118.397143      -90.575616         0.307589   \n",
       "4    0.042215   81.394545       13.653750         0.162729   \n",
       "\n",
       "   fast_trough_t_long_square  fast_trough_t_ramp  fast_trough_t_short_square  \\\n",
       "0                   1.126905            2.768700                    1.025464   \n",
       "1                   1.102660            4.005247                    1.024873   \n",
       "2                   1.104820            9.092507                    1.025024   \n",
       "3                   1.069770            7.203945                    1.024593   \n",
       "4                   1.089750            2.336427                    1.027302   \n",
       "\n",
       "   fast_trough_v_long_square  fast_trough_v_ramp  fast_trough_v_short_square  \\\n",
       "0                 -51.187504          -50.328125                  -55.312504   \n",
       "1                 -48.718750          -49.875001                  -51.500004   \n",
       "2                 -48.093750          -49.541669                  -50.312503   \n",
       "3                 -45.968754          -49.093754                  -53.800002   \n",
       "4                 -48.906250          -51.083335                  -55.800002   \n",
       "\n",
       "           ...            trough_v_long_square  trough_v_ramp  \\\n",
       "0          ...                      -56.531254     -56.812502   \n",
       "1          ...                      -48.843754     -50.093753   \n",
       "2          ...                      -49.531250     -49.968753   \n",
       "3          ...                      -46.156254     -49.218753   \n",
       "4          ...                      -52.093750     -57.614586   \n",
       "\n",
       "   trough_v_short_square  upstroke_downstroke_ratio_long_square  \\\n",
       "0             -69.306253                               3.904747   \n",
       "1             -67.416669                               4.231335   \n",
       "2             -75.656255                               2.154281   \n",
       "3             -66.318753                               2.026000   \n",
       "4             -73.337500                               4.208485   \n",
       "\n",
       "   upstroke_downstroke_ratio_ramp  upstroke_downstroke_ratio_short_square  \\\n",
       "0                        4.131130                                3.899439   \n",
       "1                        4.299535                                3.939083   \n",
       "2                        1.486651                                2.400687   \n",
       "3                        1.827572                                1.818158   \n",
       "4                        4.274151                                4.096372   \n",
       "\n",
       "   vm_for_sag      vrest  transgenic_line        reporter_status  \n",
       "0  -85.156258 -68.233376     Cux2-CreERT2  cre reporter negative  \n",
       "1  -78.593750 -66.085068  Chrna2-Cre_OE25  cre reporter positive  \n",
       "2  -87.156250 -75.141449             None         not applicable  \n",
       "3  -82.406250 -65.503044     Sst-IRES-Cre  cre reporter positive  \n",
       "4  -99.093758 -72.174675     Cux2-CreERT2  cre reporter positive  \n",
       "\n",
       "[5 rows x 57 columns]"
      ]
     },
     "execution_count": 10,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "ef_df['reporter_status'] = pd.Series(reporter_status, index=ef_df.index)\n",
    "ef_df.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>adaptation</th>\n",
       "      <th>avg_isi</th>\n",
       "      <th>electrode_0_pa</th>\n",
       "      <th>f_i_curve_slope</th>\n",
       "      <th>fast_trough_t_long_square</th>\n",
       "      <th>fast_trough_t_ramp</th>\n",
       "      <th>fast_trough_t_short_square</th>\n",
       "      <th>fast_trough_v_long_square</th>\n",
       "      <th>fast_trough_v_ramp</th>\n",
       "      <th>fast_trough_v_short_square</th>\n",
       "      <th>...</th>\n",
       "      <th>trough_v_ramp</th>\n",
       "      <th>trough_v_short_square</th>\n",
       "      <th>upstroke_downstroke_ratio_long_square</th>\n",
       "      <th>upstroke_downstroke_ratio_ramp</th>\n",
       "      <th>upstroke_downstroke_ratio_short_square</th>\n",
       "      <th>vm_for_sag</th>\n",
       "      <th>vrest</th>\n",
       "      <th>transgenic_line</th>\n",
       "      <th>reporter_status</th>\n",
       "      <th>hemisphere</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>0.093021</td>\n",
       "      <td>81.498750</td>\n",
       "      <td>-6.184375</td>\n",
       "      <td>0.205899</td>\n",
       "      <td>1.126905</td>\n",
       "      <td>2.768700</td>\n",
       "      <td>1.025464</td>\n",
       "      <td>-51.187504</td>\n",
       "      <td>-50.328125</td>\n",
       "      <td>-55.312504</td>\n",
       "      <td>...</td>\n",
       "      <td>-56.812502</td>\n",
       "      <td>-69.306253</td>\n",
       "      <td>3.904747</td>\n",
       "      <td>4.131130</td>\n",
       "      <td>3.899439</td>\n",
       "      <td>-85.156258</td>\n",
       "      <td>-68.233376</td>\n",
       "      <td>Cux2-CreERT2</td>\n",
       "      <td>cre reporter negative</td>\n",
       "      <td>left</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>0.064384</td>\n",
       "      <td>76.283333</td>\n",
       "      <td>26.135000</td>\n",
       "      <td>0.195247</td>\n",
       "      <td>1.102660</td>\n",
       "      <td>4.005247</td>\n",
       "      <td>1.024873</td>\n",
       "      <td>-48.718750</td>\n",
       "      <td>-49.875001</td>\n",
       "      <td>-51.500004</td>\n",
       "      <td>...</td>\n",
       "      <td>-50.093753</td>\n",
       "      <td>-67.416669</td>\n",
       "      <td>4.231335</td>\n",
       "      <td>4.299535</td>\n",
       "      <td>3.939083</td>\n",
       "      <td>-78.593750</td>\n",
       "      <td>-66.085068</td>\n",
       "      <td>Chrna2-Cre_OE25</td>\n",
       "      <td>cre reporter positive</td>\n",
       "      <td>left</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>-4.600001</td>\n",
       "      <td>0.055443</td>\n",
       "      <td>1.104820</td>\n",
       "      <td>9.092507</td>\n",
       "      <td>1.025024</td>\n",
       "      <td>-48.093750</td>\n",
       "      <td>-49.541669</td>\n",
       "      <td>-50.312503</td>\n",
       "      <td>...</td>\n",
       "      <td>-49.968753</td>\n",
       "      <td>-75.656255</td>\n",
       "      <td>2.154281</td>\n",
       "      <td>1.486651</td>\n",
       "      <td>2.400687</td>\n",
       "      <td>-87.156250</td>\n",
       "      <td>-75.141449</td>\n",
       "      <td>None</td>\n",
       "      <td>not applicable</td>\n",
       "      <td>left</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>0.048709</td>\n",
       "      <td>118.397143</td>\n",
       "      <td>-90.575616</td>\n",
       "      <td>0.307589</td>\n",
       "      <td>1.069770</td>\n",
       "      <td>7.203945</td>\n",
       "      <td>1.024593</td>\n",
       "      <td>-45.968754</td>\n",
       "      <td>-49.093754</td>\n",
       "      <td>-53.800002</td>\n",
       "      <td>...</td>\n",
       "      <td>-49.218753</td>\n",
       "      <td>-66.318753</td>\n",
       "      <td>2.026000</td>\n",
       "      <td>1.827572</td>\n",
       "      <td>1.818158</td>\n",
       "      <td>-82.406250</td>\n",
       "      <td>-65.503044</td>\n",
       "      <td>Sst-IRES-Cre</td>\n",
       "      <td>cre reporter positive</td>\n",
       "      <td>right</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>0.042215</td>\n",
       "      <td>81.394545</td>\n",
       "      <td>13.653750</td>\n",
       "      <td>0.162729</td>\n",
       "      <td>1.089750</td>\n",
       "      <td>2.336427</td>\n",
       "      <td>1.027302</td>\n",
       "      <td>-48.906250</td>\n",
       "      <td>-51.083335</td>\n",
       "      <td>-55.800002</td>\n",
       "      <td>...</td>\n",
       "      <td>-57.614586</td>\n",
       "      <td>-73.337500</td>\n",
       "      <td>4.208485</td>\n",
       "      <td>4.274151</td>\n",
       "      <td>4.096372</td>\n",
       "      <td>-99.093758</td>\n",
       "      <td>-72.174675</td>\n",
       "      <td>Cux2-CreERT2</td>\n",
       "      <td>cre reporter positive</td>\n",
       "      <td>right</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>5 rows × 58 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "   adaptation     avg_isi  electrode_0_pa  f_i_curve_slope  \\\n",
       "0    0.093021   81.498750       -6.184375         0.205899   \n",
       "1    0.064384   76.283333       26.135000         0.195247   \n",
       "2         NaN         NaN       -4.600001         0.055443   \n",
       "3    0.048709  118.397143      -90.575616         0.307589   \n",
       "4    0.042215   81.394545       13.653750         0.162729   \n",
       "\n",
       "   fast_trough_t_long_square  fast_trough_t_ramp  fast_trough_t_short_square  \\\n",
       "0                   1.126905            2.768700                    1.025464   \n",
       "1                   1.102660            4.005247                    1.024873   \n",
       "2                   1.104820            9.092507                    1.025024   \n",
       "3                   1.069770            7.203945                    1.024593   \n",
       "4                   1.089750            2.336427                    1.027302   \n",
       "\n",
       "   fast_trough_v_long_square  fast_trough_v_ramp  fast_trough_v_short_square  \\\n",
       "0                 -51.187504          -50.328125                  -55.312504   \n",
       "1                 -48.718750          -49.875001                  -51.500004   \n",
       "2                 -48.093750          -49.541669                  -50.312503   \n",
       "3                 -45.968754          -49.093754                  -53.800002   \n",
       "4                 -48.906250          -51.083335                  -55.800002   \n",
       "\n",
       "      ...      trough_v_ramp  trough_v_short_square  \\\n",
       "0     ...         -56.812502             -69.306253   \n",
       "1     ...         -50.093753             -67.416669   \n",
       "2     ...         -49.968753             -75.656255   \n",
       "3     ...         -49.218753             -66.318753   \n",
       "4     ...         -57.614586             -73.337500   \n",
       "\n",
       "   upstroke_downstroke_ratio_long_square  upstroke_downstroke_ratio_ramp  \\\n",
       "0                               3.904747                        4.131130   \n",
       "1                               4.231335                        4.299535   \n",
       "2                               2.154281                        1.486651   \n",
       "3                               2.026000                        1.827572   \n",
       "4                               4.208485                        4.274151   \n",
       "\n",
       "   upstroke_downstroke_ratio_short_square  vm_for_sag      vrest  \\\n",
       "0                                3.899439  -85.156258 -68.233376   \n",
       "1                                3.939083  -78.593750 -66.085068   \n",
       "2                                2.400687  -87.156250 -75.141449   \n",
       "3                                1.818158  -82.406250 -65.503044   \n",
       "4                                4.096372  -99.093758 -72.174675   \n",
       "\n",
       "   transgenic_line        reporter_status  hemisphere  \n",
       "0     Cux2-CreERT2  cre reporter negative        left  \n",
       "1  Chrna2-Cre_OE25  cre reporter positive        left  \n",
       "2             None         not applicable        left  \n",
       "3     Sst-IRES-Cre  cre reporter positive       right  \n",
       "4     Cux2-CreERT2  cre reporter positive       right  \n",
       "\n",
       "[5 rows x 58 columns]"
      ]
     },
     "execution_count": 11,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "ef_df['hemisphere'] = pd.Series(hemisphere, index = ef_df.index)\n",
    "ef_df.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "<class 'pandas.core.frame.DataFrame'>\n",
      "RangeIndex: 1337 entries, 0 to 1336\n",
      "Data columns (total 58 columns):\n",
      "adaptation                                1096 non-null float64\n",
      "avg_isi                                   1216 non-null float64\n",
      "electrode_0_pa                            1329 non-null float64\n",
      "f_i_curve_slope                           1337 non-null float64\n",
      "fast_trough_t_long_square                 1337 non-null float64\n",
      "fast_trough_t_ramp                        1301 non-null float64\n",
      "fast_trough_t_short_square                1337 non-null float64\n",
      "fast_trough_v_long_square                 1337 non-null float64\n",
      "fast_trough_v_ramp                        1301 non-null float64\n",
      "fast_trough_v_short_square                1337 non-null float64\n",
      "has_burst                                 1337 non-null bool\n",
      "has_delay                                 1337 non-null bool\n",
      "has_pause                                 1337 non-null bool\n",
      "id                                        1337 non-null int64\n",
      "input_resistance_mohm                     1337 non-null float64\n",
      "latency                                   1337 non-null float64\n",
      "peak_t_long_square                        1337 non-null float64\n",
      "peak_t_ramp                               1301 non-null float64\n",
      "peak_t_short_square                       1337 non-null float64\n",
      "peak_v_long_square                        1337 non-null float64\n",
      "peak_v_ramp                               1301 non-null float64\n",
      "peak_v_short_square                       1337 non-null float64\n",
      "rheobase_sweep_id                         1337 non-null int64\n",
      "rheobase_sweep_number                     1337 non-null int64\n",
      "ri                                        1337 non-null float64\n",
      "sag                                       1337 non-null float64\n",
      "seal_gohm                                 1337 non-null float64\n",
      "slow_trough_t_long_square                 877 non-null float64\n",
      "slow_trough_t_ramp                        897 non-null float64\n",
      "slow_trough_t_short_square                1049 non-null float64\n",
      "slow_trough_v_long_square                 877 non-null float64\n",
      "slow_trough_v_ramp                        897 non-null float64\n",
      "slow_trough_v_short_square                1049 non-null float64\n",
      "specimen_id                               1337 non-null int64\n",
      "threshold_i_long_square                   1337 non-null float64\n",
      "threshold_i_ramp                          1301 non-null float64\n",
      "threshold_i_short_square                  1337 non-null float64\n",
      "threshold_t_long_square                   1337 non-null float64\n",
      "threshold_t_ramp                          1301 non-null float64\n",
      "threshold_t_short_square                  1337 non-null float64\n",
      "threshold_v_long_square                   1337 non-null float64\n",
      "threshold_v_ramp                          1301 non-null float64\n",
      "threshold_v_short_square                  1337 non-null float64\n",
      "thumbnail_sweep_id                        1337 non-null int64\n",
      "trough_t_long_square                      1337 non-null float64\n",
      "trough_t_ramp                             1301 non-null float64\n",
      "trough_t_short_square                     1337 non-null float64\n",
      "trough_v_long_square                      1337 non-null float64\n",
      "trough_v_ramp                             1301 non-null float64\n",
      "trough_v_short_square                     1337 non-null float64\n",
      "upstroke_downstroke_ratio_long_square     1337 non-null float64\n",
      "upstroke_downstroke_ratio_ramp            1301 non-null float64\n",
      "upstroke_downstroke_ratio_short_square    1337 non-null float64\n",
      "vm_for_sag                                1337 non-null float64\n",
      "vrest                                     1337 non-null float64\n",
      "transgenic_line                           1058 non-null object\n",
      "reporter_status                           1316 non-null object\n",
      "hemisphere                                1337 non-null object\n",
      "dtypes: bool(3), float64(47), int64(5), object(3)\n",
      "memory usage: 578.5+ KB\n"
     ]
    }
   ],
   "source": [
    "ef_df.info()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "no_need_features = ['electrode_0_pa', 'has_burst', 'has_delay', 'has_pause', 'id', \n",
    "                    'rheobase_sweep_id', 'rheobase_sweep_number', 'seal_gohm', 'specimen_id',\n",
    "                   'thumbnail_sweep_id', 'slow_trough_t_long_square', 'slow_trough_t_ramp', \n",
    "                   'slow_trough_v_long_square', 'slow_trough_v_ramp']"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "ef_df_extracted = ef_df.drop(no_need_features, axis=1)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "<class 'pandas.core.frame.DataFrame'>\n",
      "RangeIndex: 1337 entries, 0 to 1336\n",
      "Data columns (total 44 columns):\n",
      "adaptation                                1096 non-null float64\n",
      "avg_isi                                   1216 non-null float64\n",
      "f_i_curve_slope                           1337 non-null float64\n",
      "fast_trough_t_long_square                 1337 non-null float64\n",
      "fast_trough_t_ramp                        1301 non-null float64\n",
      "fast_trough_t_short_square                1337 non-null float64\n",
      "fast_trough_v_long_square                 1337 non-null float64\n",
      "fast_trough_v_ramp                        1301 non-null float64\n",
      "fast_trough_v_short_square                1337 non-null float64\n",
      "input_resistance_mohm                     1337 non-null float64\n",
      "latency                                   1337 non-null float64\n",
      "peak_t_long_square                        1337 non-null float64\n",
      "peak_t_ramp                               1301 non-null float64\n",
      "peak_t_short_square                       1337 non-null float64\n",
      "peak_v_long_square                        1337 non-null float64\n",
      "peak_v_ramp                               1301 non-null float64\n",
      "peak_v_short_square                       1337 non-null float64\n",
      "ri                                        1337 non-null float64\n",
      "sag                                       1337 non-null float64\n",
      "slow_trough_t_short_square                1049 non-null float64\n",
      "slow_trough_v_short_square                1049 non-null float64\n",
      "threshold_i_long_square                   1337 non-null float64\n",
      "threshold_i_ramp                          1301 non-null float64\n",
      "threshold_i_short_square                  1337 non-null float64\n",
      "threshold_t_long_square                   1337 non-null float64\n",
      "threshold_t_ramp                          1301 non-null float64\n",
      "threshold_t_short_square                  1337 non-null float64\n",
      "threshold_v_long_square                   1337 non-null float64\n",
      "threshold_v_ramp                          1301 non-null float64\n",
      "threshold_v_short_square                  1337 non-null float64\n",
      "trough_t_long_square                      1337 non-null float64\n",
      "trough_t_ramp                             1301 non-null float64\n",
      "trough_t_short_square                     1337 non-null float64\n",
      "trough_v_long_square                      1337 non-null float64\n",
      "trough_v_ramp                             1301 non-null float64\n",
      "trough_v_short_square                     1337 non-null float64\n",
      "upstroke_downstroke_ratio_long_square     1337 non-null float64\n",
      "upstroke_downstroke_ratio_ramp            1301 non-null float64\n",
      "upstroke_downstroke_ratio_short_square    1337 non-null float64\n",
      "vm_for_sag                                1337 non-null float64\n",
      "vrest                                     1337 non-null float64\n",
      "transgenic_line                           1058 non-null object\n",
      "reporter_status                           1316 non-null object\n",
      "hemisphere                                1337 non-null object\n",
      "dtypes: float64(41), object(3)\n",
      "memory usage: 459.7+ KB\n"
     ]
    }
   ],
   "source": [
    "ef_df_extracted.info()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "ef_df_extracted['height'] = ef_df_extracted['peak_v_short_square'] -ef_df_extracted['fast_trough_v_short_square']\n",
    "# heigtht value was calculated with short protocol values, later corrected as height_short, and add height_long, height_ramp.\n",
    "ef_df_extracted['firing_rate'] = (1/ef_df_extracted['avg_isi'])*1000"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style>\n",
       "    .dataframe thead tr:only-child th {\n",
       "        text-align: right;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: left;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>adaptation</th>\n",
       "      <th>avg_isi</th>\n",
       "      <th>f_i_curve_slope</th>\n",
       "      <th>fast_trough_t_long_square</th>\n",
       "      <th>fast_trough_t_ramp</th>\n",
       "      <th>fast_trough_t_short_square</th>\n",
       "      <th>fast_trough_v_long_square</th>\n",
       "      <th>fast_trough_v_ramp</th>\n",
       "      <th>fast_trough_v_short_square</th>\n",
       "      <th>input_resistance_mohm</th>\n",
       "      <th>...</th>\n",
       "      <th>upstroke_downstroke_ratio_long_square</th>\n",
       "      <th>upstroke_downstroke_ratio_ramp</th>\n",
       "      <th>upstroke_downstroke_ratio_short_square</th>\n",
       "      <th>vm_for_sag</th>\n",
       "      <th>vrest</th>\n",
       "      <th>transgenic_line</th>\n",
       "      <th>reporter_status</th>\n",
       "      <th>hemisphere</th>\n",
       "      <th>height</th>\n",
       "      <th>firing_rate</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>0.093021</td>\n",
       "      <td>81.498750</td>\n",
       "      <td>0.205899</td>\n",
       "      <td>1.126905</td>\n",
       "      <td>2.768700</td>\n",
       "      <td>1.025464</td>\n",
       "      <td>-51.187504</td>\n",
       "      <td>-50.328125</td>\n",
       "      <td>-55.312504</td>\n",
       "      <td>180.243392</td>\n",
       "      <td>...</td>\n",
       "      <td>3.904747</td>\n",
       "      <td>4.131130</td>\n",
       "      <td>3.899439</td>\n",
       "      <td>-85.156258</td>\n",
       "      <td>-68.233376</td>\n",
       "      <td>Cux2-CreERT2</td>\n",
       "      <td>cre reporter negative</td>\n",
       "      <td>left</td>\n",
       "      <td>98.450006</td>\n",
       "      <td>12.270127</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>0.064384</td>\n",
       "      <td>76.283333</td>\n",
       "      <td>0.195247</td>\n",
       "      <td>1.102660</td>\n",
       "      <td>4.005247</td>\n",
       "      <td>1.024873</td>\n",
       "      <td>-48.718750</td>\n",
       "      <td>-49.875001</td>\n",
       "      <td>-51.500004</td>\n",
       "      <td>134.676480</td>\n",
       "      <td>...</td>\n",
       "      <td>4.231335</td>\n",
       "      <td>4.299535</td>\n",
       "      <td>3.939083</td>\n",
       "      <td>-78.593750</td>\n",
       "      <td>-66.085068</td>\n",
       "      <td>Chrna2-Cre_OE25</td>\n",
       "      <td>cre reporter positive</td>\n",
       "      <td>left</td>\n",
       "      <td>105.031258</td>\n",
       "      <td>13.109023</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>0.055443</td>\n",
       "      <td>1.104820</td>\n",
       "      <td>9.092507</td>\n",
       "      <td>1.025024</td>\n",
       "      <td>-48.093750</td>\n",
       "      <td>-49.541669</td>\n",
       "      <td>-50.312503</td>\n",
       "      <td>189.801760</td>\n",
       "      <td>...</td>\n",
       "      <td>2.154281</td>\n",
       "      <td>1.486651</td>\n",
       "      <td>2.400687</td>\n",
       "      <td>-87.156250</td>\n",
       "      <td>-75.141449</td>\n",
       "      <td>None</td>\n",
       "      <td>not applicable</td>\n",
       "      <td>left</td>\n",
       "      <td>89.918754</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>0.048709</td>\n",
       "      <td>118.397143</td>\n",
       "      <td>0.307589</td>\n",
       "      <td>1.069770</td>\n",
       "      <td>7.203945</td>\n",
       "      <td>1.024593</td>\n",
       "      <td>-45.968754</td>\n",
       "      <td>-49.093754</td>\n",
       "      <td>-53.800002</td>\n",
       "      <td>164.745728</td>\n",
       "      <td>...</td>\n",
       "      <td>2.026000</td>\n",
       "      <td>1.827572</td>\n",
       "      <td>1.818158</td>\n",
       "      <td>-82.406250</td>\n",
       "      <td>-65.503044</td>\n",
       "      <td>Sst-IRES-Cre</td>\n",
       "      <td>cre reporter positive</td>\n",
       "      <td>right</td>\n",
       "      <td>81.287503</td>\n",
       "      <td>8.446150</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>0.042215</td>\n",
       "      <td>81.394545</td>\n",
       "      <td>0.162729</td>\n",
       "      <td>1.089750</td>\n",
       "      <td>2.336427</td>\n",
       "      <td>1.027302</td>\n",
       "      <td>-48.906250</td>\n",
       "      <td>-51.083335</td>\n",
       "      <td>-55.800002</td>\n",
       "      <td>289.122080</td>\n",
       "      <td>...</td>\n",
       "      <td>4.208485</td>\n",
       "      <td>4.274151</td>\n",
       "      <td>4.096372</td>\n",
       "      <td>-99.093758</td>\n",
       "      <td>-72.174675</td>\n",
       "      <td>Cux2-CreERT2</td>\n",
       "      <td>cre reporter positive</td>\n",
       "      <td>right</td>\n",
       "      <td>84.887503</td>\n",
       "      <td>12.285836</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>5 rows × 46 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "   adaptation     avg_isi  f_i_curve_slope  fast_trough_t_long_square  \\\n",
       "0    0.093021   81.498750         0.205899                   1.126905   \n",
       "1    0.064384   76.283333         0.195247                   1.102660   \n",
       "2         NaN         NaN         0.055443                   1.104820   \n",
       "3    0.048709  118.397143         0.307589                   1.069770   \n",
       "4    0.042215   81.394545         0.162729                   1.089750   \n",
       "\n",
       "   fast_trough_t_ramp  fast_trough_t_short_square  fast_trough_v_long_square  \\\n",
       "0            2.768700                    1.025464                 -51.187504   \n",
       "1            4.005247                    1.024873                 -48.718750   \n",
       "2            9.092507                    1.025024                 -48.093750   \n",
       "3            7.203945                    1.024593                 -45.968754   \n",
       "4            2.336427                    1.027302                 -48.906250   \n",
       "\n",
       "   fast_trough_v_ramp  fast_trough_v_short_square  input_resistance_mohm  \\\n",
       "0          -50.328125                  -55.312504             180.243392   \n",
       "1          -49.875001                  -51.500004             134.676480   \n",
       "2          -49.541669                  -50.312503             189.801760   \n",
       "3          -49.093754                  -53.800002             164.745728   \n",
       "4          -51.083335                  -55.800002             289.122080   \n",
       "\n",
       "      ...       upstroke_downstroke_ratio_long_square  \\\n",
       "0     ...                                    3.904747   \n",
       "1     ...                                    4.231335   \n",
       "2     ...                                    2.154281   \n",
       "3     ...                                    2.026000   \n",
       "4     ...                                    4.208485   \n",
       "\n",
       "   upstroke_downstroke_ratio_ramp  upstroke_downstroke_ratio_short_square  \\\n",
       "0                        4.131130                                3.899439   \n",
       "1                        4.299535                                3.939083   \n",
       "2                        1.486651                                2.400687   \n",
       "3                        1.827572                                1.818158   \n",
       "4                        4.274151                                4.096372   \n",
       "\n",
       "   vm_for_sag      vrest  transgenic_line        reporter_status  hemisphere  \\\n",
       "0  -85.156258 -68.233376     Cux2-CreERT2  cre reporter negative        left   \n",
       "1  -78.593750 -66.085068  Chrna2-Cre_OE25  cre reporter positive        left   \n",
       "2  -87.156250 -75.141449             None         not applicable        left   \n",
       "3  -82.406250 -65.503044     Sst-IRES-Cre  cre reporter positive       right   \n",
       "4  -99.093758 -72.174675     Cux2-CreERT2  cre reporter positive       right   \n",
       "\n",
       "       height  firing_rate  \n",
       "0   98.450006    12.270127  \n",
       "1  105.031258    13.109023  \n",
       "2   89.918754          NaN  \n",
       "3   81.287503     8.446150  \n",
       "4   84.887503    12.285836  \n",
       "\n",
       "[5 rows x 46 columns]"
      ]
     },
     "execution_count": 17,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "ef_df_extracted.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "def dis_EI(cre_line): # labelling for excitory vs inbihitory cre line\n",
    "    output = []\n",
    "    for item in cre_line:\n",
    "        if (item == 'Pvalb-IRES-Cre' or item == 'Sst-IRES-Cre' or\n",
    "            item == 'Htr3a-Cre_NO152' or item == 'Vip-IRES-Cre' or\n",
    "            item == 'Gad2-IRES-Cre' or item == 'Chat-IRES-Cre-neo' or\n",
    "            item == 'Chrna2-Cre_OE25' or item == 'Nkx2-1-CreERT2'):\n",
    "            # missed Ndnf-IRES2-dgCre - will be corrected later in rmd\n",
    "                output = output + ['Inhibitory']\n",
    "        else:\n",
    "            output = output + ['Excitatory']\n",
    "    return output\n",
    "ef_df_extracted['binary_neuron'] = pd.DataFrame(dis_EI(ef_df_extracted['transgenic_line']))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "\n",
       "    .dataframe tbody tr th {\n",
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       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>adaptation</th>\n",
       "      <th>avg_isi</th>\n",
       "      <th>f_i_curve_slope</th>\n",
       "      <th>fast_trough_t_long_square</th>\n",
       "      <th>fast_trough_t_ramp</th>\n",
       "      <th>fast_trough_t_short_square</th>\n",
       "      <th>fast_trough_v_long_square</th>\n",
       "      <th>fast_trough_v_ramp</th>\n",
       "      <th>fast_trough_v_short_square</th>\n",
       "      <th>input_resistance_mohm</th>\n",
       "      <th>...</th>\n",
       "      <th>upstroke_downstroke_ratio_ramp</th>\n",
       "      <th>upstroke_downstroke_ratio_short_square</th>\n",
       "      <th>vm_for_sag</th>\n",
       "      <th>vrest</th>\n",
       "      <th>transgenic_line</th>\n",
       "      <th>reporter_status</th>\n",
       "      <th>hemisphere</th>\n",
       "      <th>height</th>\n",
       "      <th>firing_rate</th>\n",
       "      <th>binary_neuron</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>1332</th>\n",
       "      <td>0.033096</td>\n",
       "      <td>127.260000</td>\n",
       "      <td>0.141466</td>\n",
       "      <td>1.30392</td>\n",
       "      <td>2.453470</td>\n",
       "      <td>1.027433</td>\n",
       "      <td>-51.062504</td>\n",
       "      <td>-51.468752</td>\n",
       "      <td>-51.916668</td>\n",
       "      <td>152.173744</td>\n",
       "      <td>...</td>\n",
       "      <td>4.406138</td>\n",
       "      <td>4.282831</td>\n",
       "      <td>-88.031258</td>\n",
       "      <td>-63.121693</td>\n",
       "      <td>None</td>\n",
       "      <td>not applicable</td>\n",
       "      <td>left</td>\n",
       "      <td>102.000005</td>\n",
       "      <td>7.857929</td>\n",
       "      <td>Excitatory</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1333</th>\n",
       "      <td>0.021331</td>\n",
       "      <td>55.857500</td>\n",
       "      <td>0.126190</td>\n",
       "      <td>1.14522</td>\n",
       "      <td>4.860593</td>\n",
       "      <td>1.024965</td>\n",
       "      <td>-46.093750</td>\n",
       "      <td>-47.020835</td>\n",
       "      <td>-48.492190</td>\n",
       "      <td>251.630560</td>\n",
       "      <td>...</td>\n",
       "      <td>3.710321</td>\n",
       "      <td>3.378424</td>\n",
       "      <td>-96.781250</td>\n",
       "      <td>-78.259277</td>\n",
       "      <td>Scnn1a-Tg3-Cre</td>\n",
       "      <td>cre reporter positive</td>\n",
       "      <td>left</td>\n",
       "      <td>89.195316</td>\n",
       "      <td>17.902699</td>\n",
       "      <td>Excitatory</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1334</th>\n",
       "      <td>0.047917</td>\n",
       "      <td>112.735625</td>\n",
       "      <td>0.079324</td>\n",
       "      <td>1.16643</td>\n",
       "      <td>7.605778</td>\n",
       "      <td>1.025228</td>\n",
       "      <td>-57.000004</td>\n",
       "      <td>-57.572918</td>\n",
       "      <td>-58.762502</td>\n",
       "      <td>66.813688</td>\n",
       "      <td>...</td>\n",
       "      <td>3.010267</td>\n",
       "      <td>3.396610</td>\n",
       "      <td>-89.718750</td>\n",
       "      <td>-73.232635</td>\n",
       "      <td>None</td>\n",
       "      <td>not applicable</td>\n",
       "      <td>left</td>\n",
       "      <td>99.037505</td>\n",
       "      <td>8.870311</td>\n",
       "      <td>Excitatory</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1335</th>\n",
       "      <td>0.028293</td>\n",
       "      <td>84.403636</td>\n",
       "      <td>0.122825</td>\n",
       "      <td>1.13298</td>\n",
       "      <td>7.115233</td>\n",
       "      <td>1.025576</td>\n",
       "      <td>-44.125000</td>\n",
       "      <td>-48.250003</td>\n",
       "      <td>-51.337503</td>\n",
       "      <td>165.862832</td>\n",
       "      <td>...</td>\n",
       "      <td>3.481667</td>\n",
       "      <td>4.269691</td>\n",
       "      <td>-93.000000</td>\n",
       "      <td>-79.386765</td>\n",
       "      <td>Rorb-IRES2-Cre</td>\n",
       "      <td>cre reporter positive</td>\n",
       "      <td>left</td>\n",
       "      <td>92.687505</td>\n",
       "      <td>11.847831</td>\n",
       "      <td>Excitatory</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1336</th>\n",
       "      <td>NaN</td>\n",
       "      <td>6.260000</td>\n",
       "      <td>0.010326</td>\n",
       "      <td>1.13888</td>\n",
       "      <td>15.949200</td>\n",
       "      <td>1.025120</td>\n",
       "      <td>-52.125004</td>\n",
       "      <td>-58.218753</td>\n",
       "      <td>-55.331253</td>\n",
       "      <td>62.743816</td>\n",
       "      <td>...</td>\n",
       "      <td>3.705363</td>\n",
       "      <td>3.634396</td>\n",
       "      <td>-78.687508</td>\n",
       "      <td>-72.151871</td>\n",
       "      <td>None</td>\n",
       "      <td>not applicable</td>\n",
       "      <td>right</td>\n",
       "      <td>106.300006</td>\n",
       "      <td>159.744409</td>\n",
       "      <td>Excitatory</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>5 rows × 47 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "      adaptation     avg_isi  f_i_curve_slope  fast_trough_t_long_square  \\\n",
       "1332    0.033096  127.260000         0.141466                    1.30392   \n",
       "1333    0.021331   55.857500         0.126190                    1.14522   \n",
       "1334    0.047917  112.735625         0.079324                    1.16643   \n",
       "1335    0.028293   84.403636         0.122825                    1.13298   \n",
       "1336         NaN    6.260000         0.010326                    1.13888   \n",
       "\n",
       "      fast_trough_t_ramp  fast_trough_t_short_square  \\\n",
       "1332            2.453470                    1.027433   \n",
       "1333            4.860593                    1.024965   \n",
       "1334            7.605778                    1.025228   \n",
       "1335            7.115233                    1.025576   \n",
       "1336           15.949200                    1.025120   \n",
       "\n",
       "      fast_trough_v_long_square  fast_trough_v_ramp  \\\n",
       "1332                 -51.062504          -51.468752   \n",
       "1333                 -46.093750          -47.020835   \n",
       "1334                 -57.000004          -57.572918   \n",
       "1335                 -44.125000          -48.250003   \n",
       "1336                 -52.125004          -58.218753   \n",
       "\n",
       "      fast_trough_v_short_square  input_resistance_mohm      ...        \\\n",
       "1332                  -51.916668             152.173744      ...         \n",
       "1333                  -48.492190             251.630560      ...         \n",
       "1334                  -58.762502              66.813688      ...         \n",
       "1335                  -51.337503             165.862832      ...         \n",
       "1336                  -55.331253              62.743816      ...         \n",
       "\n",
       "      upstroke_downstroke_ratio_ramp  upstroke_downstroke_ratio_short_square  \\\n",
       "1332                        4.406138                                4.282831   \n",
       "1333                        3.710321                                3.378424   \n",
       "1334                        3.010267                                3.396610   \n",
       "1335                        3.481667                                4.269691   \n",
       "1336                        3.705363                                3.634396   \n",
       "\n",
       "      vm_for_sag      vrest  transgenic_line        reporter_status  \\\n",
       "1332  -88.031258 -63.121693             None         not applicable   \n",
       "1333  -96.781250 -78.259277   Scnn1a-Tg3-Cre  cre reporter positive   \n",
       "1334  -89.718750 -73.232635             None         not applicable   \n",
       "1335  -93.000000 -79.386765   Rorb-IRES2-Cre  cre reporter positive   \n",
       "1336  -78.687508 -72.151871             None         not applicable   \n",
       "\n",
       "      hemisphere      height  firing_rate  binary_neuron  \n",
       "1332        left  102.000005     7.857929     Excitatory  \n",
       "1333        left   89.195316    17.902699     Excitatory  \n",
       "1334        left   99.037505     8.870311     Excitatory  \n",
       "1335        left   92.687505    11.847831     Excitatory  \n",
       "1336       right  106.300006   159.744409     Excitatory  \n",
       "\n",
       "[5 rows x 47 columns]"
      ]
     },
     "execution_count": 19,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "ef_df_extracted.tail()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "969"
      ]
     },
     "execution_count": 20,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "ef_df_cre = ef_df_extracted[ef_df_extracted['reporter_status']=='cre reporter positive']\n",
    "len(ef_df_cre)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style>\n",
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       "        text-align: right;\n",
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       "\n",
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       "        text-align: left;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>transgenic_line</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>Pvalb-IRES-Cre</th>\n",
       "      <td>142</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Rorb-IRES2-Cre</th>\n",
       "      <td>120</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Sst-IRES-Cre</th>\n",
       "      <td>111</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Htr3a-Cre_NO152</th>\n",
       "      <td>89</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Cux2-CreERT2</th>\n",
       "      <td>73</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Rbp4-Cre_KL100</th>\n",
       "      <td>72</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Nr5a1-Cre</th>\n",
       "      <td>69</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Scnn1a-Tg3-Cre</th>\n",
       "      <td>60</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Ntsr1-Cre_GN220</th>\n",
       "      <td>48</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Scnn1a-Tg2-Cre</th>\n",
       "      <td>36</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Chrna2-Cre_OE25</th>\n",
       "      <td>31</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Ctgf-T2A-dgCre</th>\n",
       "      <td>26</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Nkx2-1-CreERT2</th>\n",
       "      <td>23</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Vip-IRES-Cre</th>\n",
       "      <td>20</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Chat-IRES-Cre-neo</th>\n",
       "      <td>20</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Ndnf-IRES2-dgCre</th>\n",
       "      <td>15</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Gad2-IRES-Cre</th>\n",
       "      <td>11</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Slc17a6-IRES-Cre</th>\n",
       "      <td>3</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "                   transgenic_line\n",
       "Pvalb-IRES-Cre                 142\n",
       "Rorb-IRES2-Cre                 120\n",
       "Sst-IRES-Cre                   111\n",
       "Htr3a-Cre_NO152                 89\n",
       "Cux2-CreERT2                    73\n",
       "Rbp4-Cre_KL100                  72\n",
       "Nr5a1-Cre                       69\n",
       "Scnn1a-Tg3-Cre                  60\n",
       "Ntsr1-Cre_GN220                 48\n",
       "Scnn1a-Tg2-Cre                  36\n",
       "Chrna2-Cre_OE25                 31\n",
       "Ctgf-T2A-dgCre                  26\n",
       "Nkx2-1-CreERT2                  23\n",
       "Vip-IRES-Cre                    20\n",
       "Chat-IRES-Cre-neo               20\n",
       "Ndnf-IRES2-dgCre                15\n",
       "Gad2-IRES-Cre                   11\n",
       "Slc17a6-IRES-Cre                 3"
      ]
     },
     "execution_count": 21,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "pd.DataFrame(ef_df_cre['transgenic_line'].value_counts())"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 22,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "    .dataframe thead th {\n",
       "        text-align: left;\n",
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       "\n",
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       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>binary_neuron</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>Excitatory</th>\n",
       "      <td>522</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Inhibitory</th>\n",
       "      <td>447</td>\n",
       "    </tr>\n",
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       "</table>\n",
       "</div>"
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      "text/plain": [
       "            binary_neuron\n",
       "Excitatory            522\n",
       "Inhibitory            447"
      ]
     },
     "execution_count": 22,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "pd.DataFrame(ef_df_cre['binary_neuron'].value_counts())"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 23,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "ef_df_cre.to_csv('ephys_data_cre_hemisphere.csv', index = False)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 24,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "ef_df_extracted.to_csv('ephys_data_hemisphere.csv', index = False)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "collapsed": true
   },
   "source": [
    "* ephys_data_cre.csv \n",
    "- missing hemisphere col, in further data process using these data.\n",
    "- hemisphere feature was tested for pilot."
   ]
  }
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