visualize_analysis.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "1ce58901",
   "metadata": {},
   "outputs": [],
   "source": [
    "import pandas as pd\n",
    "import numpy as np\n",
    "import UpdateME \n",
    "from UpdateME import cellfinder_output_path"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "id": "446ad22d",
   "metadata": {},
   "outputs": [],
   "source": [
    "mouse_id = 'test_000'\n",
    "cellfinder_output_path = '/Users/grant/Desktop/work/Denman_Lab/Cal_Light/LifeCanvas/cellfinder_outputs/G21/Combined/G21_cellfinder_gfp_rfp_031223/'\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "id": "3cdcc4cc",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "(6656, 3)\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "array([[ 9150.,   250.,  6950.],\n",
       "       [ 9200.,   250.,  6850.],\n",
       "       [ 9000.,   350.,  4100.],\n",
       "       ...,\n",
       "       [12750., 10000.,  4650.],\n",
       "       [13300., 10050.,  6150.],\n",
       "       [13000., 10000.,  5950.]])"
      ]
     },
     "execution_count": 19,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# Path to cellfinder_output shared cells .npy file\n",
    "shared_cells_path = '/Users/grant/Desktop/shared_cells_test_001_.npy'\n",
    "shared_cells_path\n",
    "points = np.load(shared_cells_path)\n",
    "print(np.shape(points))\n",
    "points"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "id": "a355dcad",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "(132950, 3)\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "array([[ 9350.,   450.,  3550.],\n",
       "       [ 9200.,   400.,  3550.],\n",
       "       [ 9250.,   450.,  3600.],\n",
       "       ...,\n",
       "       [ 7950.,  8300., 12050.],\n",
       "       [ 9150.,  8750., 11550.],\n",
       "       [10100.,  9000., 11200.]])"
      ]
     },
     "execution_count": 17,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# Path to cellfinder_output points.npy file\n",
    "cells_path = cellfinder_output_path + 'points/tdTomato_points.npy'\n",
    "cells_path\n",
    "points = np.load(cells_path)\n",
    "print(np.shape(points))\n",
    "points\n"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "ce00a448",
   "metadata": {},
   "source": [
    "### if you want to visualize data from a different mouse\n",
    "#### update the cellfinder_output_path and mouse_id variables in the variables.py file in this repository"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "id": "f5d35c2a",
   "metadata": {},
   "outputs": [],
   "source": [
    "# import cellfinder inital data\n",
    "gfp_df = pd.read_csv(cellfinder_output_path + 'analysis/' + 'gfp_summary.csv')\n",
    "# summary_df_0 = pd.read_csv(cellfinder_output_path + 'analysis/' + 'summary.csv')\n",
    "tdTomato_df = pd.read_csv(cellfinder_output_path + 'analysis/' + 'tdTomato_summary.csv')\n",
    "\n",
    "# import analyized data\n",
    "# labled_cells_df = pd.read_csv(cellfinder_output_path + mouse_id +'_Completed_Analysis/' + mouse_id + '_labled_cells.csv')\n",
    "# summary_df = pd.read_csv(cellfinder_output_path + mouse_id + '_Completed_Analysis/'+ mouse_id + '_summary_df.csv')"
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "id": "e8e4baad",
   "metadata": {},
   "source": [
    "# Compare GFP to tdTomato labled cells\n",
    "#### This was organized using the brain regions containing the most gfp cells in row 1 "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "id": "3af253d0",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "You are currently looking at the following cellfinder output folder, and evaluating the following mouse_id\n",
      "\n",
      "/Users/grant/Desktop/cellfinder_gf_wholebrain_030723_33/\n",
      "\n",
      "test_000\n"
     ]
    }
   ],
   "source": [
    "print('You are currently looking at the following cellfinder output folder, and evaluating the following mouse_id')\n",
    "print('')\n",
    "print(cellfinder_output_path)\n",
    "\n",
    "print('')\n",
    "print(mouse_id)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "e71967c6",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>structure_name</th>\n",
       "      <th>left_cell_count</th>\n",
       "      <th>right_cell_count</th>\n",
       "      <th>total_cells</th>\n",
       "      <th>left_volume_mm3</th>\n",
       "      <th>right_volume_mm3</th>\n",
       "      <th>total_volume_mm3</th>\n",
       "      <th>left_cells_per_mm3</th>\n",
       "      <th>right_cells_per_mm3</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>Main olfactory bulb</td>\n",
       "      <td>105.0</td>\n",
       "      <td>140.0</td>\n",
       "      <td>245.0</td>\n",
       "      <td>7.999125</td>\n",
       "      <td>8.035750</td>\n",
       "      <td>16.034875</td>\n",
       "      <td>13.126436</td>\n",
       "      <td>17.422145</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>Retrosplenial area, dorsal part, layer 5</td>\n",
       "      <td>48.0</td>\n",
       "      <td>164.0</td>\n",
       "      <td>212.0</td>\n",
       "      <td>0.644750</td>\n",
       "      <td>0.626500</td>\n",
       "      <td>1.271250</td>\n",
       "      <td>74.447460</td>\n",
       "      <td>261.771748</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>Retrosplenial area, dorsal part, layer 2/3</td>\n",
       "      <td>39.0</td>\n",
       "      <td>148.0</td>\n",
       "      <td>187.0</td>\n",
       "      <td>0.515875</td>\n",
       "      <td>0.511125</td>\n",
       "      <td>1.027000</td>\n",
       "      <td>75.599709</td>\n",
       "      <td>289.557349</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>Primary visual area, layer 2/3</td>\n",
       "      <td>32.0</td>\n",
       "      <td>124.0</td>\n",
       "      <td>156.0</td>\n",
       "      <td>1.117625</td>\n",
       "      <td>1.094000</td>\n",
       "      <td>2.211625</td>\n",
       "      <td>28.632144</td>\n",
       "      <td>113.345521</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>olfactory nerve layer of main olfactory bulb</td>\n",
       "      <td>41.0</td>\n",
       "      <td>108.0</td>\n",
       "      <td>149.0</td>\n",
       "      <td>1.978500</td>\n",
       "      <td>2.041000</td>\n",
       "      <td>4.019500</td>\n",
       "      <td>20.722770</td>\n",
       "      <td>52.915238</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>Retrosplenial area, lateral agranular part, la...</td>\n",
       "      <td>21.0</td>\n",
       "      <td>104.0</td>\n",
       "      <td>125.0</td>\n",
       "      <td>0.366750</td>\n",
       "      <td>0.353875</td>\n",
       "      <td>0.720625</td>\n",
       "      <td>57.259714</td>\n",
       "      <td>293.889085</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>Retrosplenial area, ventral part, layer 5</td>\n",
       "      <td>27.0</td>\n",
       "      <td>93.0</td>\n",
       "      <td>120.0</td>\n",
       "      <td>0.890625</td>\n",
       "      <td>0.854000</td>\n",
       "      <td>1.744625</td>\n",
       "      <td>30.315789</td>\n",
       "      <td>108.899297</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>Secondary motor area, layer 5</td>\n",
       "      <td>39.0</td>\n",
       "      <td>79.0</td>\n",
       "      <td>118.0</td>\n",
       "      <td>2.285000</td>\n",
       "      <td>2.316000</td>\n",
       "      <td>4.601000</td>\n",
       "      <td>17.067834</td>\n",
       "      <td>34.110535</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>Retrosplenial area, lateral agranular part, la...</td>\n",
       "      <td>30.0</td>\n",
       "      <td>84.0</td>\n",
       "      <td>114.0</td>\n",
       "      <td>0.400125</td>\n",
       "      <td>0.388375</td>\n",
       "      <td>0.788500</td>\n",
       "      <td>74.976570</td>\n",
       "      <td>216.285806</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>Primary visual area, layer 5</td>\n",
       "      <td>23.0</td>\n",
       "      <td>86.0</td>\n",
       "      <td>109.0</td>\n",
       "      <td>0.868750</td>\n",
       "      <td>0.855750</td>\n",
       "      <td>1.724500</td>\n",
       "      <td>26.474820</td>\n",
       "      <td>100.496640</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>10</th>\n",
       "      <td>Retrosplenial area, ventral part, layer 2/3</td>\n",
       "      <td>10.0</td>\n",
       "      <td>92.0</td>\n",
       "      <td>102.0</td>\n",
       "      <td>0.551875</td>\n",
       "      <td>0.539750</td>\n",
       "      <td>1.091625</td>\n",
       "      <td>18.120045</td>\n",
       "      <td>170.449282</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>11</th>\n",
       "      <td>Secondary motor area, layer 2/3</td>\n",
       "      <td>30.0</td>\n",
       "      <td>65.0</td>\n",
       "      <td>95.0</td>\n",
       "      <td>1.827250</td>\n",
       "      <td>1.871625</td>\n",
       "      <td>3.698875</td>\n",
       "      <td>16.418115</td>\n",
       "      <td>34.729179</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>12</th>\n",
       "      <td>Primary visual area, layer 4</td>\n",
       "      <td>17.0</td>\n",
       "      <td>63.0</td>\n",
       "      <td>80.0</td>\n",
       "      <td>0.567500</td>\n",
       "      <td>0.562875</td>\n",
       "      <td>1.130375</td>\n",
       "      <td>29.955947</td>\n",
       "      <td>111.925383</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>13</th>\n",
       "      <td>Visceral area, layer 2/3</td>\n",
       "      <td>2.0</td>\n",
       "      <td>68.0</td>\n",
       "      <td>70.0</td>\n",
       "      <td>0.291375</td>\n",
       "      <td>0.281875</td>\n",
       "      <td>0.573250</td>\n",
       "      <td>6.864007</td>\n",
       "      <td>241.241685</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>14</th>\n",
       "      <td>Uvula (IX)</td>\n",
       "      <td>47.0</td>\n",
       "      <td>22.0</td>\n",
       "      <td>69.0</td>\n",
       "      <td>0.977125</td>\n",
       "      <td>1.022875</td>\n",
       "      <td>2.000000</td>\n",
       "      <td>48.100294</td>\n",
       "      <td>21.508004</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>15</th>\n",
       "      <td>Spinal nucleus of the trigeminal, caudal part</td>\n",
       "      <td>13.0</td>\n",
       "      <td>51.0</td>\n",
       "      <td>64.0</td>\n",
       "      <td>0.798500</td>\n",
       "      <td>0.798750</td>\n",
       "      <td>1.597250</td>\n",
       "      <td>16.280526</td>\n",
       "      <td>63.849765</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>16</th>\n",
       "      <td>Olfactory areas</td>\n",
       "      <td>22.0</td>\n",
       "      <td>39.0</td>\n",
       "      <td>61.0</td>\n",
       "      <td>2.497250</td>\n",
       "      <td>2.588375</td>\n",
       "      <td>5.085625</td>\n",
       "      <td>8.809691</td>\n",
       "      <td>15.067369</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>17</th>\n",
       "      <td>Primary motor area, Layer 5</td>\n",
       "      <td>31.0</td>\n",
       "      <td>28.0</td>\n",
       "      <td>59.0</td>\n",
       "      <td>1.645875</td>\n",
       "      <td>1.632375</td>\n",
       "      <td>3.278250</td>\n",
       "      <td>18.834966</td>\n",
       "      <td>17.152921</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>18</th>\n",
       "      <td>Retrosplenial area, ventral part, layer 1</td>\n",
       "      <td>9.0</td>\n",
       "      <td>47.0</td>\n",
       "      <td>56.0</td>\n",
       "      <td>0.429625</td>\n",
       "      <td>0.537375</td>\n",
       "      <td>0.967000</td>\n",
       "      <td>20.948502</td>\n",
       "      <td>87.462201</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>19</th>\n",
       "      <td>choroid plexus</td>\n",
       "      <td>35.0</td>\n",
       "      <td>20.0</td>\n",
       "      <td>55.0</td>\n",
       "      <td>0.685875</td>\n",
       "      <td>0.733250</td>\n",
       "      <td>1.419125</td>\n",
       "      <td>51.029707</td>\n",
       "      <td>27.275827</td>\n",
       "    </tr>\n",
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      ],
      "text/plain": [
       "                                       structure_name  left_cell_count  \\\n",
       "0                                 Main olfactory bulb            105.0   \n",
       "1            Retrosplenial area, dorsal part, layer 5             48.0   \n",
       "2          Retrosplenial area, dorsal part, layer 2/3             39.0   \n",
       "3                      Primary visual area, layer 2/3             32.0   \n",
       "4        olfactory nerve layer of main olfactory bulb             41.0   \n",
       "5   Retrosplenial area, lateral agranular part, la...             21.0   \n",
       "6           Retrosplenial area, ventral part, layer 5             27.0   \n",
       "7                       Secondary motor area, layer 5             39.0   \n",
       "8   Retrosplenial area, lateral agranular part, la...             30.0   \n",
       "9                        Primary visual area, layer 5             23.0   \n",
       "10        Retrosplenial area, ventral part, layer 2/3             10.0   \n",
       "11                    Secondary motor area, layer 2/3             30.0   \n",
       "12                       Primary visual area, layer 4             17.0   \n",
       "13                           Visceral area, layer 2/3              2.0   \n",
       "14                                         Uvula (IX)             47.0   \n",
       "15      Spinal nucleus of the trigeminal, caudal part             13.0   \n",
       "16                                    Olfactory areas             22.0   \n",
       "17                        Primary motor area, Layer 5             31.0   \n",
       "18          Retrosplenial area, ventral part, layer 1              9.0   \n",
       "19                                     choroid plexus             35.0   \n",
       "\n",
       "    right_cell_count  total_cells  left_volume_mm3  right_volume_mm3  \\\n",
       "0              140.0        245.0         7.999125          8.035750   \n",
       "1              164.0        212.0         0.644750          0.626500   \n",
       "2              148.0        187.0         0.515875          0.511125   \n",
       "3              124.0        156.0         1.117625          1.094000   \n",
       "4              108.0        149.0         1.978500          2.041000   \n",
       "5              104.0        125.0         0.366750          0.353875   \n",
       "6               93.0        120.0         0.890625          0.854000   \n",
       "7               79.0        118.0         2.285000          2.316000   \n",
       "8               84.0        114.0         0.400125          0.388375   \n",
       "9               86.0        109.0         0.868750          0.855750   \n",
       "10              92.0        102.0         0.551875          0.539750   \n",
       "11              65.0         95.0         1.827250          1.871625   \n",
       "12              63.0         80.0         0.567500          0.562875   \n",
       "13              68.0         70.0         0.291375          0.281875   \n",
       "14              22.0         69.0         0.977125          1.022875   \n",
       "15              51.0         64.0         0.798500          0.798750   \n",
       "16              39.0         61.0         2.497250          2.588375   \n",
       "17              28.0         59.0         1.645875          1.632375   \n",
       "18              47.0         56.0         0.429625          0.537375   \n",
       "19              20.0         55.0         0.685875          0.733250   \n",
       "\n",
       "    total_volume_mm3  left_cells_per_mm3  right_cells_per_mm3  \n",
       "0          16.034875           13.126436            17.422145  \n",
       "1           1.271250           74.447460           261.771748  \n",
       "2           1.027000           75.599709           289.557349  \n",
       "3           2.211625           28.632144           113.345521  \n",
       "4           4.019500           20.722770            52.915238  \n",
       "5           0.720625           57.259714           293.889085  \n",
       "6           1.744625           30.315789           108.899297  \n",
       "7           4.601000           17.067834            34.110535  \n",
       "8           0.788500           74.976570           216.285806  \n",
       "9           1.724500           26.474820           100.496640  \n",
       "10          1.091625           18.120045           170.449282  \n",
       "11          3.698875           16.418115            34.729179  \n",
       "12          1.130375           29.955947           111.925383  \n",
       "13          0.573250            6.864007           241.241685  \n",
       "14          2.000000           48.100294            21.508004  \n",
       "15          1.597250           16.280526            63.849765  \n",
       "16          5.085625            8.809691            15.067369  \n",
       "17          3.278250           18.834966            17.152921  \n",
       "18          0.967000           20.948502            87.462201  \n",
       "19          1.419125           51.029707            27.275827  "
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "gfp_df.head(20)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "id": "a4148f38",
   "metadata": {},
   "outputs": [
    {
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       "      <th></th>\n",
       "      <th>structure_name</th>\n",
       "      <th>left_cell_count</th>\n",
       "      <th>right_cell_count</th>\n",
       "      <th>total_cells</th>\n",
       "      <th>left_volume_mm3</th>\n",
       "      <th>right_volume_mm3</th>\n",
       "      <th>total_volume_mm3</th>\n",
       "      <th>left_cells_per_mm3</th>\n",
       "      <th>right_cells_per_mm3</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>Primary visual area, layer 2/3</td>\n",
       "      <td>5.0</td>\n",
       "      <td>12.0</td>\n",
       "      <td>17.0</td>\n",
       "      <td>1.117625</td>\n",
       "      <td>1.094000</td>\n",
       "      <td>2.211625</td>\n",
       "      <td>4.473773</td>\n",
       "      <td>10.968921</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>Retrosplenial area, lateral agranular part, la...</td>\n",
       "      <td>1.0</td>\n",
       "      <td>11.0</td>\n",
       "      <td>12.0</td>\n",
       "      <td>0.366750</td>\n",
       "      <td>0.353875</td>\n",
       "      <td>0.720625</td>\n",
       "      <td>2.726653</td>\n",
       "      <td>31.084422</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>Retrosplenial area, dorsal part, layer 2/3</td>\n",
       "      <td>2.0</td>\n",
       "      <td>4.0</td>\n",
       "      <td>6.0</td>\n",
       "      <td>0.515875</td>\n",
       "      <td>0.511125</td>\n",
       "      <td>1.027000</td>\n",
       "      <td>3.876908</td>\n",
       "      <td>7.825874</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>posteromedial visual area, layer 2/3</td>\n",
       "      <td>1.0</td>\n",
       "      <td>5.0</td>\n",
       "      <td>6.0</td>\n",
       "      <td>0.160125</td>\n",
       "      <td>0.157875</td>\n",
       "      <td>0.318000</td>\n",
       "      <td>6.245121</td>\n",
       "      <td>31.670625</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>Retrosplenial area, dorsal part, layer 1</td>\n",
       "      <td>0.0</td>\n",
       "      <td>5.0</td>\n",
       "      <td>5.0</td>\n",
       "      <td>0.432375</td>\n",
       "      <td>0.427250</td>\n",
       "      <td>0.859625</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>11.702750</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>Tuberomammillary nucleus, ventral part</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.064875</td>\n",
       "      <td>0.062000</td>\n",
       "      <td>0.126875</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>Primary somatosensory area, mouth, layer 6b</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.059375</td>\n",
       "      <td>0.059625</td>\n",
       "      <td>0.119000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>internal capsule</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>1.207875</td>\n",
       "      <td>1.195125</td>\n",
       "      <td>2.403000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>Principal sensory nucleus of the trigeminal</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.481000</td>\n",
       "      <td>0.493000</td>\n",
       "      <td>0.974000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>Primary somatosensory area, trunk, layer 6a</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.117500</td>\n",
       "      <td>0.116375</td>\n",
       "      <td>0.233875</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>10</th>\n",
       "      <td>Superior colliculus, motor related, intermedia...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>1.074625</td>\n",
       "      <td>1.023250</td>\n",
       "      <td>2.097875</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>11</th>\n",
       "      <td>Interfascicular nucleus raphe</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.036125</td>\n",
       "      <td>0.047125</td>\n",
       "      <td>0.083250</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>12</th>\n",
       "      <td>Parataenial nucleus</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.133000</td>\n",
       "      <td>0.132125</td>\n",
       "      <td>0.265125</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>13</th>\n",
       "      <td>Superior colliculus, motor related, intermedia...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>1.054625</td>\n",
       "      <td>1.039000</td>\n",
       "      <td>2.093625</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>14</th>\n",
       "      <td>Induseum griseum</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.056000</td>\n",
       "      <td>0.081875</td>\n",
       "      <td>0.137875</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>15</th>\n",
       "      <td>Entorhinal area, lateral part, layer 2</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.909125</td>\n",
       "      <td>0.903625</td>\n",
       "      <td>1.812750</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>16</th>\n",
       "      <td>Anterior amygdalar area</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.278000</td>\n",
       "      <td>0.278250</td>\n",
       "      <td>0.556250</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>17</th>\n",
       "      <td>Superior colliculus, motor related, deep gray ...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.585875</td>\n",
       "      <td>0.575875</td>\n",
       "      <td>1.161750</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>18</th>\n",
       "      <td>Intergeniculate leaflet of the lateral genicul...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.038875</td>\n",
       "      <td>0.036125</td>\n",
       "      <td>0.075000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>19</th>\n",
       "      <td>Entorhinal area, lateral part, layer 6a</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.592250</td>\n",
       "      <td>0.592875</td>\n",
       "      <td>1.185125</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "                                       structure_name  left_cell_count  \\\n",
       "0                      Primary visual area, layer 2/3              5.0   \n",
       "1   Retrosplenial area, lateral agranular part, la...              1.0   \n",
       "2          Retrosplenial area, dorsal part, layer 2/3              2.0   \n",
       "3                posteromedial visual area, layer 2/3              1.0   \n",
       "4            Retrosplenial area, dorsal part, layer 1              0.0   \n",
       "5              Tuberomammillary nucleus, ventral part              0.0   \n",
       "6         Primary somatosensory area, mouth, layer 6b              0.0   \n",
       "7                                    internal capsule              0.0   \n",
       "8         Principal sensory nucleus of the trigeminal              0.0   \n",
       "9         Primary somatosensory area, trunk, layer 6a              0.0   \n",
       "10  Superior colliculus, motor related, intermedia...              0.0   \n",
       "11                      Interfascicular nucleus raphe              0.0   \n",
       "12                                Parataenial nucleus              0.0   \n",
       "13  Superior colliculus, motor related, intermedia...              0.0   \n",
       "14                                   Induseum griseum              0.0   \n",
       "15             Entorhinal area, lateral part, layer 2              0.0   \n",
       "16                            Anterior amygdalar area              0.0   \n",
       "17  Superior colliculus, motor related, deep gray ...              0.0   \n",
       "18  Intergeniculate leaflet of the lateral genicul...              0.0   \n",
       "19            Entorhinal area, lateral part, layer 6a              0.0   \n",
       "\n",
       "    right_cell_count  total_cells  left_volume_mm3  right_volume_mm3  \\\n",
       "0               12.0         17.0         1.117625          1.094000   \n",
       "1               11.0         12.0         0.366750          0.353875   \n",
       "2                4.0          6.0         0.515875          0.511125   \n",
       "3                5.0          6.0         0.160125          0.157875   \n",
       "4                5.0          5.0         0.432375          0.427250   \n",
       "5                0.0          0.0         0.064875          0.062000   \n",
       "6                0.0          0.0         0.059375          0.059625   \n",
       "7                0.0          0.0         1.207875          1.195125   \n",
       "8                0.0          0.0         0.481000          0.493000   \n",
       "9                0.0          0.0         0.117500          0.116375   \n",
       "10               0.0          0.0         1.074625          1.023250   \n",
       "11               0.0          0.0         0.036125          0.047125   \n",
       "12               0.0          0.0         0.133000          0.132125   \n",
       "13               0.0          0.0         1.054625          1.039000   \n",
       "14               0.0          0.0         0.056000          0.081875   \n",
       "15               0.0          0.0         0.909125          0.903625   \n",
       "16               0.0          0.0         0.278000          0.278250   \n",
       "17               0.0          0.0         0.585875          0.575875   \n",
       "18               0.0          0.0         0.038875          0.036125   \n",
       "19               0.0          0.0         0.592250          0.592875   \n",
       "\n",
       "    total_volume_mm3  left_cells_per_mm3  right_cells_per_mm3  \n",
       "0           2.211625            4.473773            10.968921  \n",
       "1           0.720625            2.726653            31.084422  \n",
       "2           1.027000            3.876908             7.825874  \n",
       "3           0.318000            6.245121            31.670625  \n",
       "4           0.859625            0.000000            11.702750  \n",
       "5           0.126875            0.000000             0.000000  \n",
       "6           0.119000            0.000000             0.000000  \n",
       "7           2.403000            0.000000             0.000000  \n",
       "8           0.974000            0.000000             0.000000  \n",
       "9           0.233875            0.000000             0.000000  \n",
       "10          2.097875            0.000000             0.000000  \n",
       "11          0.083250            0.000000             0.000000  \n",
       "12          0.265125            0.000000             0.000000  \n",
       "13          2.093625            0.000000             0.000000  \n",
       "14          0.137875            0.000000             0.000000  \n",
       "15          1.812750            0.000000             0.000000  \n",
       "16          0.556250            0.000000             0.000000  \n",
       "17          1.161750            0.000000             0.000000  \n",
       "18          0.075000            0.000000             0.000000  \n",
       "19          1.185125            0.000000             0.000000  "
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "tdTomato_df.head(20)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "id": "4306ef93",
   "metadata": {},
   "outputs": [
    {
     "ename": "NameError",
     "evalue": "name 'labled_cells_df' is not defined",
     "output_type": "error",
     "traceback": [
      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[0;31mNameError\u001b[0m                                 Traceback (most recent call last)",
      "\u001b[0;32m/var/folders/mc/qbcjsrl16h3gf6t6xvz8czzw0000gn/T/ipykernel_2919/1504546251.py\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0mlabled_cells_df\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
      "\u001b[0;31mNameError\u001b[0m: name 'labled_cells_df' is not defined"
     ]
    }
   ],
   "source": [
    "labled_cells_df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 27,
   "id": "a6226aac",
   "metadata": {},
   "outputs": [
    {
     "ename": "NameError",
     "evalue": "name 'summary_df' is not defined",
     "output_type": "error",
     "traceback": [
      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[0;31mNameError\u001b[0m                                 Traceback (most recent call last)",
      "\u001b[0;32m/var/folders/mc/qbcjsrl16h3gf6t6xvz8czzw0000gn/T/ipykernel_71449/1328616635.py\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0msummary_df\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
      "\u001b[0;31mNameError\u001b[0m: name 'summary_df' is not defined"
     ]
    }
   ],
   "source": [
    "summary_df"
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "id": "1580af3f",
   "metadata": {},
   "source": [
    "# Cellfinders inital outputs"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 28,
   "id": "e177468e",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
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       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>structure_name</th>\n",
       "      <th>left_cell_count</th>\n",
       "      <th>right_cell_count</th>\n",
       "      <th>total_cells</th>\n",
       "      <th>left_volume_mm3</th>\n",
       "      <th>right_volume_mm3</th>\n",
       "      <th>total_volume_mm3</th>\n",
       "      <th>left_cells_per_mm3</th>\n",
       "      <th>right_cells_per_mm3</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>Primary visual area, layer 5</td>\n",
       "      <td>2686.0</td>\n",
       "      <td>6761.0</td>\n",
       "      <td>9447.0</td>\n",
       "      <td>0.868750</td>\n",
       "      <td>0.855750</td>\n",
       "      <td>1.724500</td>\n",
       "      <td>3091.798561</td>\n",
       "      <td>7900.671925</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>Retrosplenial area, dorsal part, layer 5</td>\n",
       "      <td>1346.0</td>\n",
       "      <td>2328.0</td>\n",
       "      <td>3674.0</td>\n",
       "      <td>0.644750</td>\n",
       "      <td>0.626500</td>\n",
       "      <td>1.271250</td>\n",
       "      <td>2087.630865</td>\n",
       "      <td>3715.881883</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>Primary visual area, layer 4</td>\n",
       "      <td>647.0</td>\n",
       "      <td>2409.0</td>\n",
       "      <td>3056.0</td>\n",
       "      <td>0.567500</td>\n",
       "      <td>0.562875</td>\n",
       "      <td>1.130375</td>\n",
       "      <td>1140.088106</td>\n",
       "      <td>4279.813458</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>posteromedial visual area, layer 5</td>\n",
       "      <td>1122.0</td>\n",
       "      <td>1673.0</td>\n",
       "      <td>2795.0</td>\n",
       "      <td>0.159250</td>\n",
       "      <td>0.152125</td>\n",
       "      <td>0.311375</td>\n",
       "      <td>7045.525903</td>\n",
       "      <td>10997.534922</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>Retrosplenial area, lateral agranular part, la...</td>\n",
       "      <td>1002.0</td>\n",
       "      <td>1736.0</td>\n",
       "      <td>2738.0</td>\n",
       "      <td>0.400125</td>\n",
       "      <td>0.388375</td>\n",
       "      <td>0.788500</td>\n",
       "      <td>2504.217432</td>\n",
       "      <td>4469.906662</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>663</th>\n",
       "      <td>Interpeduncular nucleus, intermediate</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.016375</td>\n",
       "      <td>0.017250</td>\n",
       "      <td>0.033625</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>664</th>\n",
       "      <td>Interpeduncular nucleus, dorsomedial</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.008625</td>\n",
       "      <td>0.009375</td>\n",
       "      <td>0.018000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>665</th>\n",
       "      <td>Interpeduncular nucleus, dorsolateral</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.018000</td>\n",
       "      <td>0.019625</td>\n",
       "      <td>0.037625</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>666</th>\n",
       "      <td>Interpeduncular nucleus, rostrolateral</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.009000</td>\n",
       "      <td>0.011125</td>\n",
       "      <td>0.020125</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>667</th>\n",
       "      <td>Supraoculomotor periaqueductal gray</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.019500</td>\n",
       "      <td>0.018875</td>\n",
       "      <td>0.038375</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>668 rows × 9 columns</p>\n",
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      ],
      "text/plain": [
       "                                        structure_name  left_cell_count  \\\n",
       "0                         Primary visual area, layer 5           2686.0   \n",
       "1             Retrosplenial area, dorsal part, layer 5           1346.0   \n",
       "2                         Primary visual area, layer 4            647.0   \n",
       "3                   posteromedial visual area, layer 5           1122.0   \n",
       "4    Retrosplenial area, lateral agranular part, la...           1002.0   \n",
       "..                                                 ...              ...   \n",
       "663              Interpeduncular nucleus, intermediate              0.0   \n",
       "664               Interpeduncular nucleus, dorsomedial              0.0   \n",
       "665              Interpeduncular nucleus, dorsolateral              0.0   \n",
       "666             Interpeduncular nucleus, rostrolateral              0.0   \n",
       "667                Supraoculomotor periaqueductal gray              0.0   \n",
       "\n",
       "     right_cell_count  total_cells  left_volume_mm3  right_volume_mm3  \\\n",
       "0              6761.0       9447.0         0.868750          0.855750   \n",
       "1              2328.0       3674.0         0.644750          0.626500   \n",
       "2              2409.0       3056.0         0.567500          0.562875   \n",
       "3              1673.0       2795.0         0.159250          0.152125   \n",
       "4              1736.0       2738.0         0.400125          0.388375   \n",
       "..                ...          ...              ...               ...   \n",
       "663               0.0          0.0         0.016375          0.017250   \n",
       "664               0.0          0.0         0.008625          0.009375   \n",
       "665               0.0          0.0         0.018000          0.019625   \n",
       "666               0.0          0.0         0.009000          0.011125   \n",
       "667               0.0          0.0         0.019500          0.018875   \n",
       "\n",
       "     total_volume_mm3  left_cells_per_mm3  right_cells_per_mm3  \n",
       "0            1.724500         3091.798561          7900.671925  \n",
       "1            1.271250         2087.630865          3715.881883  \n",
       "2            1.130375         1140.088106          4279.813458  \n",
       "3            0.311375         7045.525903         10997.534922  \n",
       "4            0.788500         2504.217432          4469.906662  \n",
       "..                ...                 ...                  ...  \n",
       "663          0.033625            0.000000             0.000000  \n",
       "664          0.018000            0.000000             0.000000  \n",
       "665          0.037625            0.000000             0.000000  \n",
       "666          0.020125            0.000000             0.000000  \n",
       "667          0.038375            0.000000             0.000000  \n",
       "\n",
       "[668 rows x 9 columns]"
      ]
     },
     "execution_count": 28,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "gfp_df "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 49,
   "id": "2802aea2",
   "metadata": {},
   "outputs": [
    {
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       "      <th>Unnamed: 0</th>\n",
       "      <th>structure_name</th>\n",
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       "      <th>0</th>\n",
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       "      <td>6771.0</td>\n",
       "      <td>5166.0</td>\n",
       "      <td>50706</td>\n",
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       "      <th>1</th>\n",
       "      <td>1</td>\n",
       "      <td>Piriform area</td>\n",
       "      <td>5348.0</td>\n",
       "      <td>5904.0</td>\n",
       "      <td>1188</td>\n",
       "      <td>7.430750</td>\n",
       "      <td>7.541750</td>\n",
       "      <td>14.972500</td>\n",
       "      <td>719.712008</td>\n",
       "      <td>782.842179</td>\n",
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       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>2</td>\n",
       "      <td>Retrosplenial area, dorsal part, layer 1</td>\n",
       "      <td>2026.0</td>\n",
       "      <td>1420.0</td>\n",
       "      <td>16233</td>\n",
       "      <td>0.536000</td>\n",
       "      <td>0.553500</td>\n",
       "      <td>1.089500</td>\n",
       "      <td>3779.850746</td>\n",
       "      <td>2565.492322</td>\n",
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       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>3</td>\n",
       "      <td>Retrosplenial area, dorsal part, layer 2/3</td>\n",
       "      <td>1575.0</td>\n",
       "      <td>1281.0</td>\n",
       "      <td>9762</td>\n",
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       "      <td>1993.386501</td>\n",
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       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>4</td>\n",
       "      <td>Retrosplenial area, lateral agranular part, la...</td>\n",
       "      <td>1413.0</td>\n",
       "      <td>929.0</td>\n",
       "      <td>84720</td>\n",
       "      <td>0.333000</td>\n",
       "      <td>0.330250</td>\n",
       "      <td>0.663250</td>\n",
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       "    <tr>\n",
       "      <th>663</th>\n",
       "      <td>663</td>\n",
       "      <td>Interpeduncular nucleus, intermediate</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>25648</td>\n",
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       "      <td>0.000000</td>\n",
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       "      <th>664</th>\n",
       "      <td>664</td>\n",
       "      <td>Interpeduncular nucleus, dorsomedial</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>37459</td>\n",
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       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
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       "      <th>665</th>\n",
       "      <td>665</td>\n",
       "      <td>Interpeduncular nucleus, dorsolateral</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>56380</td>\n",
       "      <td>0.025250</td>\n",
       "      <td>0.025625</td>\n",
       "      <td>0.050875</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
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       "      <th>666</th>\n",
       "      <td>666</td>\n",
       "      <td>Interpeduncular nucleus, rostrolateral</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>88194</td>\n",
       "      <td>0.011250</td>\n",
       "      <td>0.012000</td>\n",
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       "      <td>0.000000</td>\n",
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       "      <th>667</th>\n",
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       "      <td>75532</td>\n",
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       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
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       "     Unnamed: 0                                     structure_name  \\\n",
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       "2             2           Retrosplenial area, dorsal part, layer 1   \n",
       "3             3         Retrosplenial area, dorsal part, layer 2/3   \n",
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       "..          ...                                                ...   \n",
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       "667         667                Supraoculomotor periaqueductal gray   \n",
       "\n",
       "     left_cell_count  right_cell_count  total_cells  left_volume_mm3  \\\n",
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       "1             5348.0            5904.0         1188         7.430750   \n",
       "2             2026.0            1420.0        16233         0.536000   \n",
       "3             1575.0            1281.0         9762         0.649250   \n",
       "4             1413.0             929.0        84720         0.333000   \n",
       "..               ...               ...          ...              ...   \n",
       "663              0.0               0.0        25648         0.025500   \n",
       "664              0.0               0.0        37459         0.013125   \n",
       "665              0.0               0.0        56380         0.025250   \n",
       "666              0.0               0.0        88194         0.011250   \n",
       "667              0.0               0.0        75532         0.028625   \n",
       "\n",
       "     right_volume_mm3  total_volume_mm3  left_cells_per_mm3  \\\n",
       "0            2.452250          4.941125         2720.506253   \n",
       "1            7.541750         14.972500          719.712008   \n",
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       "3            0.642625          1.291875         2425.876011   \n",
       "4            0.330250          0.663250         4243.243243   \n",
       "..                ...               ...                 ...   \n",
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       "2            2565.492322  \n",
       "3            1993.386501  \n",
       "4            2813.020439  \n",
       "..                   ...  \n",
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       "664             0.000000  \n",
       "665             0.000000  \n",
       "666             0.000000  \n",
       "667             0.000000  \n",
       "\n",
       "[668 rows x 10 columns]"
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     "execution_count": 49,
     "metadata": {},
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   "source": [
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   ]
  },
  {
   "cell_type": "code",
   "execution_count": 50,
   "id": "0066c268",
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "      <td>Olfactory tubercle</td>\n",
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       "      <th>1</th>\n",
       "      <td>Piriform area</td>\n",
       "      <td>5348.0</td>\n",
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       "      <td>11252.0</td>\n",
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       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>Retrosplenial area, dorsal part, layer 1</td>\n",
       "      <td>2026.0</td>\n",
       "      <td>1420.0</td>\n",
       "      <td>3446.0</td>\n",
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       "      <th>3</th>\n",
       "      <td>Retrosplenial area, dorsal part, layer 2/3</td>\n",
       "      <td>1575.0</td>\n",
       "      <td>1281.0</td>\n",
       "      <td>2856.0</td>\n",
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       "      <td>1.291875</td>\n",
       "      <td>2425.876011</td>\n",
       "      <td>1993.386501</td>\n",
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       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>Retrosplenial area, lateral agranular part, la...</td>\n",
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       "      <th>663</th>\n",
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       "      <th>664</th>\n",
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       "    </tr>\n",
       "    <tr>\n",
       "      <th>666</th>\n",
       "      <td>Interpeduncular nucleus, rostrolateral</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.011250</td>\n",
       "      <td>0.012000</td>\n",
       "      <td>0.023250</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>667</th>\n",
       "      <td>Supraoculomotor periaqueductal gray</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.028625</td>\n",
       "      <td>0.026125</td>\n",
       "      <td>0.054750</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>668 rows × 9 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                                        structure_name  left_cell_count  \\\n",
       "0                                   Olfactory tubercle           6771.0   \n",
       "1                                        Piriform area           5348.0   \n",
       "2             Retrosplenial area, dorsal part, layer 1           2026.0   \n",
       "3           Retrosplenial area, dorsal part, layer 2/3           1575.0   \n",
       "4    Retrosplenial area, lateral agranular part, la...           1413.0   \n",
       "..                                                 ...              ...   \n",
       "663              Interpeduncular nucleus, intermediate              0.0   \n",
       "664               Interpeduncular nucleus, dorsomedial              0.0   \n",
       "665              Interpeduncular nucleus, dorsolateral              0.0   \n",
       "666             Interpeduncular nucleus, rostrolateral              0.0   \n",
       "667                Supraoculomotor periaqueductal gray              0.0   \n",
       "\n",
       "     right_cell_count  total_cells  left_volume_mm3  right_volume_mm3  \\\n",
       "0              5166.0      11937.0         2.488875          2.452250   \n",
       "1              5904.0      11252.0         7.430750          7.541750   \n",
       "2              1420.0       3446.0         0.536000          0.553500   \n",
       "3              1281.0       2856.0         0.649250          0.642625   \n",
       "4               929.0       2342.0         0.333000          0.330250   \n",
       "..                ...          ...              ...               ...   \n",
       "663               0.0          0.0         0.025500          0.022750   \n",
       "664               0.0          0.0         0.013125          0.011875   \n",
       "665               0.0          0.0         0.025250          0.025625   \n",
       "666               0.0          0.0         0.011250          0.012000   \n",
       "667               0.0          0.0         0.028625          0.026125   \n",
       "\n",
       "     total_volume_mm3  left_cells_per_mm3  right_cells_per_mm3  \n",
       "0            4.941125         2720.506253          2106.636762  \n",
       "1           14.972500          719.712008           782.842179  \n",
       "2            1.089500         3779.850746          2565.492322  \n",
       "3            1.291875         2425.876011          1993.386501  \n",
       "4            0.663250         4243.243243          2813.020439  \n",
       "..                ...                 ...                  ...  \n",
       "663          0.048250            0.000000             0.000000  \n",
       "664          0.025000            0.000000             0.000000  \n",
       "665          0.050875            0.000000             0.000000  \n",
       "666          0.023250            0.000000             0.000000  \n",
       "667          0.054750            0.000000             0.000000  \n",
       "\n",
       "[668 rows x 9 columns]"
      ]
     },
     "execution_count": 50,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "summary_df_0"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "b82d4de5",
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "5c180a46",
   "metadata": {},
   "outputs": [],
   "source": []
  }
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