view_points_directory_files.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "1ce58901",
   "metadata": {},
   "outputs": [],
   "source": [
    "import pandas as pd\n",
    "import numpy as np\n",
    "import UpdateME \n",
    "from UpdateME import cellfinder_output_path\n",
    "import xml.etree.ElementTree as ET\n",
    "import pandas as pd"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "de87f7df",
   "metadata": {},
   "source": [
    "# UPDATE"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "id": "a75f1ef3",
   "metadata": {},
   "outputs": [],
   "source": [
    "\n",
    "cellfinder_output_path = '/Users/denmanlab/Desktop/Grant/cellfinder/LlifeCanvas/Denman_G21_antiGFP-tdTomato-Autofluorescence/cellfinder_output_gfp_Planes_400-450_032623'\n"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "6f4c9a04",
   "metadata": {},
   "source": [
    "# Cells.xml\n",
    "\n",
    "### cells.xml - Cell candidate positions in the coordinate space of the raw data"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "id": "d19bb89a",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "num rows with type 1: 1670\n",
      "num rows with type 2: 0\n"
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       "       Image_Filename Type MarkerX MarkerY MarkerZ\n",
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     "execution_count": 15,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# Parse the XML file\n",
    "\n",
    "# XML file from G21\n",
    "tree = ET.parse(cellfinder_output_path + \"/points/cells.xml\")\n",
    "\n",
    "# XML file from cellfinder training data\n",
    "# tree = ET.parse('C:/Users/denmanlab/serial2p/332/list2.xml')\n",
    "\n",
    "# Get the root element\n",
    "root = tree.getroot()\n",
    "\n",
    "# Get the Image_Filename\n",
    "image_filename = root.find('Image_Properties/Image_Filename').text\n",
    "\n",
    "# Create a list of dictionaries to store the data\n",
    "data = []\n",
    "for marker_type in root.findall('Marker_Data/Marker_Type'):\n",
    "    type_id = marker_type.find('Type').text\n",
    "    for marker in marker_type.findall('Marker'):\n",
    "        row = {'Image_Filename': image_filename,\n",
    "               'Type': type_id,\n",
    "               'MarkerX': marker.find('MarkerX').text,\n",
    "               'MarkerY': marker.find('MarkerY').text,\n",
    "               'MarkerZ': marker.find('MarkerZ').text}\n",
    "        data.append(row)\n",
    "\n",
    "# Create a pandas DataFrame from the data\n",
    "cells_df = pd.DataFrame(data, columns=['Image_Filename', 'Type', 'MarkerX', 'MarkerY', 'MarkerZ'])\n",
    "\n",
    "# Assuming your DataFrame is called \"df\"\n",
    "num_rows_with_type_1 = len(cells_df[cells_df['Type'] == '1'])\n",
    "print(\"num rows with type 1: \" + str(num_rows_with_type_1))\n",
    "\n",
    "# Assuming your DataFrame is called \"df\"\n",
    "num_rows_with_type_2 = len(cells_df[cells_df['Type'] == '2'])\n",
    "print(\"num rows with type 2: \" + str(num_rows_with_type_2))\n",
    "cells_df.to_csv(cellfinder_output_path+ '/points/csv/cells_df.csv', index=False)\n",
    "\n",
    "\n",
    "cells_df\n"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "2778a7ec",
   "metadata": {},
   "source": [
    "# Cell_classification.xml\n",
    "\n",
    "### cell_classification.xml - Same as cells.xml, but after classification (i.e. each cell candidate has a cell/no_cell label)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "id": "2f2d7354",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "num rows with type 1 / non-cells: 1393\n",
      "num rows with type 2 / cells: 278\n"
     ]
    },
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       "       Image_Filename Type MarkerX MarkerY MarkerZ\n",
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    }
   ],
   "source": [
    "\n",
    "# XML file from G21\n",
    "# tree = ET.parse('C:/Users/denmanlab/Desktop/Grant/cellfinder/LlifeCanvas/Denman_G21_antiGFP-tdTomato-Autofluorescence/cell_canidate_dection_testing/old/cellfinder_output_gfp_planes90_190_030323_29/points/cell_classification.xml')\n",
    "tree = ET.parse(cellfinder_output_path+\"/points/cell_classification.xml\")\n",
    "\n",
    "# Get the root element\n",
    "root = tree.getroot()\n",
    "\n",
    "# Get the Image_Filename\n",
    "image_filename = root.find('Image_Properties/Image_Filename').text\n",
    "\n",
    "# Get the Image_Filename\n",
    "image_filename = root.find('Image_Properties/Image_Filename').text\n",
    "\n",
    "# Create a list of dictionaries to store the data\n",
    "data = []\n",
    "for marker_type in root.findall('Marker_Data/Marker_Type'):\n",
    "    type_id = marker_type.find('Type').text\n",
    "    for marker in marker_type.findall('Marker'):\n",
    "        row = {'Image_Filename': image_filename,\n",
    "               'Type': type_id,\n",
    "               'MarkerX': marker.find('MarkerX').text,\n",
    "               'MarkerY': marker.find('MarkerY').text,\n",
    "               'MarkerZ': marker.find('MarkerZ').text}\n",
    "        data.append(row)\n",
    "\n",
    "# Create a pandas DataFrame from the data\n",
    "cellClassification_df = pd.DataFrame(data, columns=['Image_Filename', 'Type', 'MarkerX', 'MarkerY', 'MarkerZ'])\n",
    "\n",
    "# Assuming your DataFrame is called \"df\"\n",
    "num_rows_with_type_1 = len(cellClassification_df[cellClassification_df['Type'] == '1'])\n",
    "print(\"num rows with type 1 / non-cells: \" + str(num_rows_with_type_1))\n",
    "\n",
    "# Assuming your DataFrame is called \"df\"\n",
    "num_rows_with_type_2 = len(cellClassification_df[cellClassification_df['Type'] == '2'])\n",
    "print(\"num rows with type 2 / cells: \" + str(num_rows_with_type_2))\n",
    "cellClassification_df.sort_values(by='MarkerZ', inplace=True)\n",
    "\n",
    "cellClassification_df.to_csv(cellfinder_output_path+ '/points/csv/cellClassification_df.csv', index=False)\n",
    "\n",
    "cellClassification_df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "id": "4d605c23",
   "metadata": {},
   "outputs": [
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       "      <td>2</td>\n",
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       "      <td>1654</td>\n",
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       "      <th>64736</th>\n",
       "      <td>placeholder.tif</td>\n",
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       "      <th>64476</th>\n",
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       "      <td>4114</td>\n",
       "      <td>1043</td>\n",
       "      <td>1504</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>64737</th>\n",
       "      <td>placeholder.tif</td>\n",
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       "      <td>5064</td>\n",
       "      <td>1043</td>\n",
       "      <td>1667</td>\n",
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       "    <tr>\n",
       "      <th>64669</th>\n",
       "      <td>placeholder.tif</td>\n",
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       "      <td>1043</td>\n",
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       "      <td>1044</td>\n",
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       "      <td>placeholder.tif</td>\n",
       "      <td>2</td>\n",
       "      <td>3585</td>\n",
       "      <td>1046</td>\n",
       "      <td>1625</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "        Image_Filename Type MarkerX MarkerY  MarkerZ\n",
       "64904  placeholder.tif    2    4147    1000     1713\n",
       "65352  placeholder.tif    2    4779    1000     1824\n",
       "64826  placeholder.tif    2    4117    1002     1685\n",
       "64919  placeholder.tif    2    4149    1005     1718\n",
       "64953  placeholder.tif    2    4170    1011     1731\n",
       "65216  placeholder.tif    2    4850    1014     1800\n",
       "64849  placeholder.tif    2    4111    1015     1697\n",
       "64598  placeholder.tif    2    4129    1020     1580\n",
       "64898  placeholder.tif    2    4161    1020     1725\n",
       "64191  placeholder.tif    2    3298    1021     1310\n",
       "64137  placeholder.tif    2    4164    1022     1296\n",
       "64712  placeholder.tif    2    3602    1023     1644\n",
       "65447  placeholder.tif    2    4417    1026     1837\n",
       "64859  placeholder.tif    2    2605    1030     1714\n",
       "65264  placeholder.tif    2    4780    1032     1794\n",
       "64701  placeholder.tif    2    4121    1033     1634\n",
       "65452  placeholder.tif    2    4432    1033     1835\n",
       "64241  placeholder.tif    2    3243    1034     1343\n",
       "64992  placeholder.tif    2    5168    1035     1746\n",
       "65243  placeholder.tif    2    4790    1038     1790\n",
       "64662  placeholder.tif    2    3606    1038     1618\n",
       "64057  placeholder.tif    2    4241    1040     1266\n",
       "64730  placeholder.tif    2    4141    1041     1654\n",
       "64736  placeholder.tif    2    5063    1042     1667\n",
       "64476  placeholder.tif    2    4114    1043     1504\n",
       "64737  placeholder.tif    2    5064    1043     1667\n",
       "64669  placeholder.tif    2    4129    1043     1640\n",
       "64608  placeholder.tif    2    4127    1043     1596\n",
       "65233  placeholder.tif    2    4843    1044     1788\n",
       "64689  placeholder.tif    2    3585    1046     1625"
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# Create a new DataFrame that only contains rows with Type == 2 and sort by MarkerZ\n",
    "cellClassification_df_type2 = cellClassification_df[cellClassification_df['Type'] == '2']\n",
    "cellClassification_df_type2 = cellClassification_df_type2.astype({'MarkerZ': 'int32'}) # convert MarkerZ column to int\n",
    "cellClassification_df_type2 = cellClassification_df_type2.sort_values(by=['MarkerY'], ascending=True)\n",
    "\n",
    "# Write the DataFrame to a CSV file\n",
    "cellClassification_df_type2.to_csv(cellfinder_output_path+ '/points/csv/cellClassification_df_type2_markerY.csv', index=False)\n",
    "\n",
    "# Print the first 30 rows of the sorted DataFrame\n",
    "cellClassification_df_type2.head(30)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "5640db1c",
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "markdown",
   "id": "446ad22d",
   "metadata": {},
   "source": [
    "# Atlat.points"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "5a582d4c",
   "metadata": {},
   "outputs": [
    {
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       "      <th>6655</th>\n",
       "      <td>260</td>\n",
       "      <td>200</td>\n",
       "      <td>119</td>\n",
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       "  </tbody>\n",
       "</table>\n",
       "<p>6656 rows × 3 columns</p>\n",
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      ],
      "text/plain": [
       "        0    1    2\n",
       "0     183    5  139\n",
       "1     184    5  137\n",
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       "3     180   11   68\n",
       "4     243   23  117\n",
       "...   ...  ...  ...\n",
       "6651  269  202  125\n",
       "6652  254  206   -4\n",
       "6653  255  200   93\n",
       "6654  266  201  123\n",
       "6655  260  200  119\n",
       "\n",
       "[6656 rows x 3 columns]"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "atlas_points_path = cellfinder_output_path+'/points/atlas.points'\n",
    "atlas_points = pd.read_hdf(atlas_points_path)\n",
    "atlas_points.to_csv(cellfinder_output_path+ '/points/csv/atlas_points.csv', index=False)\n",
    "\n",
    "atlas_points"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "231ce1cd",
   "metadata": {},
   "source": [
    "# abc4d"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "id": "a355dcad",
   "metadata": {},
   "outputs": [
    {
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       "      <th>y</th>\n",
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       "      <td>6950.0</td>\n",
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       "      <td>6.0</td>\n",
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       "      <td>7200.0</td>\n",
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       "      <td>3250.0</td>\n",
       "      <td>6.0</td>\n",
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       "      <th>3814</th>\n",
       "      <td>7250.0</td>\n",
       "      <td>4750.0</td>\n",
       "      <td>8350.0</td>\n",
       "      <td>6.0</td>\n",
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       "      <td>6750.0</td>\n",
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       "      <td>6.0</td>\n",
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       "      <th>3593</th>\n",
       "      <td>6950.0</td>\n",
       "      <td>4450.0</td>\n",
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       "      <td>6.0</td>\n",
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       "      <th>4630</th>\n",
       "      <td>-600.0</td>\n",
       "      <td>5100.0</td>\n",
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       "      <th>3308</th>\n",
       "      <td>12700.0</td>\n",
       "      <td>5150.0</td>\n",
       "      <td>3900.0</td>\n",
       "      <td>589508451.0</td>\n",
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       "      <th>4624</th>\n",
       "      <td>-750.0</td>\n",
       "      <td>5050.0</td>\n",
       "      <td>3900.0</td>\n",
       "      <td>589508451.0</td>\n",
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       "    <tr>\n",
       "      <th>4659</th>\n",
       "      <td>-550.0</td>\n",
       "      <td>5200.0</td>\n",
       "      <td>3950.0</td>\n",
       "      <td>589508451.0</td>\n",
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       "    <tr>\n",
       "      <th>4620</th>\n",
       "      <td>-600.0</td>\n",
       "      <td>5100.0</td>\n",
       "      <td>3850.0</td>\n",
       "      <td>589508451.0</td>\n",
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       "  </tbody>\n",
       "</table>\n",
       "<p>5029 rows × 4 columns</p>\n",
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      ],
      "text/plain": [
       "            y       x       z        image\n",
       "3633   6950.0  4500.0  3200.0          6.0\n",
       "3661   7200.0  4650.0  3250.0          6.0\n",
       "3814   7250.0  4750.0  8350.0          6.0\n",
       "3572   6750.0  4250.0  3100.0          6.0\n",
       "3593   6950.0  4450.0  3150.0          6.0\n",
       "...       ...     ...     ...          ...\n",
       "4630   -600.0  5100.0  3900.0  589508451.0\n",
       "3308  12700.0  5150.0  3900.0  589508451.0\n",
       "4624   -750.0  5050.0  3900.0  589508451.0\n",
       "4659   -550.0  5200.0  3950.0  589508451.0\n",
       "4620   -600.0  5100.0  3850.0  589508451.0\n",
       "\n",
       "[5029 rows x 4 columns]"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# Path to cellfinder_output points.npy file\n",
    "cells_path = cellfinder_output_path + '/points/abc4d.npy'\n",
    "cells_path\n",
    "points = np.load(cells_path)\n",
    "df = pd.DataFrame(points, columns=['y', 'x', 'z','image'])\n",
    "df.sort_values(by='image', inplace=True)\n",
    "# df.to_csv('C:/Users/denmanlab/Desktop/cellfinder_gfp_wholebrain_030723_G21/points/points.csv', index=False)\n",
    "df.to_csv(cellfinder_output_path+'/points/csv/abc4d.csv', index=False)\n",
    "df\n",
    "\n"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "fa59bde7",
   "metadata": {},
   "source": [
    "# points"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 55,
   "id": "ac739eb5",
   "metadata": {},
   "outputs": [
    {
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       "      <td>10250.0</td>\n",
       "      <td>-100.0</td>\n",
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       "      <th>6591</th>\n",
       "      <td>13950.0</td>\n",
       "      <td>10250.0</td>\n",
       "      <td>5900.0</td>\n",
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       "      <th>6652</th>\n",
       "      <td>12700.0</td>\n",
       "      <td>10300.0</td>\n",
       "      <td>-200.0</td>\n",
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       "  </tbody>\n",
       "</table>\n",
       "<p>6656 rows × 3 columns</p>\n",
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       "440    3800.0   -800.0   9350.0\n",
       "29     8200.0     50.0   4550.0\n",
       "2035   3800.0     50.0  11050.0\n",
       "...       ...      ...      ...\n",
       "6602  13900.0  10200.0   5850.0\n",
       "6645  12700.0  10250.0   -150.0\n",
       "6646  12700.0  10250.0   -100.0\n",
       "6591  13950.0  10250.0   5900.0\n",
       "6652  12700.0  10300.0   -200.0\n",
       "\n",
       "[6656 rows x 3 columns]"
      ]
     },
     "execution_count": 55,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# Path to cellfinder_output points.npy file\n",
    "cells_path = cellfinder_output_path + '/points/points.npy'\n",
    "cells_path\n",
    "points = np.load(cells_path)\n",
    "df = pd.DataFrame(points, columns=['y', 'x', 'z',])\n",
    "df.sort_values(by='x', inplace=True)\n",
    "# df.to_csv('C:/Users/denmanlab/Desktop/cellfinder_gfp_wholebrain_030723_G21/points/points.csv', index=False)\n",
    "df.to_csv(cellfinder_output_path+'/points/csv/points.csv', index=False)\n",
    "df"
   ]
  },
  {
   "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": 31,
   "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": 32,
   "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/denmanlab/Desktop/cellfinder_output_gfp_planes001_400_030423_31/\n",
      "\n",
      "test000\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": 33,
   "id": "e71967c6",
   "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",
       "    }\n",
       "\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>Retrosplenial area, dorsal part, layer 5</td>\n",
       "      <td>47.0</td>\n",
       "      <td>164.0</td>\n",
       "      <td>211.0</td>\n",
       "      <td>0.644750</td>\n",
       "      <td>0.626500</td>\n",
       "      <td>1.271250</td>\n",
       "      <td>72.896472</td>\n",
       "      <td>261.771748</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</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>2</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>3</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>4</th>\n",
       "      <td>Retrosplenial area, ventral part, layer 5</td>\n",
       "      <td>25.0</td>\n",
       "      <td>90.0</td>\n",
       "      <td>115.0</td>\n",
       "      <td>0.890625</td>\n",
       "      <td>0.854000</td>\n",
       "      <td>1.744625</td>\n",
       "      <td>28.070175</td>\n",
       "      <td>105.386417</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</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>6</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>7</th>\n",
       "      <td>Retrosplenial area, ventral part, layer 2/3</td>\n",
       "      <td>9.0</td>\n",
       "      <td>88.0</td>\n",
       "      <td>97.0</td>\n",
       "      <td>0.551875</td>\n",
       "      <td>0.539750</td>\n",
       "      <td>1.091625</td>\n",
       "      <td>16.308041</td>\n",
       "      <td>163.038444</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8</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>9</th>\n",
       "      <td>Retrosplenial area, ventral part, layer 1</td>\n",
       "      <td>9.0</td>\n",
       "      <td>46.0</td>\n",
       "      <td>55.0</td>\n",
       "      <td>0.429625</td>\n",
       "      <td>0.537375</td>\n",
       "      <td>0.967000</td>\n",
       "      <td>20.948502</td>\n",
       "      <td>85.601303</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>10</th>\n",
       "      <td>posteromedial visual area, layer 2/3</td>\n",
       "      <td>10.0</td>\n",
       "      <td>37.0</td>\n",
       "      <td>47.0</td>\n",
       "      <td>0.160125</td>\n",
       "      <td>0.157875</td>\n",
       "      <td>0.318000</td>\n",
       "      <td>62.451210</td>\n",
       "      <td>234.362629</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>11</th>\n",
       "      <td>posteromedial visual area, layer 5</td>\n",
       "      <td>9.0</td>\n",
       "      <td>33.0</td>\n",
       "      <td>42.0</td>\n",
       "      <td>0.159250</td>\n",
       "      <td>0.152125</td>\n",
       "      <td>0.311375</td>\n",
       "      <td>56.514914</td>\n",
       "      <td>216.926869</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>12</th>\n",
       "      <td>Retrosplenial area, lateral agranular part, la...</td>\n",
       "      <td>7.0</td>\n",
       "      <td>32.0</td>\n",
       "      <td>39.0</td>\n",
       "      <td>0.264875</td>\n",
       "      <td>0.254125</td>\n",
       "      <td>0.519000</td>\n",
       "      <td>26.427560</td>\n",
       "      <td>125.922282</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>13</th>\n",
       "      <td>Retrosplenial area, dorsal part, layer 1</td>\n",
       "      <td>7.0</td>\n",
       "      <td>31.0</td>\n",
       "      <td>38.0</td>\n",
       "      <td>0.432375</td>\n",
       "      <td>0.427250</td>\n",
       "      <td>0.859625</td>\n",
       "      <td>16.189650</td>\n",
       "      <td>72.557051</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>14</th>\n",
       "      <td>Retrosplenial area, dorsal part, layer 6a</td>\n",
       "      <td>6.0</td>\n",
       "      <td>29.0</td>\n",
       "      <td>35.0</td>\n",
       "      <td>0.417750</td>\n",
       "      <td>0.384375</td>\n",
       "      <td>0.802125</td>\n",
       "      <td>14.362657</td>\n",
       "      <td>75.447154</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>15</th>\n",
       "      <td>Primary visual area, layer 1</td>\n",
       "      <td>4.0</td>\n",
       "      <td>29.0</td>\n",
       "      <td>33.0</td>\n",
       "      <td>0.684250</td>\n",
       "      <td>0.677750</td>\n",
       "      <td>1.362000</td>\n",
       "      <td>5.845817</td>\n",
       "      <td>42.788639</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>16</th>\n",
       "      <td>Lobules IV-V</td>\n",
       "      <td>12.0</td>\n",
       "      <td>13.0</td>\n",
       "      <td>25.0</td>\n",
       "      <td>3.019500</td>\n",
       "      <td>3.028000</td>\n",
       "      <td>6.047500</td>\n",
       "      <td>3.974168</td>\n",
       "      <td>4.293263</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>17</th>\n",
       "      <td>Simple lobule</td>\n",
       "      <td>16.0</td>\n",
       "      <td>8.0</td>\n",
       "      <td>24.0</td>\n",
       "      <td>2.704875</td>\n",
       "      <td>2.588375</td>\n",
       "      <td>5.293250</td>\n",
       "      <td>5.915246</td>\n",
       "      <td>3.090742</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>18</th>\n",
       "      <td>Primary visual area, layer 6a</td>\n",
       "      <td>1.0</td>\n",
       "      <td>23.0</td>\n",
       "      <td>24.0</td>\n",
       "      <td>0.604000</td>\n",
       "      <td>0.587750</td>\n",
       "      <td>1.191750</td>\n",
       "      <td>1.655629</td>\n",
       "      <td>39.132284</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>19</th>\n",
       "      <td>Area prostriata</td>\n",
       "      <td>2.0</td>\n",
       "      <td>21.0</td>\n",
       "      <td>23.0</td>\n",
       "      <td>0.179875</td>\n",
       "      <td>0.172875</td>\n",
       "      <td>0.352750</td>\n",
       "      <td>11.118833</td>\n",
       "      <td>121.475054</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>20</th>\n",
       "      <td>Postsubiculum</td>\n",
       "      <td>2.0</td>\n",
       "      <td>20.0</td>\n",
       "      <td>22.0</td>\n",
       "      <td>0.591375</td>\n",
       "      <td>0.564750</td>\n",
       "      <td>1.156125</td>\n",
       "      <td>3.381949</td>\n",
       "      <td>35.413900</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>21</th>\n",
       "      <td>posteromedial visual area, layer 1</td>\n",
       "      <td>0.0</td>\n",
       "      <td>21.0</td>\n",
       "      <td>21.0</td>\n",
       "      <td>0.104000</td>\n",
       "      <td>0.099625</td>\n",
       "      <td>0.203625</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>210.790464</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>22</th>\n",
       "      <td>Retrosplenial area, lateral agranular part, la...</td>\n",
       "      <td>4.0</td>\n",
       "      <td>15.0</td>\n",
       "      <td>19.0</td>\n",
       "      <td>0.215000</td>\n",
       "      <td>0.223125</td>\n",
       "      <td>0.438125</td>\n",
       "      <td>18.604651</td>\n",
       "      <td>67.226891</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>23</th>\n",
       "      <td>Crus 1</td>\n",
       "      <td>4.0</td>\n",
       "      <td>15.0</td>\n",
       "      <td>19.0</td>\n",
       "      <td>2.701750</td>\n",
       "      <td>2.576375</td>\n",
       "      <td>5.278125</td>\n",
       "      <td>1.480522</td>\n",
       "      <td>5.822134</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>24</th>\n",
       "      <td>Superior colliculus, motor related, intermedia...</td>\n",
       "      <td>7.0</td>\n",
       "      <td>11.0</td>\n",
       "      <td>18.0</td>\n",
       "      <td>1.074625</td>\n",
       "      <td>1.023250</td>\n",
       "      <td>2.097875</td>\n",
       "      <td>6.513900</td>\n",
       "      <td>10.750061</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>25</th>\n",
       "      <td>Superior colliculus, optic layer</td>\n",
       "      <td>6.0</td>\n",
       "      <td>11.0</td>\n",
       "      <td>17.0</td>\n",
       "      <td>0.335000</td>\n",
       "      <td>0.329250</td>\n",
       "      <td>0.664250</td>\n",
       "      <td>17.910448</td>\n",
       "      <td>33.409263</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>26</th>\n",
       "      <td>posteromedial visual area, layer 4</td>\n",
       "      <td>3.0</td>\n",
       "      <td>14.0</td>\n",
       "      <td>17.0</td>\n",
       "      <td>0.054250</td>\n",
       "      <td>0.052500</td>\n",
       "      <td>0.106750</td>\n",
       "      <td>55.299539</td>\n",
       "      <td>266.666667</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>27</th>\n",
       "      <td>Posterolateral visual area, layer 2/3</td>\n",
       "      <td>0.0</td>\n",
       "      <td>16.0</td>\n",
       "      <td>16.0</td>\n",
       "      <td>0.118125</td>\n",
       "      <td>0.117125</td>\n",
       "      <td>0.235250</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>136.606190</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>28</th>\n",
       "      <td>Primary somatosensory area, barrel field, layer 4</td>\n",
       "      <td>4.0</td>\n",
       "      <td>10.0</td>\n",
       "      <td>14.0</td>\n",
       "      <td>0.652625</td>\n",
       "      <td>0.631750</td>\n",
       "      <td>1.284375</td>\n",
       "      <td>6.129094</td>\n",
       "      <td>15.829046</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>29</th>\n",
       "      <td>Declive (VI)</td>\n",
       "      <td>8.0</td>\n",
       "      <td>6.0</td>\n",
       "      <td>14.0</td>\n",
       "      <td>1.438375</td>\n",
       "      <td>1.469250</td>\n",
       "      <td>2.907625</td>\n",
       "      <td>5.561832</td>\n",
       "      <td>4.083716</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>30</th>\n",
       "      <td>Primary somatosensory area, trunk, layer 2/3</td>\n",
       "      <td>3.0</td>\n",
       "      <td>11.0</td>\n",
       "      <td>14.0</td>\n",
       "      <td>0.212750</td>\n",
       "      <td>0.209500</td>\n",
       "      <td>0.422250</td>\n",
       "      <td>14.101058</td>\n",
       "      <td>52.505967</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>31</th>\n",
       "      <td>Field CA1</td>\n",
       "      <td>1.0</td>\n",
       "      <td>12.0</td>\n",
       "      <td>13.0</td>\n",
       "      <td>5.749625</td>\n",
       "      <td>5.587000</td>\n",
       "      <td>11.336625</td>\n",
       "      <td>0.173924</td>\n",
       "      <td>2.147843</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>32</th>\n",
       "      <td>Parasubiculum</td>\n",
       "      <td>0.0</td>\n",
       "      <td>13.0</td>\n",
       "      <td>13.0</td>\n",
       "      <td>0.484000</td>\n",
       "      <td>0.474875</td>\n",
       "      <td>0.958875</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>27.375625</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>33</th>\n",
       "      <td>Anterior area, layer 5</td>\n",
       "      <td>3.0</td>\n",
       "      <td>10.0</td>\n",
       "      <td>13.0</td>\n",
       "      <td>0.185750</td>\n",
       "      <td>0.180125</td>\n",
       "      <td>0.365875</td>\n",
       "      <td>16.150740</td>\n",
       "      <td>55.517002</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>34</th>\n",
       "      <td>Anterior area, layer 2/3</td>\n",
       "      <td>6.0</td>\n",
       "      <td>7.0</td>\n",
       "      <td>13.0</td>\n",
       "      <td>0.225000</td>\n",
       "      <td>0.211375</td>\n",
       "      <td>0.436375</td>\n",
       "      <td>26.666667</td>\n",
       "      <td>33.116499</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>35</th>\n",
       "      <td>Crus 2</td>\n",
       "      <td>3.0</td>\n",
       "      <td>10.0</td>\n",
       "      <td>13.0</td>\n",
       "      <td>2.357625</td>\n",
       "      <td>2.245625</td>\n",
       "      <td>4.603250</td>\n",
       "      <td>1.272467</td>\n",
       "      <td>4.453103</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>36</th>\n",
       "      <td>Superior colliculus, superficial gray layer</td>\n",
       "      <td>3.0</td>\n",
       "      <td>9.0</td>\n",
       "      <td>12.0</td>\n",
       "      <td>0.607125</td>\n",
       "      <td>0.586125</td>\n",
       "      <td>1.193250</td>\n",
       "      <td>4.941322</td>\n",
       "      <td>15.355086</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>37</th>\n",
       "      <td>Posterolateral visual area, layer 1</td>\n",
       "      <td>0.0</td>\n",
       "      <td>11.0</td>\n",
       "      <td>11.0</td>\n",
       "      <td>0.101375</td>\n",
       "      <td>0.102375</td>\n",
       "      <td>0.203750</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>107.448107</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>38</th>\n",
       "      <td>Primary somatosensory area, trunk, layer 4</td>\n",
       "      <td>1.0</td>\n",
       "      <td>10.0</td>\n",
       "      <td>11.0</td>\n",
       "      <td>0.076250</td>\n",
       "      <td>0.074000</td>\n",
       "      <td>0.150250</td>\n",
       "      <td>13.114754</td>\n",
       "      <td>135.135135</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>39</th>\n",
       "      <td>Primary somatosensory area, barrel field, layer 5</td>\n",
       "      <td>2.0</td>\n",
       "      <td>9.0</td>\n",
       "      <td>11.0</td>\n",
       "      <td>0.608500</td>\n",
       "      <td>0.604000</td>\n",
       "      <td>1.212500</td>\n",
       "      <td>3.286771</td>\n",
       "      <td>14.900662</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>40</th>\n",
       "      <td>Primary somatosensory area, trunk, layer 5</td>\n",
       "      <td>0.0</td>\n",
       "      <td>10.0</td>\n",
       "      <td>10.0</td>\n",
       "      <td>0.183875</td>\n",
       "      <td>0.173000</td>\n",
       "      <td>0.356875</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>57.803468</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>41</th>\n",
       "      <td>Posterolateral visual area, layer 5</td>\n",
       "      <td>0.0</td>\n",
       "      <td>10.0</td>\n",
       "      <td>10.0</td>\n",
       "      <td>0.130250</td>\n",
       "      <td>0.129375</td>\n",
       "      <td>0.259625</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>77.294686</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>42</th>\n",
       "      <td>Retrosplenial area, ventral part, layer 6a</td>\n",
       "      <td>3.0</td>\n",
       "      <td>7.0</td>\n",
       "      <td>10.0</td>\n",
       "      <td>0.360125</td>\n",
       "      <td>0.354500</td>\n",
       "      <td>0.714625</td>\n",
       "      <td>8.330441</td>\n",
       "      <td>19.746121</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>43</th>\n",
       "      <td>Primary somatosensory area, barrel field, laye...</td>\n",
       "      <td>2.0</td>\n",
       "      <td>8.0</td>\n",
       "      <td>10.0</td>\n",
       "      <td>0.759250</td>\n",
       "      <td>0.739375</td>\n",
       "      <td>1.498625</td>\n",
       "      <td>2.634178</td>\n",
       "      <td>10.819949</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>44</th>\n",
       "      <td>Primary somatosensory area, lower limb, layer 2/3</td>\n",
       "      <td>3.0</td>\n",
       "      <td>6.0</td>\n",
       "      <td>9.0</td>\n",
       "      <td>0.318625</td>\n",
       "      <td>0.314875</td>\n",
       "      <td>0.633500</td>\n",
       "      <td>9.415457</td>\n",
       "      <td>19.055181</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>45</th>\n",
       "      <td>Inferior colliculus, external nucleus</td>\n",
       "      <td>2.0</td>\n",
       "      <td>6.0</td>\n",
       "      <td>8.0</td>\n",
       "      <td>0.990375</td>\n",
       "      <td>0.954625</td>\n",
       "      <td>1.945000</td>\n",
       "      <td>2.019437</td>\n",
       "      <td>6.285191</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>46</th>\n",
       "      <td>Subiculum</td>\n",
       "      <td>1.0</td>\n",
       "      <td>7.0</td>\n",
       "      <td>8.0</td>\n",
       "      <td>1.170250</td>\n",
       "      <td>1.146875</td>\n",
       "      <td>2.317125</td>\n",
       "      <td>0.854518</td>\n",
       "      <td>6.103542</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>47</th>\n",
       "      <td>Anteromedial visual area, layer 5</td>\n",
       "      <td>0.0</td>\n",
       "      <td>8.0</td>\n",
       "      <td>8.0</td>\n",
       "      <td>0.118750</td>\n",
       "      <td>0.118250</td>\n",
       "      <td>0.237000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>67.653277</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>48</th>\n",
       "      <td>Anteromedial visual area, layer 2/3</td>\n",
       "      <td>2.0</td>\n",
       "      <td>5.0</td>\n",
       "      <td>7.0</td>\n",
       "      <td>0.110125</td>\n",
       "      <td>0.107375</td>\n",
       "      <td>0.217500</td>\n",
       "      <td>18.161180</td>\n",
       "      <td>46.565774</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>49</th>\n",
       "      <td>posteromedial visual area, layer 6a</td>\n",
       "      <td>0.0</td>\n",
       "      <td>7.0</td>\n",
       "      <td>7.0</td>\n",
       "      <td>0.086125</td>\n",
       "      <td>0.079000</td>\n",
       "      <td>0.165125</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>88.607595</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "                                       structure_name  left_cell_count  \\\n",
       "0            Retrosplenial area, dorsal part, layer 5             47.0   \n",
       "1          Retrosplenial area, dorsal part, layer 2/3             39.0   \n",
       "2                      Primary visual area, layer 2/3             32.0   \n",
       "3   Retrosplenial area, lateral agranular part, la...             21.0   \n",
       "4           Retrosplenial area, ventral part, layer 5             25.0   \n",
       "5   Retrosplenial area, lateral agranular part, la...             30.0   \n",
       "6                        Primary visual area, layer 5             23.0   \n",
       "7         Retrosplenial area, ventral part, layer 2/3              9.0   \n",
       "8                        Primary visual area, layer 4             17.0   \n",
       "9           Retrosplenial area, ventral part, layer 1              9.0   \n",
       "10               posteromedial visual area, layer 2/3             10.0   \n",
       "11                 posteromedial visual area, layer 5              9.0   \n",
       "12  Retrosplenial area, lateral agranular part, la...              7.0   \n",
       "13           Retrosplenial area, dorsal part, layer 1              7.0   \n",
       "14          Retrosplenial area, dorsal part, layer 6a              6.0   \n",
       "15                       Primary visual area, layer 1              4.0   \n",
       "16                                       Lobules IV-V             12.0   \n",
       "17                                      Simple lobule             16.0   \n",
       "18                      Primary visual area, layer 6a              1.0   \n",
       "19                                    Area prostriata              2.0   \n",
       "20                                      Postsubiculum              2.0   \n",
       "21                 posteromedial visual area, layer 1              0.0   \n",
       "22  Retrosplenial area, lateral agranular part, la...              4.0   \n",
       "23                                             Crus 1              4.0   \n",
       "24  Superior colliculus, motor related, intermedia...              7.0   \n",
       "25                   Superior colliculus, optic layer              6.0   \n",
       "26                 posteromedial visual area, layer 4              3.0   \n",
       "27              Posterolateral visual area, layer 2/3              0.0   \n",
       "28  Primary somatosensory area, barrel field, layer 4              4.0   \n",
       "29                                       Declive (VI)              8.0   \n",
       "30       Primary somatosensory area, trunk, layer 2/3              3.0   \n",
       "31                                          Field CA1              1.0   \n",
       "32                                      Parasubiculum              0.0   \n",
       "33                             Anterior area, layer 5              3.0   \n",
       "34                           Anterior area, layer 2/3              6.0   \n",
       "35                                             Crus 2              3.0   \n",
       "36        Superior colliculus, superficial gray layer              3.0   \n",
       "37                Posterolateral visual area, layer 1              0.0   \n",
       "38         Primary somatosensory area, trunk, layer 4              1.0   \n",
       "39  Primary somatosensory area, barrel field, layer 5              2.0   \n",
       "40         Primary somatosensory area, trunk, layer 5              0.0   \n",
       "41                Posterolateral visual area, layer 5              0.0   \n",
       "42         Retrosplenial area, ventral part, layer 6a              3.0   \n",
       "43  Primary somatosensory area, barrel field, laye...              2.0   \n",
       "44  Primary somatosensory area, lower limb, layer 2/3              3.0   \n",
       "45              Inferior colliculus, external nucleus              2.0   \n",
       "46                                          Subiculum              1.0   \n",
       "47                  Anteromedial visual area, layer 5              0.0   \n",
       "48                Anteromedial visual area, layer 2/3              2.0   \n",
       "49                posteromedial visual area, layer 6a              0.0   \n",
       "\n",
       "    right_cell_count  total_cells  left_volume_mm3  right_volume_mm3  \\\n",
       "0              164.0        211.0         0.644750          0.626500   \n",
       "1              148.0        187.0         0.515875          0.511125   \n",
       "2              124.0        156.0         1.117625          1.094000   \n",
       "3              104.0        125.0         0.366750          0.353875   \n",
       "4               90.0        115.0         0.890625          0.854000   \n",
       "5               84.0        114.0         0.400125          0.388375   \n",
       "6               86.0        109.0         0.868750          0.855750   \n",
       "7               88.0         97.0         0.551875          0.539750   \n",
       "8               63.0         80.0         0.567500          0.562875   \n",
       "9               46.0         55.0         0.429625          0.537375   \n",
       "10              37.0         47.0         0.160125          0.157875   \n",
       "11              33.0         42.0         0.159250          0.152125   \n",
       "12              32.0         39.0         0.264875          0.254125   \n",
       "13              31.0         38.0         0.432375          0.427250   \n",
       "14              29.0         35.0         0.417750          0.384375   \n",
       "15              29.0         33.0         0.684250          0.677750   \n",
       "16              13.0         25.0         3.019500          3.028000   \n",
       "17               8.0         24.0         2.704875          2.588375   \n",
       "18              23.0         24.0         0.604000          0.587750   \n",
       "19              21.0         23.0         0.179875          0.172875   \n",
       "20              20.0         22.0         0.591375          0.564750   \n",
       "21              21.0         21.0         0.104000          0.099625   \n",
       "22              15.0         19.0         0.215000          0.223125   \n",
       "23              15.0         19.0         2.701750          2.576375   \n",
       "24              11.0         18.0         1.074625          1.023250   \n",
       "25              11.0         17.0         0.335000          0.329250   \n",
       "26              14.0         17.0         0.054250          0.052500   \n",
       "27              16.0         16.0         0.118125          0.117125   \n",
       "28              10.0         14.0         0.652625          0.631750   \n",
       "29               6.0         14.0         1.438375          1.469250   \n",
       "30              11.0         14.0         0.212750          0.209500   \n",
       "31              12.0         13.0         5.749625          5.587000   \n",
       "32              13.0         13.0         0.484000          0.474875   \n",
       "33              10.0         13.0         0.185750          0.180125   \n",
       "34               7.0         13.0         0.225000          0.211375   \n",
       "35              10.0         13.0         2.357625          2.245625   \n",
       "36               9.0         12.0         0.607125          0.586125   \n",
       "37              11.0         11.0         0.101375          0.102375   \n",
       "38              10.0         11.0         0.076250          0.074000   \n",
       "39               9.0         11.0         0.608500          0.604000   \n",
       "40              10.0         10.0         0.183875          0.173000   \n",
       "41              10.0         10.0         0.130250          0.129375   \n",
       "42               7.0         10.0         0.360125          0.354500   \n",
       "43               8.0         10.0         0.759250          0.739375   \n",
       "44               6.0          9.0         0.318625          0.314875   \n",
       "45               6.0          8.0         0.990375          0.954625   \n",
       "46               7.0          8.0         1.170250          1.146875   \n",
       "47               8.0          8.0         0.118750          0.118250   \n",
       "48               5.0          7.0         0.110125          0.107375   \n",
       "49               7.0          7.0         0.086125          0.079000   \n",
       "\n",
       "    total_volume_mm3  left_cells_per_mm3  right_cells_per_mm3  \n",
       "0           1.271250           72.896472           261.771748  \n",
       "1           1.027000           75.599709           289.557349  \n",
       "2           2.211625           28.632144           113.345521  \n",
       "3           0.720625           57.259714           293.889085  \n",
       "4           1.744625           28.070175           105.386417  \n",
       "5           0.788500           74.976570           216.285806  \n",
       "6           1.724500           26.474820           100.496640  \n",
       "7           1.091625           16.308041           163.038444  \n",
       "8           1.130375           29.955947           111.925383  \n",
       "9           0.967000           20.948502            85.601303  \n",
       "10          0.318000           62.451210           234.362629  \n",
       "11          0.311375           56.514914           216.926869  \n",
       "12          0.519000           26.427560           125.922282  \n",
       "13          0.859625           16.189650            72.557051  \n",
       "14          0.802125           14.362657            75.447154  \n",
       "15          1.362000            5.845817            42.788639  \n",
       "16          6.047500            3.974168             4.293263  \n",
       "17          5.293250            5.915246             3.090742  \n",
       "18          1.191750            1.655629            39.132284  \n",
       "19          0.352750           11.118833           121.475054  \n",
       "20          1.156125            3.381949            35.413900  \n",
       "21          0.203625            0.000000           210.790464  \n",
       "22          0.438125           18.604651            67.226891  \n",
       "23          5.278125            1.480522             5.822134  \n",
       "24          2.097875            6.513900            10.750061  \n",
       "25          0.664250           17.910448            33.409263  \n",
       "26          0.106750           55.299539           266.666667  \n",
       "27          0.235250            0.000000           136.606190  \n",
       "28          1.284375            6.129094            15.829046  \n",
       "29          2.907625            5.561832             4.083716  \n",
       "30          0.422250           14.101058            52.505967  \n",
       "31         11.336625            0.173924             2.147843  \n",
       "32          0.958875            0.000000            27.375625  \n",
       "33          0.365875           16.150740            55.517002  \n",
       "34          0.436375           26.666667            33.116499  \n",
       "35          4.603250            1.272467             4.453103  \n",
       "36          1.193250            4.941322            15.355086  \n",
       "37          0.203750            0.000000           107.448107  \n",
       "38          0.150250           13.114754           135.135135  \n",
       "39          1.212500            3.286771            14.900662  \n",
       "40          0.356875            0.000000            57.803468  \n",
       "41          0.259625            0.000000            77.294686  \n",
       "42          0.714625            8.330441            19.746121  \n",
       "43          1.498625            2.634178            10.819949  \n",
       "44          0.633500            9.415457            19.055181  \n",
       "45          1.945000            2.019437             6.285191  \n",
       "46          2.317125            0.854518             6.103542  \n",
       "47          0.237000            0.000000            67.653277  \n",
       "48          0.217500           18.161180            46.565774  \n",
       "49          0.165125            0.000000            88.607595  "
      ]
     },
     "execution_count": 33,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "gfp_df.head(50)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 34,
   "id": "a4148f38",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "<style scoped>\n",
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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>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": 34,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "tdTomato_df.head(20)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 35,
   "id": "4306ef93",
   "metadata": {},
   "outputs": [
    {
     "ename": "NameError",
     "evalue": "name 'labled_cells_df' is not defined",
     "output_type": "error",
     "traceback": [
      "\u001b[1;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[1;31mNameError\u001b[0m                                 Traceback (most recent call last)",
      "\u001b[1;32m~\\AppData\\Local\\Temp\\ipykernel_2740\\1504546251.py\u001b[0m in \u001b[0;36m<module>\u001b[1;34m\u001b[0m\n\u001b[1;32m----> 1\u001b[1;33m \u001b[0mlabled_cells_df\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m",
      "\u001b[1;31mNameError\u001b[0m: name 'labled_cells_df' is not defined"
     ]
    }
   ],
   "source": [
    "labled_cells_df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 36,
   "id": "a6226aac",
   "metadata": {},
   "outputs": [
    {
     "ename": "NameError",
     "evalue": "name 'summary_df' is not defined",
     "output_type": "error",
     "traceback": [
      "\u001b[1;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[1;31mNameError\u001b[0m                                 Traceback (most recent call last)",
      "\u001b[1;32m~\\AppData\\Local\\Temp\\ipykernel_2740\\1328616635.py\u001b[0m in \u001b[0;36m<module>\u001b[1;34m\u001b[0m\n\u001b[1;32m----> 1\u001b[1;33m \u001b[0msummary_df\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m",
      "\u001b[1;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": 23,
   "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",
       "    }\n",
       "\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>Retrosplenial area, dorsal part, layer 5</td>\n",
       "      <td>47.0</td>\n",
       "      <td>164.0</td>\n",
       "      <td>211.0</td>\n",
       "      <td>0.644750</td>\n",
       "      <td>0.626500</td>\n",
       "      <td>1.271250</td>\n",
       "      <td>72.896472</td>\n",
       "      <td>261.771748</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</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>2</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>3</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>4</th>\n",
       "      <td>Retrosplenial area, ventral part, layer 5</td>\n",
       "      <td>25.0</td>\n",
       "      <td>90.0</td>\n",
       "      <td>115.0</td>\n",
       "      <td>0.890625</td>\n",
       "      <td>0.854000</td>\n",
       "      <td>1.744625</td>\n",
       "      <td>28.070175</td>\n",
       "      <td>105.386417</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",
       "</div>"
      ],
      "text/plain": [
       "                                        structure_name  left_cell_count  \\\n",
       "0             Retrosplenial area, dorsal part, layer 5             47.0   \n",
       "1           Retrosplenial area, dorsal part, layer 2/3             39.0   \n",
       "2                       Primary visual area, layer 2/3             32.0   \n",
       "3    Retrosplenial area, lateral agranular part, la...             21.0   \n",
       "4            Retrosplenial area, ventral part, layer 5             25.0   \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               164.0        211.0         0.644750          0.626500   \n",
       "1               148.0        187.0         0.515875          0.511125   \n",
       "2               124.0        156.0         1.117625          1.094000   \n",
       "3               104.0        125.0         0.366750          0.353875   \n",
       "4                90.0        115.0         0.890625          0.854000   \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            1.271250           72.896472           261.771748  \n",
       "1            1.027000           75.599709           289.557349  \n",
       "2            2.211625           28.632144           113.345521  \n",
       "3            0.720625           57.259714           293.889085  \n",
       "4            1.744625           28.070175           105.386417  \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": 23,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "gfp_df "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 24,
   "id": "2802aea2",
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "  <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",
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       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>Retrosplenial area, dorsal part, layer 5</td>\n",
       "      <td>47.0</td>\n",
       "      <td>164.0</td>\n",
       "      <td>211.0</td>\n",
       "      <td>0.644750</td>\n",
       "      <td>0.626500</td>\n",
       "      <td>1.271250</td>\n",
       "      <td>72.896472</td>\n",
       "      <td>261.771748</td>\n",
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       "    <tr>\n",
       "      <th>1</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>2</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>3</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>4</th>\n",
       "      <td>Retrosplenial area, ventral part, layer 5</td>\n",
       "      <td>25.0</td>\n",
       "      <td>90.0</td>\n",
       "      <td>115.0</td>\n",
       "      <td>0.890625</td>\n",
       "      <td>0.854000</td>\n",
       "      <td>1.744625</td>\n",
       "      <td>28.070175</td>\n",
       "      <td>105.386417</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",
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      ],
      "text/plain": [
       "                                        structure_name  left_cell_count  \\\n",
       "0             Retrosplenial area, dorsal part, layer 5             47.0   \n",
       "1           Retrosplenial area, dorsal part, layer 2/3             39.0   \n",
       "2                       Primary visual area, layer 2/3             32.0   \n",
       "3    Retrosplenial area, lateral agranular part, la...             21.0   \n",
       "4            Retrosplenial area, ventral part, layer 5             25.0   \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               164.0        211.0         0.644750          0.626500   \n",
       "1               148.0        187.0         0.515875          0.511125   \n",
       "2               124.0        156.0         1.117625          1.094000   \n",
       "3               104.0        125.0         0.366750          0.353875   \n",
       "4                90.0        115.0         0.890625          0.854000   \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            1.271250           72.896472           261.771748  \n",
       "1            1.027000           75.599709           289.557349  \n",
       "2            2.211625           28.632144           113.345521  \n",
       "3            0.720625           57.259714           293.889085  \n",
       "4            1.744625           28.070175           105.386417  \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": 24,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "tdTomato_df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 25,
   "id": "0066c268",
   "metadata": {},
   "outputs": [
    {
     "ename": "NameError",
     "evalue": "name 'summary_df_0' is not defined",
     "output_type": "error",
     "traceback": [
      "\u001b[1;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[1;31mNameError\u001b[0m                                 Traceback (most recent call last)",
      "\u001b[1;32m~\\AppData\\Local\\Temp\\ipykernel_2740\\3934315072.py\u001b[0m in \u001b[0;36m<module>\u001b[1;34m\u001b[0m\n\u001b[1;32m----> 1\u001b[1;33m \u001b[0msummary_df_0\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m",
      "\u001b[1;31mNameError\u001b[0m: name 'summary_df_0' is not defined"
     ]
    }
   ],
   "source": [
    "summary_df_0"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "b82d4de5",
   "metadata": {},
   "outputs": [],
   "source": []
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  {
   "cell_type": "code",
   "execution_count": null,
   "id": "5c180a46",
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   "outputs": [],
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