vtk_nuclei_visualizer_with_vasculature.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "fa10355e",
   "metadata": {},
   "outputs": [],
   "source": [
    "import pandas as pd\n",
    "import numpy as np\n",
    "import os"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "c54d77b4",
   "metadata": {},
   "outputs": [],
   "source": [
    "from meshparty import trimesh_io, trimesh_vtk, skeleton, utils"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "cb04bb66",
   "metadata": {},
   "outputs": [],
   "source": [
    "import vtk"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "4e3edf25",
   "metadata": {},
   "outputs": [],
   "source": [
    "pd.set_option('display.max_columns', None)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "id": "d34dcc0b",
   "metadata": {},
   "outputs": [],
   "source": [
    "# setup the mesh meta to handle downloads and caching for cell bodies\n",
    "mesh_dir = 'data/neuron_meshes_v185/' # or change to your desired folder\n",
    "seg_source = \"precomputed://https://storage.googleapis.com/microns_public_datasets/pinky100_v185/seg\"\n",
    "mm = trimesh_io.MeshMeta(cv_path=seg_source,\n",
    "                         disk_cache_path=mesh_dir, \n",
    "                         cache_size=20)\n",
    "\n",
    "# setup the mesh meta to handle downloads and caching for mitochondria\n",
    "mito_mesh_dir = 'data/meshes/'\n",
    "mito_source = \"precomputed://https://td.princeton.edu/sseung-archive/pinky100-mito/seg_191220\"\n",
    "mito_mm = trimesh_io.MeshMeta(cv_path=mito_source,\n",
    "                         disk_cache_path=mito_mesh_dir)\n",
    "\n",
    "# setup the mesh meta to handle downloads and caching for nuclei\n",
    "nuc_mesh_dir = 'data/nuclei_meshes/'\n",
    "nuc_source = \"precomputed://https://td.princeton.edu/sseung-archive/pinky100-nuclei/seg\"\n",
    "nuc_mm = trimesh_io.MeshMeta(cv_path=nuc_source,\n",
    "                         disk_cache_path=nuc_mesh_dir)\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "0dc4641e",
   "metadata": {
    "scrolled": true
   },
   "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>id</th>\n",
       "      <th>cell_type</th>\n",
       "      <th>pt_position</th>\n",
       "      <th>pt_root_id</th>\n",
       "      <th>soma_x_nm</th>\n",
       "      <th>soma_y_nm</th>\n",
       "      <th>soma_z_nm</th>\n",
       "      <th>nuc_id</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>17</td>\n",
       "      <td>e</td>\n",
       "      <td>[103860  44385    891]</td>\n",
       "      <td>648518346349540057</td>\n",
       "      <td>415440</td>\n",
       "      <td>177540</td>\n",
       "      <td>35640</td>\n",
       "      <td>4809</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>453</td>\n",
       "      <td>e</td>\n",
       "      <td>[84054 50604  1424]</td>\n",
       "      <td>648518346349538466</td>\n",
       "      <td>336216</td>\n",
       "      <td>202416</td>\n",
       "      <td>56960</td>\n",
       "      <td>6097</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>35</td>\n",
       "      <td>e</td>\n",
       "      <td>[103728  54333    304]</td>\n",
       "      <td>648518346349538711</td>\n",
       "      <td>414912</td>\n",
       "      <td>217332</td>\n",
       "      <td>12160</td>\n",
       "      <td>6582</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>74</td>\n",
       "      <td>e</td>\n",
       "      <td>[51543 57568   155]</td>\n",
       "      <td>648518346349538715</td>\n",
       "      <td>206172</td>\n",
       "      <td>230272</td>\n",
       "      <td>6200</td>\n",
       "      <td>7498</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>231</td>\n",
       "      <td>e</td>\n",
       "      <td>[77197 61773   428]</td>\n",
       "      <td>648518346349537038</td>\n",
       "      <td>308788</td>\n",
       "      <td>247092</td>\n",
       "      <td>17120</td>\n",
       "      <td>8610</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",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>451</th>\n",
       "      <td>298</td>\n",
       "      <td>e</td>\n",
       "      <td>[116314  58234    933]</td>\n",
       "      <td>648518346349537961</td>\n",
       "      <td>465256</td>\n",
       "      <td>232936</td>\n",
       "      <td>37320</td>\n",
       "      <td>7570</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>452</th>\n",
       "      <td>444</td>\n",
       "      <td>e</td>\n",
       "      <td>[70253 54531  1752]</td>\n",
       "      <td>648518346349538336</td>\n",
       "      <td>281012</td>\n",
       "      <td>218124</td>\n",
       "      <td>70080</td>\n",
       "      <td>6877</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>453</th>\n",
       "      <td>69</td>\n",
       "      <td>e</td>\n",
       "      <td>[75256 56402   571]</td>\n",
       "      <td>648518346349537509</td>\n",
       "      <td>301024</td>\n",
       "      <td>225608</td>\n",
       "      <td>22840</td>\n",
       "      <td>7525</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>454</th>\n",
       "      <td>116</td>\n",
       "      <td>e</td>\n",
       "      <td>[77180 55980   185]</td>\n",
       "      <td>648518346349537641</td>\n",
       "      <td>308720</td>\n",
       "      <td>223920</td>\n",
       "      <td>7400</td>\n",
       "      <td>6557</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>455</th>\n",
       "      <td>13</td>\n",
       "      <td>e</td>\n",
       "      <td>[67633 56398  1056]</td>\n",
       "      <td>648518346349537516</td>\n",
       "      <td>270532</td>\n",
       "      <td>225592</td>\n",
       "      <td>42240</td>\n",
       "      <td>7514</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>456 rows × 8 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "      id cell_type             pt_position          pt_root_id  soma_x_nm  \\\n",
       "0     17         e  [103860  44385    891]  648518346349540057     415440   \n",
       "1    453         e     [84054 50604  1424]  648518346349538466     336216   \n",
       "2     35         e  [103728  54333    304]  648518346349538711     414912   \n",
       "3     74         e     [51543 57568   155]  648518346349538715     206172   \n",
       "4    231         e     [77197 61773   428]  648518346349537038     308788   \n",
       "..   ...       ...                     ...                 ...        ...   \n",
       "451  298         e  [116314  58234    933]  648518346349537961     465256   \n",
       "452  444         e     [70253 54531  1752]  648518346349538336     281012   \n",
       "453   69         e     [75256 56402   571]  648518346349537509     301024   \n",
       "454  116         e     [77180 55980   185]  648518346349537641     308720   \n",
       "455   13         e     [67633 56398  1056]  648518346349537516     270532   \n",
       "\n",
       "     soma_y_nm  soma_z_nm  nuc_id  \n",
       "0       177540      35640    4809  \n",
       "1       202416      56960    6097  \n",
       "2       217332      12160    6582  \n",
       "3       230272       6200    7498  \n",
       "4       247092      17120    8610  \n",
       "..         ...        ...     ...  \n",
       "451     232936      37320    7570  \n",
       "452     218124      70080    6877  \n",
       "453     225608      22840    7525  \n",
       "454     223920       7400    6557  \n",
       "455     225592      42240    7514  \n",
       "\n",
       "[456 rows x 8 columns]"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "nuc = pd.read_csv(\"data/230106_soma_valence_v185.csv\", index_col=[0])\n",
    "nuc"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "id": "362bd759",
   "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>id</th>\n",
       "      <th>cell_type</th>\n",
       "      <th>pt_position</th>\n",
       "      <th>pt_root_id</th>\n",
       "      <th>soma_x_nm</th>\n",
       "      <th>soma_y_nm</th>\n",
       "      <th>soma_z_nm</th>\n",
       "      <th>nuc_id</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>86</th>\n",
       "      <td>196</td>\n",
       "      <td>e</td>\n",
       "      <td>[62316 63307  2085]</td>\n",
       "      <td>648518346349539390</td>\n",
       "      <td>249264</td>\n",
       "      <td>253228</td>\n",
       "      <td>83400</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>172</th>\n",
       "      <td>315</td>\n",
       "      <td>e</td>\n",
       "      <td>[100322  38374   2074]</td>\n",
       "      <td>648518346349493874</td>\n",
       "      <td>401288</td>\n",
       "      <td>153496</td>\n",
       "      <td>82960</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>196</th>\n",
       "      <td>346</td>\n",
       "      <td>i</td>\n",
       "      <td>[70079 48099   356]</td>\n",
       "      <td>648518346349515985</td>\n",
       "      <td>280316</td>\n",
       "      <td>192396</td>\n",
       "      <td>14240</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>299</th>\n",
       "      <td>288</td>\n",
       "      <td>e</td>\n",
       "      <td>[52102 44781  1091]</td>\n",
       "      <td>648518346349523667</td>\n",
       "      <td>208408</td>\n",
       "      <td>179124</td>\n",
       "      <td>43640</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>356</th>\n",
       "      <td>362</td>\n",
       "      <td>i</td>\n",
       "      <td>[99769 54014  2156]</td>\n",
       "      <td>648518346349522740</td>\n",
       "      <td>399076</td>\n",
       "      <td>216056</td>\n",
       "      <td>86240</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>427</th>\n",
       "      <td>262</td>\n",
       "      <td>e</td>\n",
       "      <td>[110245  59258     92]</td>\n",
       "      <td>648518346349536391</td>\n",
       "      <td>440980</td>\n",
       "      <td>237032</td>\n",
       "      <td>3680</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "      id cell_type             pt_position          pt_root_id  soma_x_nm  \\\n",
       "86   196         e     [62316 63307  2085]  648518346349539390     249264   \n",
       "172  315         e  [100322  38374   2074]  648518346349493874     401288   \n",
       "196  346         i     [70079 48099   356]  648518346349515985     280316   \n",
       "299  288         e     [52102 44781  1091]  648518346349523667     208408   \n",
       "356  362         i     [99769 54014  2156]  648518346349522740     399076   \n",
       "427  262         e  [110245  59258     92]  648518346349536391     440980   \n",
       "\n",
       "     soma_y_nm  soma_z_nm  nuc_id  \n",
       "86      253228      83400       0  \n",
       "172     153496      82960       0  \n",
       "196     192396      14240       0  \n",
       "299     179124      43640       0  \n",
       "356     216056      86240       0  \n",
       "427     237032       3680       0  "
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "zeroes = nuc[nuc['nuc_id'] == 0]\n",
    "zeroes"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "id": "90f7cd94",
   "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>id</th>\n",
       "      <th>cell_type</th>\n",
       "      <th>pt_position</th>\n",
       "      <th>pt_root_id</th>\n",
       "      <th>soma_x_nm</th>\n",
       "      <th>soma_y_nm</th>\n",
       "      <th>soma_z_nm</th>\n",
       "      <th>nuc_id</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>17</td>\n",
       "      <td>e</td>\n",
       "      <td>[103860  44385    891]</td>\n",
       "      <td>648518346349540057</td>\n",
       "      <td>415440</td>\n",
       "      <td>177540</td>\n",
       "      <td>35640</td>\n",
       "      <td>4809</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>453</td>\n",
       "      <td>e</td>\n",
       "      <td>[84054 50604  1424]</td>\n",
       "      <td>648518346349538466</td>\n",
       "      <td>336216</td>\n",
       "      <td>202416</td>\n",
       "      <td>56960</td>\n",
       "      <td>6097</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>35</td>\n",
       "      <td>e</td>\n",
       "      <td>[103728  54333    304]</td>\n",
       "      <td>648518346349538711</td>\n",
       "      <td>414912</td>\n",
       "      <td>217332</td>\n",
       "      <td>12160</td>\n",
       "      <td>6582</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>74</td>\n",
       "      <td>e</td>\n",
       "      <td>[51543 57568   155]</td>\n",
       "      <td>648518346349538715</td>\n",
       "      <td>206172</td>\n",
       "      <td>230272</td>\n",
       "      <td>6200</td>\n",
       "      <td>7498</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>231</td>\n",
       "      <td>e</td>\n",
       "      <td>[77197 61773   428]</td>\n",
       "      <td>648518346349537038</td>\n",
       "      <td>308788</td>\n",
       "      <td>247092</td>\n",
       "      <td>17120</td>\n",
       "      <td>8610</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",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>451</th>\n",
       "      <td>298</td>\n",
       "      <td>e</td>\n",
       "      <td>[116314  58234    933]</td>\n",
       "      <td>648518346349537961</td>\n",
       "      <td>465256</td>\n",
       "      <td>232936</td>\n",
       "      <td>37320</td>\n",
       "      <td>7570</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>452</th>\n",
       "      <td>444</td>\n",
       "      <td>e</td>\n",
       "      <td>[70253 54531  1752]</td>\n",
       "      <td>648518346349538336</td>\n",
       "      <td>281012</td>\n",
       "      <td>218124</td>\n",
       "      <td>70080</td>\n",
       "      <td>6877</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>453</th>\n",
       "      <td>69</td>\n",
       "      <td>e</td>\n",
       "      <td>[75256 56402   571]</td>\n",
       "      <td>648518346349537509</td>\n",
       "      <td>301024</td>\n",
       "      <td>225608</td>\n",
       "      <td>22840</td>\n",
       "      <td>7525</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>454</th>\n",
       "      <td>116</td>\n",
       "      <td>e</td>\n",
       "      <td>[77180 55980   185]</td>\n",
       "      <td>648518346349537641</td>\n",
       "      <td>308720</td>\n",
       "      <td>223920</td>\n",
       "      <td>7400</td>\n",
       "      <td>6557</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>455</th>\n",
       "      <td>13</td>\n",
       "      <td>e</td>\n",
       "      <td>[67633 56398  1056]</td>\n",
       "      <td>648518346349537516</td>\n",
       "      <td>270532</td>\n",
       "      <td>225592</td>\n",
       "      <td>42240</td>\n",
       "      <td>7514</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>450 rows × 8 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "      id cell_type             pt_position          pt_root_id  soma_x_nm  \\\n",
       "0     17         e  [103860  44385    891]  648518346349540057     415440   \n",
       "1    453         e     [84054 50604  1424]  648518346349538466     336216   \n",
       "2     35         e  [103728  54333    304]  648518346349538711     414912   \n",
       "3     74         e     [51543 57568   155]  648518346349538715     206172   \n",
       "4    231         e     [77197 61773   428]  648518346349537038     308788   \n",
       "..   ...       ...                     ...                 ...        ...   \n",
       "451  298         e  [116314  58234    933]  648518346349537961     465256   \n",
       "452  444         e     [70253 54531  1752]  648518346349538336     281012   \n",
       "453   69         e     [75256 56402   571]  648518346349537509     301024   \n",
       "454  116         e     [77180 55980   185]  648518346349537641     308720   \n",
       "455   13         e     [67633 56398  1056]  648518346349537516     270532   \n",
       "\n",
       "     soma_y_nm  soma_z_nm  nuc_id  \n",
       "0       177540      35640    4809  \n",
       "1       202416      56960    6097  \n",
       "2       217332      12160    6582  \n",
       "3       230272       6200    7498  \n",
       "4       247092      17120    8610  \n",
       "..         ...        ...     ...  \n",
       "451     232936      37320    7570  \n",
       "452     218124      70080    6877  \n",
       "453     225608      22840    7525  \n",
       "454     223920       7400    6557  \n",
       "455     225592      42240    7514  \n",
       "\n",
       "[450 rows x 8 columns]"
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "nuc_removezeroes = nuc[nuc['nuc_id'] != 0]\n",
    "nuc_removezeroes"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "id": "bcc67ecd",
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "e            358\n",
       "g             59\n",
       "i             32\n",
       "uncertain      1\n",
       "Name: cell_type, dtype: int64"
      ]
     },
     "execution_count": 9,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "nuc_removezeroes.cell_type.value_counts()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "id": "0ef08513",
   "metadata": {},
   "outputs": [],
   "source": [
    "nuc_all_list = nuc_removezeroes.nuc_id.to_list()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "id": "0b682fb2",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "450"
      ]
     },
     "execution_count": 11,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "len(nuc_all_list)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "id": "96476e40",
   "metadata": {},
   "outputs": [],
   "source": [
    "nuc_all_list.sort()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "id": "5d805b24",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "[123,\n",
       " 375,\n",
       " 642,\n",
       " 1318,\n",
       " 1889,\n",
       " 1890,\n",
       " 1892,\n",
       " 1911,\n",
       " 1914,\n",
       " 2256,\n",
       " 2730,\n",
       " 3118,\n",
       " 3181,\n",
       " 3511,\n",
       " 3531,\n",
       " 3536,\n",
       " 3539,\n",
       " 3540,\n",
       " 3541,\n",
       " 3542,\n",
       " 3543,\n",
       " 3545,\n",
       " 3546,\n",
       " 3550,\n",
       " 3551,\n",
       " 3554,\n",
       " 3564,\n",
       " 3567,\n",
       " 3575,\n",
       " 3670,\n",
       " 3673,\n",
       " 3798,\n",
       " 3854,\n",
       " 4029,\n",
       " 4306,\n",
       " 4308,\n",
       " 4309,\n",
       " 4310,\n",
       " 4312,\n",
       " 4313,\n",
       " 4316,\n",
       " 4317,\n",
       " 4330,\n",
       " 4332,\n",
       " 4333,\n",
       " 4335,\n",
       " 4336,\n",
       " 4337,\n",
       " 4338,\n",
       " 4339,\n",
       " 4340,\n",
       " 4341,\n",
       " 4342,\n",
       " 4344,\n",
       " 4349,\n",
       " 4351,\n",
       " 4369,\n",
       " 4378,\n",
       " 4381,\n",
       " 4597,\n",
       " 4624,\n",
       " 4762,\n",
       " 4763,\n",
       " 4764,\n",
       " 4766,\n",
       " 4768,\n",
       " 4769,\n",
       " 4774,\n",
       " 4775,\n",
       " 4778,\n",
       " 4782,\n",
       " 4784,\n",
       " 4786,\n",
       " 4793,\n",
       " 4794,\n",
       " 4795,\n",
       " 4796,\n",
       " 4797,\n",
       " 4799,\n",
       " 4801,\n",
       " 4802,\n",
       " 4804,\n",
       " 4805,\n",
       " 4808,\n",
       " 4809,\n",
       " 4810,\n",
       " 4811,\n",
       " 4812,\n",
       " 4813,\n",
       " 4815,\n",
       " 4820,\n",
       " 4887,\n",
       " 5080,\n",
       " 5081,\n",
       " 5084,\n",
       " 5085,\n",
       " 5086,\n",
       " 5088,\n",
       " 5092,\n",
       " 5093,\n",
       " 5116,\n",
       " 5121,\n",
       " 5123,\n",
       " 5125,\n",
       " 5126,\n",
       " 5128,\n",
       " 5130,\n",
       " 5131,\n",
       " 5132,\n",
       " 5134,\n",
       " 5135,\n",
       " 5136,\n",
       " 5137,\n",
       " 5143,\n",
       " 5145,\n",
       " 5146,\n",
       " 5156,\n",
       " 5158,\n",
       " 5160,\n",
       " 5161,\n",
       " 5162,\n",
       " 5327,\n",
       " 5441,\n",
       " 5626,\n",
       " 5629,\n",
       " 5631,\n",
       " 5637,\n",
       " 5639,\n",
       " 5640,\n",
       " 5642,\n",
       " 5643,\n",
       " 5648,\n",
       " 5649,\n",
       " 5650,\n",
       " 5651,\n",
       " 5652,\n",
       " 5660,\n",
       " 5672,\n",
       " 5680,\n",
       " 5682,\n",
       " 5684,\n",
       " 5689,\n",
       " 5692,\n",
       " 5702,\n",
       " 5704,\n",
       " 5705,\n",
       " 5708,\n",
       " 5709,\n",
       " 5711,\n",
       " 5712,\n",
       " 5714,\n",
       " 5718,\n",
       " 5719,\n",
       " 5720,\n",
       " 5729,\n",
       " 6048,\n",
       " 6062,\n",
       " 6066,\n",
       " 6074,\n",
       " 6082,\n",
       " 6083,\n",
       " 6084,\n",
       " 6088,\n",
       " 6090,\n",
       " 6096,\n",
       " 6097,\n",
       " 6099,\n",
       " 6120,\n",
       " 6121,\n",
       " 6124,\n",
       " 6125,\n",
       " 6130,\n",
       " 6131,\n",
       " 6132,\n",
       " 6146,\n",
       " 6147,\n",
       " 6151,\n",
       " 6152,\n",
       " 6154,\n",
       " 6155,\n",
       " 6411,\n",
       " 6537,\n",
       " 6542,\n",
       " 6545,\n",
       " 6551,\n",
       " 6553,\n",
       " 6554,\n",
       " 6556,\n",
       " 6557,\n",
       " 6558,\n",
       " 6559,\n",
       " 6560,\n",
       " 6565,\n",
       " 6580,\n",
       " 6581,\n",
       " 6582,\n",
       " 6588,\n",
       " 6589,\n",
       " 6591,\n",
       " 6592,\n",
       " 6593,\n",
       " 6709,\n",
       " 6857,\n",
       " 6862,\n",
       " 6864,\n",
       " 6866,\n",
       " 6867,\n",
       " 6868,\n",
       " 6871,\n",
       " 6873,\n",
       " 6875,\n",
       " 6877,\n",
       " 6880,\n",
       " 6881,\n",
       " 6882,\n",
       " 6902,\n",
       " 6908,\n",
       " 6909,\n",
       " 6911,\n",
       " 6917,\n",
       " 6919,\n",
       " 6923,\n",
       " 6928,\n",
       " 6934,\n",
       " 6958,\n",
       " 7496,\n",
       " 7498,\n",
       " 7506,\n",
       " 7508,\n",
       " 7510,\n",
       " 7511,\n",
       " 7512,\n",
       " 7513,\n",
       " 7514,\n",
       " 7515,\n",
       " 7517,\n",
       " 7518,\n",
       " 7523,\n",
       " 7524,\n",
       " 7525,\n",
       " 7528,\n",
       " 7529,\n",
       " 7533,\n",
       " 7538,\n",
       " 7539,\n",
       " 7540,\n",
       " 7541,\n",
       " 7542,\n",
       " 7543,\n",
       " 7544,\n",
       " 7549,\n",
       " 7553,\n",
       " 7554,\n",
       " 7557,\n",
       " 7559,\n",
       " 7564,\n",
       " 7566,\n",
       " 7570,\n",
       " 7669,\n",
       " 7937,\n",
       " 7951,\n",
       " 7955,\n",
       " 7974,\n",
       " 7981,\n",
       " 7983,\n",
       " 7986,\n",
       " 7987,\n",
       " 7989,\n",
       " 7999,\n",
       " 8013,\n",
       " 8016,\n",
       " 8017,\n",
       " 8018,\n",
       " 8579,\n",
       " 8583,\n",
       " 8589,\n",
       " 8596,\n",
       " 8598,\n",
       " 8600,\n",
       " 8601,\n",
       " 8602,\n",
       " 8603,\n",
       " 8604,\n",
       " 8610,\n",
       " 8616,\n",
       " 8617,\n",
       " 8618,\n",
       " 8619,\n",
       " 8621,\n",
       " 8622,\n",
       " 8623,\n",
       " 8627,\n",
       " 8636,\n",
       " 8642,\n",
       " 8656,\n",
       " 8657,\n",
       " 8658,\n",
       " 8659,\n",
       " 8668,\n",
       " 9028,\n",
       " 9035,\n",
       " 9047,\n",
       " 9049,\n",
       " 9050,\n",
       " 9056,\n",
       " 9062,\n",
       " 9077,\n",
       " 9079,\n",
       " 9080,\n",
       " 9110,\n",
       " 9118,\n",
       " 9120,\n",
       " 9122,\n",
       " 9129,\n",
       " 9137,\n",
       " 9141,\n",
       " 9142,\n",
       " 9144,\n",
       " 9145,\n",
       " 9146,\n",
       " 9149,\n",
       " 9150,\n",
       " 9151,\n",
       " 9152,\n",
       " 9153,\n",
       " 9154,\n",
       " 9161,\n",
       " 9574,\n",
       " 9655,\n",
       " 9659,\n",
       " 9662,\n",
       " 9664,\n",
       " 9670,\n",
       " 9671,\n",
       " 9672,\n",
       " 9673,\n",
       " 9675,\n",
       " 9676,\n",
       " 9679,\n",
       " 9680,\n",
       " 9681,\n",
       " 9689,\n",
       " 9691,\n",
       " 9696,\n",
       " 9703,\n",
       " 9705,\n",
       " 9706,\n",
       " 9707,\n",
       " 9710,\n",
       " 9712,\n",
       " 9713,\n",
       " 9715,\n",
       " 9716,\n",
       " 9719,\n",
       " 9720,\n",
       " 10113,\n",
       " 10124,\n",
       " 10126,\n",
       " 10132,\n",
       " 10135,\n",
       " 10136,\n",
       " 10143,\n",
       " 10147,\n",
       " 10148,\n",
       " 10149,\n",
       " 10150,\n",
       " 10151,\n",
       " 10167,\n",
       " 10169,\n",
       " 10176,\n",
       " 10177,\n",
       " 10181,\n",
       " 10183,\n",
       " 10202,\n",
       " 10969,\n",
       " 11008,\n",
       " 11015,\n",
       " 11042,\n",
       " 11048,\n",
       " 11051,\n",
       " 11054,\n",
       " 11055,\n",
       " 11059,\n",
       " 11061,\n",
       " 11064,\n",
       " 11075,\n",
       " 11076,\n",
       " 11077,\n",
       " 11079,\n",
       " 11080,\n",
       " 11082,\n",
       " 11083,\n",
       " 11084,\n",
       " 11765,\n",
       " 11780,\n",
       " 11782,\n",
       " 11787,\n",
       " 11788,\n",
       " 11792,\n",
       " 11799,\n",
       " 11804,\n",
       " 11828,\n",
       " 11831,\n",
       " 11832,\n",
       " 11834,\n",
       " 11836,\n",
       " 11839,\n",
       " 11841,\n",
       " 11842,\n",
       " 11843,\n",
       " 11845,\n",
       " 11847,\n",
       " 11851,\n",
       " 11856,\n",
       " 11857,\n",
       " 11859,\n",
       " 12724,\n",
       " 12784,\n",
       " 12805,\n",
       " 12810,\n",
       " 12849,\n",
       " 12882,\n",
       " 12883,\n",
       " 12892,\n",
       " 12893,\n",
       " 12894,\n",
       " 12900,\n",
       " 12905,\n",
       " 12907,\n",
       " 12921,\n",
       " 12950,\n",
       " 12955,\n",
       " 12962,\n",
       " 13776,\n",
       " 13829,\n",
       " 13900,\n",
       " 13907,\n",
       " 13913,\n",
       " 13935,\n",
       " 13941,\n",
       " 13951,\n",
       " 13952,\n",
       " 13959,\n",
       " 13961,\n",
       " 13963,\n",
       " 13968,\n",
       " 15557,\n",
       " 15575,\n",
       " 15592,\n",
       " 15593]"
      ]
     },
     "execution_count": 13,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "nuc_all_list"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "id": "e626a9cf",
   "metadata": {},
   "outputs": [],
   "source": [
    "# download nuclei meshes to local drive as specified above\n",
    "\n",
    "for i in range(len(nuc_all_list)):\n",
    "    nuc_seg_id = nuc_all_list[i]\n",
    "    nuc_downloadmesh = nuc_mm.mesh(seg_id = nuc_seg_id, remove_duplicate_vertices=True)\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "id": "e70c6092",
   "metadata": {},
   "outputs": [],
   "source": [
    "# manual download for cells not in the soma table\n",
    "# nuc_id not in soma table: 7986,7987\n",
    "\n",
    "manual_nucid = 7986\n",
    "nuc_downloadmesh = nuc_mm.mesh(seg_id = manual_nucid, remove_duplicate_vertices=True)\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "id": "81493e1e",
   "metadata": {},
   "outputs": [],
   "source": [
    "# iterate the nuc_mesh for each nuclei in list\n",
    "# from https://python-forum.io/thread-23500.html\n",
    "\n",
    "nuc_iterator = {}\n",
    "for i in range(len(nuc_all_list)):\n",
    "    nuc_seg_id = nuc_all_list[i] \n",
    "    nuc_mesh_file = os.path.join(nuc_mesh_dir, str(nuc_seg_id)+'.h5')\n",
    "    nuc_iterator['nuc_mesh_' + str(i)] = nuc_mm.mesh(filename = nuc_mesh_file)\n",
    "    \n",
    "locals().update(nuc_iterator)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "id": "173d8541",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "setting up renderer\n",
      "done setting up\n",
      "actors added\n",
      "camera set\n",
      "render done\n",
      "finalizing..\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "<vtkmodules.vtkRenderingOpenGL2.vtkOpenGLRenderer(0x000001B2613A0860) at 0x000001B23BEB4B88>"
      ]
     },
     "execution_count": 17,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# opacity and color settings for nuclei meshes\n",
    "cell_opac = 0.025 # 0.075\n",
    "cell_color = (0.7, 0.7, 0.7) # (0.2, 0.4, 0.7) blue\n",
    "nuc_opac = 0.40 # 0.35\n",
    "\n",
    "# cell membrane mesh\n",
    "#mesh_actor = trimesh_vtk.mesh_actor(mesh, opacity=cell_opac, color=cell_color)\n",
    "\n",
    "# mito meshes\n",
    "#actor_iterator = {}\n",
    "#for i in range(len(mito_query_mitolist)):\n",
    "#    random_color = list(np.random.random(size=3))\n",
    "#    actor_iterator['mito_mesh_actor_' + str(i)] = trimesh_vtk.mesh_actor(var_iterator['mito_mesh_'+str(i)], opacity=mito_opac, color=(random_color))\n",
    "    \n",
    "#locals().update(actor_iterator)\n",
    "\n",
    "# nuclei meshes\n",
    "nuc_actor_iterator = {}\n",
    "for i in range(len(nuc_all_list)):\n",
    "    random_color = list(np.random.random(size=3))\n",
    "    nuc_actor_iterator['nuc_mesh_actor_' + str(i)] = trimesh_vtk.mesh_actor(nuc_iterator['nuc_mesh_'+str(i)], opacity=nuc_opac, color=(random_color))\n",
    "    \n",
    "locals().update(nuc_actor_iterator)\n",
    "\n",
    "\n",
    "# update dictionary for the render actors code below\n",
    "#actor_iterator['mesh_actor'] = mesh_actor\n",
    "\n",
    "#creating a camera object and defining the view\n",
    "camera = trimesh_vtk.oriented_camera((nuc_mesh_165.centroid), backoff=500) # this nuclei is near the center of the volume\n",
    "\n",
    "#render the actors, will open a pop up python window\n",
    "trimesh_vtk.render_actors(nuc_actor_iterator.values(), camera=camera)\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "id": "09032c91",
   "metadata": {},
   "outputs": [],
   "source": [
    "# color by cell type (e,i,g)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "id": "829c8568",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "358"
      ]
     },
     "execution_count": 19,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "exc = nuc_removezeroes[nuc_removezeroes['cell_type'] == 'e']\n",
    "exc_list = exc.nuc_id.to_list()\n",
    "len(exc_list)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "id": "ed41b7dc",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "32"
      ]
     },
     "execution_count": 20,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "inh = nuc_removezeroes[nuc_removezeroes['cell_type'] == 'i']\n",
    "inh_list = inh.nuc_id.to_list()\n",
    "len(inh_list)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "id": "797590ca",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "59"
      ]
     },
     "execution_count": 21,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "glia = nuc_removezeroes[nuc_removezeroes['cell_type'] == 'g']\n",
    "glia_list = glia.nuc_id.to_list()\n",
    "len(glia_list)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 22,
   "id": "0a28b837",
   "metadata": {},
   "outputs": [],
   "source": [
    "# iterate the nuc_mesh for each nuclei in list by cell type\n",
    "# from https://python-forum.io/thread-23500.html\n",
    "\n",
    "exc_iterator = {}\n",
    "for i in range(len(exc_list)):\n",
    "    nuc_seg_id = exc_list[i] \n",
    "    nuc_mesh_file = os.path.join(nuc_mesh_dir, str(nuc_seg_id)+'.h5')\n",
    "    exc_iterator['exc_mesh_' + str(i)] = nuc_mm.mesh(filename = nuc_mesh_file)\n",
    "\n",
    "locals().update(exc_iterator)\n",
    "\n",
    "inh_iterator = {}\n",
    "for i in range(len(inh_list)):\n",
    "    nuc_seg_id = inh_list[i] \n",
    "    nuc_mesh_file = os.path.join(nuc_mesh_dir, str(nuc_seg_id)+'.h5')\n",
    "    inh_iterator['inh_mesh_' + str(i)] = nuc_mm.mesh(filename = nuc_mesh_file)\n",
    "\n",
    "locals().update(inh_iterator)\n",
    "\n",
    "glia_iterator = {}\n",
    "for i in range(len(glia_list)):\n",
    "    nuc_seg_id = glia_list[i] \n",
    "    nuc_mesh_file = os.path.join(nuc_mesh_dir, str(nuc_seg_id)+'.h5')\n",
    "    glia_iterator['glia_mesh_' + str(i)] = nuc_mm.mesh(filename = nuc_mesh_file)\n",
    "\n",
    "locals().update(glia_iterator)\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 23,
   "id": "a575b50d",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "setting up renderer\n",
      "done setting up\n",
      "actors added\n",
      "camera set\n",
      "render done\n",
      "finalizing..\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "<vtkmodules.vtkRenderingOpenGL2.vtkOpenGLRenderer(0x000001B28F859720) at 0x000001B239CAEA08>"
      ]
     },
     "execution_count": 23,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# opacity and color settings for nuclei meshes\n",
    "exc_opac = 0.10 # 0.075\n",
    "exc_color = (0.2, 0.4, 0.7) # (0.2, 0.4, 0.7) blue\n",
    "inh_opac = 0.10 # 0.35\n",
    "inh_color = (0.7, 0.4, 0.2)\n",
    "glia_opac = 0.75\n",
    "glia_color = (0.7, 0.7, 0.2)\n",
    "\n",
    "# exc meshes\n",
    "exc_actor_iterator = {}\n",
    "for i in range(len(exc_list)):\n",
    "    #random_color = list(np.random.random(size=3))\n",
    "    exc_actor_iterator['exc_mesh_actor_' + str(i)] = trimesh_vtk.mesh_actor(exc_iterator['exc_mesh_'+str(i)], opacity=exc_opac, color=exc_color)\n",
    "    \n",
    "locals().update(exc_actor_iterator)\n",
    "\n",
    "# inh meshes\n",
    "inh_actor_iterator = {}\n",
    "for i in range(len(inh_list)):\n",
    "    #random_color = list(np.random.random(size=3))\n",
    "    inh_actor_iterator['inh_mesh_actor_' + str(i)] = trimesh_vtk.mesh_actor(inh_iterator['inh_mesh_'+str(i)], opacity=inh_opac, color=inh_color)\n",
    "    \n",
    "locals().update(inh_actor_iterator)\n",
    "\n",
    "# glia meshes\n",
    "glia_actor_iterator = {}\n",
    "for i in range(len(glia_list)):\n",
    "    #random_color = list(np.random.random(size=3))\n",
    "    glia_actor_iterator['glia_mesh_actor_' + str(i)] = trimesh_vtk.mesh_actor(glia_iterator['glia_mesh_'+str(i)], opacity=glia_opac, color=glia_color)\n",
    "    \n",
    "locals().update(glia_actor_iterator)\n",
    "\n",
    "\n",
    "# update dictionary for the render actors code below\n",
    "actor_iterator = {}\n",
    "actor_iterator.update(exc_actor_iterator)\n",
    "actor_iterator.update(inh_actor_iterator)\n",
    "actor_iterator.update(glia_actor_iterator)\n",
    "locals().update(actor_iterator)\n",
    "\n",
    "#creating a camera object and defining the view\n",
    "camera = trimesh_vtk.oriented_camera((nuc_mesh_165.centroid), backoff=500) # this nuclei is near the center of the volume\n",
    "\n",
    "#render the actors, will open a pop up python window\n",
    "trimesh_vtk.render_actors(actor_iterator.values(), camera=camera)\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 24,
   "id": "6646e155",
   "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>centroid_x</th>\n",
       "      <th>centroid_y</th>\n",
       "      <th>centroid_z</th>\n",
       "      <th>cell_segid</th>\n",
       "      <th>cell_type</th>\n",
       "      <th>cell_subtype</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>41760</td>\n",
       "      <td>60256</td>\n",
       "      <td>1702</td>\n",
       "      <td>648518346349538237</td>\n",
       "      <td>pyramidal</td>\n",
       "      <td>pyramidal cell</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>98128</td>\n",
       "      <td>39856</td>\n",
       "      <td>218</td>\n",
       "      <td>648518346349536816</td>\n",
       "      <td>pyramidal</td>\n",
       "      <td>pyramidal cell</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>51248</td>\n",
       "      <td>50608</td>\n",
       "      <td>86</td>\n",
       "      <td>648518346349539797</td>\n",
       "      <td>pyramidal</td>\n",
       "      <td>pyramidal cell</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>115392</td>\n",
       "      <td>47136</td>\n",
       "      <td>617</td>\n",
       "      <td>648518346349536744</td>\n",
       "      <td>pyramidal</td>\n",
       "      <td>pyramidal cell</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>104928</td>\n",
       "      <td>72496</td>\n",
       "      <td>1448</td>\n",
       "      <td>648518346349536851</td>\n",
       "      <td>pyramidal</td>\n",
       "      <td>pyramidal cell</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",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>68</th>\n",
       "      <td>107312</td>\n",
       "      <td>43552</td>\n",
       "      <td>2160</td>\n",
       "      <td>648518346349375478</td>\n",
       "      <td>vasculature</td>\n",
       "      <td>endothelial</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>69</th>\n",
       "      <td>104752</td>\n",
       "      <td>40768</td>\n",
       "      <td>878</td>\n",
       "      <td>648518346349061101</td>\n",
       "      <td>vasculature</td>\n",
       "      <td>endothelial</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>70</th>\n",
       "      <td>104464</td>\n",
       "      <td>40784</td>\n",
       "      <td>1867</td>\n",
       "      <td>648518346349375478</td>\n",
       "      <td>vasculature</td>\n",
       "      <td>endothelial</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>71</th>\n",
       "      <td>97377</td>\n",
       "      <td>38012</td>\n",
       "      <td>1145</td>\n",
       "      <td>648518346349375478</td>\n",
       "      <td>vasculature</td>\n",
       "      <td>endothelial</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>72</th>\n",
       "      <td>89216</td>\n",
       "      <td>38976</td>\n",
       "      <td>873</td>\n",
       "      <td>648518346349526102</td>\n",
       "      <td>vasculature</td>\n",
       "      <td>endothelial</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>619 rows × 6 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "    centroid_x  centroid_y  centroid_z          cell_segid    cell_type  \\\n",
       "1        41760       60256        1702  648518346349538237    pyramidal   \n",
       "2        98128       39856         218  648518346349536816    pyramidal   \n",
       "3        51248       50608          86  648518346349539797    pyramidal   \n",
       "5       115392       47136         617  648518346349536744    pyramidal   \n",
       "6       104928       72496        1448  648518346349536851    pyramidal   \n",
       "..         ...         ...         ...                 ...          ...   \n",
       "68      107312       43552        2160  648518346349375478  vasculature   \n",
       "69      104752       40768         878  648518346349061101  vasculature   \n",
       "70      104464       40784        1867  648518346349375478  vasculature   \n",
       "71       97377       38012        1145  648518346349375478  vasculature   \n",
       "72       89216       38976         873  648518346349526102  vasculature   \n",
       "\n",
       "      cell_subtype  \n",
       "1   pyramidal cell  \n",
       "2   pyramidal cell  \n",
       "3   pyramidal cell  \n",
       "5   pyramidal cell  \n",
       "6   pyramidal cell  \n",
       "..             ...  \n",
       "68     endothelial  \n",
       "69     endothelial  \n",
       "70     endothelial  \n",
       "71     endothelial  \n",
       "72     endothelial  \n",
       "\n",
       "[619 rows x 6 columns]"
      ]
     },
     "execution_count": 24,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# add vascular ids\n",
    "# load cell table\n",
    "\n",
    "celltypes = pd.read_csv('data/220309_cell_type_classification.csv', index_col=[0])\n",
    "celltypes"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 25,
   "id": "df9ff4a0",
   "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>centroid_x</th>\n",
       "      <th>centroid_y</th>\n",
       "      <th>centroid_z</th>\n",
       "      <th>cell_segid</th>\n",
       "      <th>cell_type</th>\n",
       "      <th>cell_subtype</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>113904</td>\n",
       "      <td>67296</td>\n",
       "      <td>24</td>\n",
       "      <td>648518346342804483</td>\n",
       "      <td>vasculature</td>\n",
       "      <td>endothelial</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>44512</td>\n",
       "      <td>71312</td>\n",
       "      <td>94</td>\n",
       "      <td>648518346341422370</td>\n",
       "      <td>vasculature</td>\n",
       "      <td>endothelial</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>76944</td>\n",
       "      <td>58784</td>\n",
       "      <td>1987</td>\n",
       "      <td>648518346349526102</td>\n",
       "      <td>vasculature</td>\n",
       "      <td>pericyte</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>104256</td>\n",
       "      <td>40800</td>\n",
       "      <td>1968</td>\n",
       "      <td>648518346349375478</td>\n",
       "      <td>vasculature</td>\n",
       "      <td>endothelial</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>45168</td>\n",
       "      <td>69328</td>\n",
       "      <td>105</td>\n",
       "      <td>648518346343497543</td>\n",
       "      <td>vasculature</td>\n",
       "      <td>endothelial</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",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>68</th>\n",
       "      <td>107312</td>\n",
       "      <td>43552</td>\n",
       "      <td>2160</td>\n",
       "      <td>648518346349375478</td>\n",
       "      <td>vasculature</td>\n",
       "      <td>endothelial</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>69</th>\n",
       "      <td>104752</td>\n",
       "      <td>40768</td>\n",
       "      <td>878</td>\n",
       "      <td>648518346349061101</td>\n",
       "      <td>vasculature</td>\n",
       "      <td>endothelial</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>70</th>\n",
       "      <td>104464</td>\n",
       "      <td>40784</td>\n",
       "      <td>1867</td>\n",
       "      <td>648518346349375478</td>\n",
       "      <td>vasculature</td>\n",
       "      <td>endothelial</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>71</th>\n",
       "      <td>97377</td>\n",
       "      <td>38012</td>\n",
       "      <td>1145</td>\n",
       "      <td>648518346349375478</td>\n",
       "      <td>vasculature</td>\n",
       "      <td>endothelial</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>72</th>\n",
       "      <td>89216</td>\n",
       "      <td>38976</td>\n",
       "      <td>873</td>\n",
       "      <td>648518346349526102</td>\n",
       "      <td>vasculature</td>\n",
       "      <td>endothelial</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>72 rows × 6 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "    centroid_x  centroid_y  centroid_z          cell_segid    cell_type  \\\n",
       "0       113904       67296          24  648518346342804483  vasculature   \n",
       "1        44512       71312          94  648518346341422370  vasculature   \n",
       "2        76944       58784        1987  648518346349526102  vasculature   \n",
       "3       104256       40800        1968  648518346349375478  vasculature   \n",
       "4        45168       69328         105  648518346343497543  vasculature   \n",
       "..         ...         ...         ...                 ...          ...   \n",
       "68      107312       43552        2160  648518346349375478  vasculature   \n",
       "69      104752       40768         878  648518346349061101  vasculature   \n",
       "70      104464       40784        1867  648518346349375478  vasculature   \n",
       "71       97377       38012        1145  648518346349375478  vasculature   \n",
       "72       89216       38976         873  648518346349526102  vasculature   \n",
       "\n",
       "   cell_subtype  \n",
       "0   endothelial  \n",
       "1   endothelial  \n",
       "2      pericyte  \n",
       "3   endothelial  \n",
       "4   endothelial  \n",
       "..          ...  \n",
       "68  endothelial  \n",
       "69  endothelial  \n",
       "70  endothelial  \n",
       "71  endothelial  \n",
       "72  endothelial  \n",
       "\n",
       "[72 rows x 6 columns]"
      ]
     },
     "execution_count": 25,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "vasc = celltypes[celltypes['cell_type'] == 'vasculature']\n",
    "vasc"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 26,
   "id": "377cd4b7",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "array([648518346342804483, 648518346341422370, 648518346349526102,\n",
       "       648518346349375478, 648518346343497543, 648518346348189552,\n",
       "       648518346344072053, 648518346348121670, 648518346344328018,\n",
       "       648518346344456391, 648518346344505300, 648518346341763956,\n",
       "       648518346345118988, 648518346342104735, 648518346343459827,\n",
       "       648518346342796989, 648518346349061101], dtype=int64)"
      ]
     },
     "execution_count": 26,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "vasc.cell_segid.unique()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 27,
   "id": "1a3abdec",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "17"
      ]
     },
     "execution_count": 27,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "len(vasc.cell_segid.unique())"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 28,
   "id": "51d5b755",
   "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>centroid_x</th>\n",
       "      <th>centroid_y</th>\n",
       "      <th>centroid_z</th>\n",
       "      <th>cell_segid</th>\n",
       "      <th>cell_type</th>\n",
       "      <th>cell_subtype</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>113904</td>\n",
       "      <td>67296</td>\n",
       "      <td>24</td>\n",
       "      <td>648518346342804483</td>\n",
       "      <td>vasculature</td>\n",
       "      <td>endothelial</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>44512</td>\n",
       "      <td>71312</td>\n",
       "      <td>94</td>\n",
       "      <td>648518346341422370</td>\n",
       "      <td>vasculature</td>\n",
       "      <td>endothelial</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>104256</td>\n",
       "      <td>40800</td>\n",
       "      <td>1968</td>\n",
       "      <td>648518346349375478</td>\n",
       "      <td>vasculature</td>\n",
       "      <td>endothelial</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>45168</td>\n",
       "      <td>69328</td>\n",
       "      <td>105</td>\n",
       "      <td>648518346343497543</td>\n",
       "      <td>vasculature</td>\n",
       "      <td>endothelial</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>107808</td>\n",
       "      <td>45904</td>\n",
       "      <td>2158</td>\n",
       "      <td>648518346348189552</td>\n",
       "      <td>vasculature</td>\n",
       "      <td>endothelial</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",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>68</th>\n",
       "      <td>107312</td>\n",
       "      <td>43552</td>\n",
       "      <td>2160</td>\n",
       "      <td>648518346349375478</td>\n",
       "      <td>vasculature</td>\n",
       "      <td>endothelial</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>69</th>\n",
       "      <td>104752</td>\n",
       "      <td>40768</td>\n",
       "      <td>878</td>\n",
       "      <td>648518346349061101</td>\n",
       "      <td>vasculature</td>\n",
       "      <td>endothelial</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>70</th>\n",
       "      <td>104464</td>\n",
       "      <td>40784</td>\n",
       "      <td>1867</td>\n",
       "      <td>648518346349375478</td>\n",
       "      <td>vasculature</td>\n",
       "      <td>endothelial</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>71</th>\n",
       "      <td>97377</td>\n",
       "      <td>38012</td>\n",
       "      <td>1145</td>\n",
       "      <td>648518346349375478</td>\n",
       "      <td>vasculature</td>\n",
       "      <td>endothelial</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>72</th>\n",
       "      <td>89216</td>\n",
       "      <td>38976</td>\n",
       "      <td>873</td>\n",
       "      <td>648518346349526102</td>\n",
       "      <td>vasculature</td>\n",
       "      <td>endothelial</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>71 rows × 6 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "    centroid_x  centroid_y  centroid_z          cell_segid    cell_type  \\\n",
       "0       113904       67296          24  648518346342804483  vasculature   \n",
       "1        44512       71312          94  648518346341422370  vasculature   \n",
       "3       104256       40800        1968  648518346349375478  vasculature   \n",
       "4        45168       69328         105  648518346343497543  vasculature   \n",
       "5       107808       45904        2158  648518346348189552  vasculature   \n",
       "..         ...         ...         ...                 ...          ...   \n",
       "68      107312       43552        2160  648518346349375478  vasculature   \n",
       "69      104752       40768         878  648518346349061101  vasculature   \n",
       "70      104464       40784        1867  648518346349375478  vasculature   \n",
       "71       97377       38012        1145  648518346349375478  vasculature   \n",
       "72       89216       38976         873  648518346349526102  vasculature   \n",
       "\n",
       "   cell_subtype  \n",
       "0   endothelial  \n",
       "1   endothelial  \n",
       "3   endothelial  \n",
       "4   endothelial  \n",
       "5   endothelial  \n",
       "..          ...  \n",
       "68  endothelial  \n",
       "69  endothelial  \n",
       "70  endothelial  \n",
       "71  endothelial  \n",
       "72  endothelial  \n",
       "\n",
       "[71 rows x 6 columns]"
      ]
     },
     "execution_count": 28,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "endo = celltypes[celltypes['cell_subtype'] == 'endothelial']\n",
    "endo"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 29,
   "id": "b09abbf4",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "array([648518346342804483, 648518346341422370, 648518346349375478,\n",
       "       648518346343497543, 648518346348189552, 648518346344072053,\n",
       "       648518346349526102, 648518346348121670, 648518346344328018,\n",
       "       648518346344456391, 648518346344505300, 648518346341763956,\n",
       "       648518346345118988, 648518346342104735, 648518346343459827,\n",
       "       648518346342796989, 648518346349061101], dtype=int64)"
      ]
     },
     "execution_count": 29,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "endo.cell_segid.unique()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 30,
   "id": "202e0313",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "17"
      ]
     },
     "execution_count": 30,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "len(endo.cell_segid.unique())"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 31,
   "id": "d909035d",
   "metadata": {},
   "outputs": [],
   "source": [
    "endo_list = endo.cell_segid.unique().tolist()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 32,
   "id": "882ed0f4",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "list"
      ]
     },
     "execution_count": 32,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "type(endo_list)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 33,
   "id": "333d06f3",
   "metadata": {},
   "outputs": [],
   "source": [
    "# download the cell meshes for the endothelial cells\n",
    "\n",
    "for i in range(len(endo_list)):\n",
    "    endo_id = endo_list[i]\n",
    "    endo_seg_id = endo_id\n",
    "    endo_downloadmesh = mm.mesh(seg_id = endo_seg_id, remove_duplicate_vertices=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 34,
   "id": "0375076b",
   "metadata": {},
   "outputs": [],
   "source": [
    "# iterate the cell meshes for endothelial cells\n",
    "# from https://python-forum.io/thread-23500.html\n",
    "\n",
    "endo_iterator = {}\n",
    "for i in range(len(endo_list)):\n",
    "    endo_seg_id = endo_list[i] \n",
    "    endo_mesh_file = os.path.join(mesh_dir, str(endo_seg_id)+'.h5')\n",
    "    endo_iterator['endo_mesh_' + str(i)] = mm.mesh(filename = endo_mesh_file)\n",
    "    \n",
    "locals().update(endo_iterator)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 35,
   "id": "e9e134b9",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "setting up renderer\n",
      "done setting up\n",
      "actors added\n",
      "camera set\n",
      "render done\n",
      "finalizing..\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "<vtkmodules.vtkRenderingOpenGL2.vtkOpenGLRenderer(0x000001B28F859D70) at 0x000001B293CE9888>"
      ]
     },
     "execution_count": 35,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# opacity and color settings for nuclei meshes\n",
    "exc_opac = 0.10 # 0.075\n",
    "exc_color = (0.2, 0.4, 0.7) # (0.2, 0.4, 0.7) blue\n",
    "inh_opac = 0.10 # 0.35\n",
    "inh_color = (0.7, 0.4, 0.2)\n",
    "glia_opac = 0.75\n",
    "glia_color = (0.7, 0.7, 0.2)\n",
    "vasc_opac = 0.15\n",
    "vasc_color = (1,1,1)\n",
    "\n",
    "# exc meshes\n",
    "exc_actor_iterator = {}\n",
    "for i in range(len(exc_list)):\n",
    "    #random_color = list(np.random.random(size=3))\n",
    "    exc_actor_iterator['exc_mesh_actor_' + str(i)] = trimesh_vtk.mesh_actor(exc_iterator['exc_mesh_'+str(i)], opacity=exc_opac, color=exc_color)\n",
    "    \n",
    "locals().update(exc_actor_iterator)\n",
    "\n",
    "# inh meshes\n",
    "inh_actor_iterator = {}\n",
    "for i in range(len(inh_list)):\n",
    "    #random_color = list(np.random.random(size=3))\n",
    "    inh_actor_iterator['inh_mesh_actor_' + str(i)] = trimesh_vtk.mesh_actor(inh_iterator['inh_mesh_'+str(i)], opacity=inh_opac, color=inh_color)\n",
    "    \n",
    "locals().update(inh_actor_iterator)\n",
    "\n",
    "# glia meshes\n",
    "glia_actor_iterator = {}\n",
    "for i in range(len(glia_list)):\n",
    "    #random_color = list(np.random.random(size=3))\n",
    "    glia_actor_iterator['glia_mesh_actor_' + str(i)] = trimesh_vtk.mesh_actor(glia_iterator['glia_mesh_'+str(i)], opacity=glia_opac, color=glia_color)\n",
    "    \n",
    "locals().update(glia_actor_iterator)\n",
    "\n",
    "# endothelial meshes\n",
    "endo_actor_iterator = {}\n",
    "for i in range(len(endo_list)):\n",
    "    #random_color = list(np.random.random(size=3))\n",
    "    endo_actor_iterator['endo_mesh_actor_' + str(i)] = trimesh_vtk.mesh_actor(endo_iterator['endo_mesh_'+str(i)], opacity=vasc_opac, color=vasc_color)\n",
    "    \n",
    "locals().update(endo_actor_iterator)\n",
    "\n",
    "# update dictionary for the render actors code below\n",
    "actor_iterator = {}\n",
    "actor_iterator.update(exc_actor_iterator)\n",
    "actor_iterator.update(inh_actor_iterator)\n",
    "actor_iterator.update(glia_actor_iterator)\n",
    "actor_iterator.update(endo_actor_iterator)\n",
    "locals().update(actor_iterator)\n",
    "\n",
    "#creating a camera object and defining the view\n",
    "camera = trimesh_vtk.oriented_camera((nuc_mesh_165.centroid), backoff=500) # this nuclei is near the center of the volume\n",
    "\n",
    "#render the actors, will open a pop up python window\n",
    "trimesh_vtk.render_actors(actor_iterator.values(), camera=camera)\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "45ea3c45",
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "Python 3 (ipykernel)",
   "language": "python",
   "name": "python3"
  },
  "language_info": {
   "codemirror_mode": {
    "name": "ipython",
    "version": 3
   },
   "file_extension": ".py",
   "mimetype": "text/x-python",
   "name": "python",
   "nbconvert_exporter": "python",
   "pygments_lexer": "ipython3",
   "version": "3.7.12"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 5
}