Intro.ipynb

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   "source": [
    "# TA3 Segmentation Pipeline\n",
    "\n",
    "This is the pipeline for EM segmentation data.\n",
    "\n",
    "To connect, obtain your credentials on `datajoint.ninai.org`."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "import numpy as np\n",
    "import datajoint as dj\n",
    "dj.config['database.user'] = 'dimitri'    #  change to your username\n",
    "dj.config['database.host'] = 'at-database'"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Connect to schemas `microns_ta3` and `microns_nda`"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Connecting dimitri@at-database:3306\n"
     ]
    }
   ],
   "source": [
    "import ta3\n",
    "nda = dj.create_virtual_module('nda', 'microns_nda')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "scrolled": false
   },
   "outputs": [
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       "                                <p id=\"primary\">synapse_id</p>\n",
       "                                <span class=\"djtooltiptext\">synapse index within the segmentation</span>\n",
       "                            </div></th><th><div class=\"djtooltip\">\n",
       "                                <p id=\"nonprimary\">presyn</p>\n",
       "                                <span class=\"djtooltiptext\">segment id unique within each Segmentation</span>\n",
       "                            </div></th><th><div class=\"djtooltip\">\n",
       "                                <p id=\"nonprimary\">postsyn</p>\n",
       "                                <span class=\"djtooltiptext\">segment id unique within each Segmentation</span>\n",
       "                            </div></th><th><div class=\"djtooltip\">\n",
       "                                <p id=\"nonprimary\">synapse_x</p>\n",
       "                                <span class=\"djtooltiptext\">(EM voxels)</span>\n",
       "                            </div></th><th><div class=\"djtooltip\">\n",
       "                                <p id=\"nonprimary\">synapse_y</p>\n",
       "                                <span class=\"djtooltiptext\">(EM voxels)</span>\n",
       "                            </div></th><th><div class=\"djtooltip\">\n",
       "                                <p id=\"nonprimary\">synapse_z</p>\n",
       "                                <span class=\"djtooltiptext\">(EM voxels)</span>\n",
       "                            </div></th><th><div class=\"djtooltip\">\n",
       "                                <p id=\"nonprimary\">syn_bbox_x1</p>\n",
       "                                <span class=\"djtooltiptext\">(EM voxels)  - bounding box</span>\n",
       "                            </div></th><th><div class=\"djtooltip\">\n",
       "                                <p id=\"nonprimary\">syn_bbox_y1</p>\n",
       "                                <span class=\"djtooltiptext\">(EM voxels)  - bounding box</span>\n",
       "                            </div></th><th><div class=\"djtooltip\">\n",
       "                                <p id=\"nonprimary\">syn_bbox_z1</p>\n",
       "                                <span class=\"djtooltiptext\">(EM voxels)  - bounding box</span>\n",
       "                            </div></th><th><div class=\"djtooltip\">\n",
       "                                <p id=\"nonprimary\">syn_bbox_x2</p>\n",
       "                                <span class=\"djtooltiptext\">(EM voxels)  - bounding box</span>\n",
       "                            </div></th><th><div class=\"djtooltip\">\n",
       "                                <p id=\"nonprimary\">syn_bbox_y2</p>\n",
       "                                <span class=\"djtooltiptext\">(EM voxels)  - bounding box</span>\n",
       "                            </div></th><th><div class=\"djtooltip\">\n",
       "                                <p id=\"nonprimary\">syn_bbox_z2</p>\n",
       "                                <span class=\"djtooltiptext\">(EM voxels)  - bounding box</span>\n",
       "                            </div> </th> </tr> </thead>\n",
       "                <tbody> <tr> <td>1</td>\n",
       "<td>1</td>\n",
       "<td>20113710</td>\n",
       "<td>129499</td>\n",
       "<td>11299</td>\n",
       "<td>8069</td>\n",
       "<td>500</td>\n",
       "<td>11285</td>\n",
       "<td>8051</td>\n",
       "<td>498</td>\n",
       "<td>11311</td>\n",
       "<td>8090</td>\n",
       "<td>502</td></tr><tr><td>1</td>\n",
       "<td>2</td>\n",
       "<td>23717036</td>\n",
       "<td>47418</td>\n",
       "<td>11881</td>\n",
       "<td>7833</td>\n",
       "<td>617</td>\n",
       "<td>11756</td>\n",
       "<td>7763</td>\n",
       "<td>613</td>\n",
       "<td>11983</td>\n",
       "<td>7910</td>\n",
       "<td>623</td></tr><tr><td>1</td>\n",
       "<td>3</td>\n",
       "<td>155693</td>\n",
       "<td>160691</td>\n",
       "<td>12130</td>\n",
       "<td>8167</td>\n",
       "<td>845</td>\n",
       "<td>12101</td>\n",
       "<td>8155</td>\n",
       "<td>843</td>\n",
       "<td>12157</td>\n",
       "<td>8180</td>\n",
       "<td>847</td></tr><tr><td>1</td>\n",
       "<td>4</td>\n",
       "<td>4165907</td>\n",
       "<td>556648</td>\n",
       "<td>11992</td>\n",
       "<td>7715</td>\n",
       "<td>342</td>\n",
       "<td>11962</td>\n",
       "<td>7694</td>\n",
       "<td>339</td>\n",
       "<td>12026</td>\n",
       "<td>7731</td>\n",
       "<td>344</td></tr><tr><td>1</td>\n",
       "<td>5</td>\n",
       "<td>60613</td>\n",
       "<td>50327</td>\n",
       "<td>11633</td>\n",
       "<td>7915</td>\n",
       "<td>612</td>\n",
       "<td>11608</td>\n",
       "<td>7901</td>\n",
       "<td>611</td>\n",
       "<td>11657</td>\n",
       "<td>7926</td>\n",
       "<td>614</td></tr><tr><td>1</td>\n",
       "<td>6</td>\n",
       "<td>4209671</td>\n",
       "<td>68592</td>\n",
       "<td>12717</td>\n",
       "<td>8038</td>\n",
       "<td>991</td>\n",
       "<td>12685</td>\n",
       "<td>7992</td>\n",
       "<td>986</td>\n",
       "<td>12751</td>\n",
       "<td>8086</td>\n",
       "<td>996</td></tr><tr><td>1</td>\n",
       "<td>7</td>\n",
       "<td>215757</td>\n",
       "<td>128075</td>\n",
       "<td>12654</td>\n",
       "<td>7713</td>\n",
       "<td>461</td>\n",
       "<td>12625</td>\n",
       "<td>7698</td>\n",
       "<td>455</td>\n",
       "<td>12684</td>\n",
       "<td>7732</td>\n",
       "<td>465</td> </tr> </tbody>\n",
       "            </table>\n",
       "            <p>...</p>\n",
       "            <p>1181196 tuples</p></div>\n",
       "            "
      ],
      "text/plain": [
       "*segmentation  *synapse_id    presyn       postsyn     synapse_x     synapse_y     synapse_z     syn_bbox_x1    syn_bbox_y1    syn_bbox_z1    syn_bbox_x2    syn_bbox_y2    syn_bbox_z2   \n",
       "+------------+ +------------+ +----------+ +---------+ +-----------+ +-----------+ +-----------+ +------------+ +------------+ +------------+ +------------+ +------------+ +------------+\n",
       "1              1              20113710     129499      11299         8069          500           11285          8051           498            11311          8090           502           \n",
       "1              2              23717036     47418       11881         7833          617           11756          7763           613            11983          7910           623           \n",
       "1              3              155693       160691      12130         8167          845           12101          8155           843            12157          8180           847           \n",
       "1              4              4165907      556648      11992         7715          342           11962          7694           339            12026          7731           344           \n",
       "1              5              60613        50327       11633         7915          612           11608          7901           611            11657          7926           614           \n",
       "1              6              4209671      68592       12717         8038          991           12685          7992           986            12751          8086           996           \n",
       "1              7              215757       128075      12654         7713          461           12625          7698           455            12684          7732           465           \n",
       "   ...\n",
       " (1181196 tuples)"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "ta3.Synapse()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Mesh                 Completed 1720929 of 1721148 (100.0%)   2017-10-10 13:52:56\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "(219, 1721148)"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "ta3.Mesh().progress()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": []
  }
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