code_calibration.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 32,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/var/folders/lc/l3h44z2d7_d98lsb5yh9d2y00000gn/T/ipykernel_36405/357318868.py:24: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  data_frame[\"State_cell\"][index]=hyper\n",
      "/var/folders/lc/l3h44z2d7_d98lsb5yh9d2y00000gn/T/ipykernel_36405/357318868.py:28: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  data_frame[\"State_cell\"][index]= norm\n"
     ]
    },
    {
     "data": {
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       "    .dataframe tbody tr th:only-of-type {\n",
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       "\n",
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>label</th>\n",
       "      <th>area</th>\n",
       "      <th>centroid-0</th>\n",
       "      <th>centroid-1</th>\n",
       "      <th>eccentricity</th>\n",
       "      <th>bbox-0</th>\n",
       "      <th>bbox-1</th>\n",
       "      <th>bbox-2</th>\n",
       "      <th>bbox-3</th>\n",
       "      <th>image</th>\n",
       "      <th>perimeter</th>\n",
       "      <th>feret_diameter_max</th>\n",
       "      <th>diameter_µm</th>\n",
       "      <th>State_cell</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>1</td>\n",
       "      <td>42573</td>\n",
       "      <td>114.372584</td>\n",
       "      <td>134.664435</td>\n",
       "      <td>0.590280</td>\n",
       "      <td>0</td>\n",
       "      <td>26</td>\n",
       "      <td>240</td>\n",
       "      <td>253</td>\n",
       "      <td>[[False False False ... False False False]\\n [...</td>\n",
       "      <td>832.315801</td>\n",
       "      <td>274.417565</td>\n",
       "      <td>85.618280</td>\n",
       "      <td>Hypertrophy</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>2</td>\n",
       "      <td>24120</td>\n",
       "      <td>63.611774</td>\n",
       "      <td>308.462935</td>\n",
       "      <td>0.641193</td>\n",
       "      <td>0</td>\n",
       "      <td>209</td>\n",
       "      <td>154</td>\n",
       "      <td>422</td>\n",
       "      <td>[[False False False ... False False False]\\n [...</td>\n",
       "      <td>644.238636</td>\n",
       "      <td>214.200840</td>\n",
       "      <td>66.830662</td>\n",
       "      <td>Normal</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>3</td>\n",
       "      <td>49842</td>\n",
       "      <td>116.046547</td>\n",
       "      <td>510.143514</td>\n",
       "      <td>0.359108</td>\n",
       "      <td>0</td>\n",
       "      <td>388</td>\n",
       "      <td>249</td>\n",
       "      <td>631</td>\n",
       "      <td>[[False False False ... False False False]\\n [...</td>\n",
       "      <td>866.748304</td>\n",
       "      <td>277.650860</td>\n",
       "      <td>86.627068</td>\n",
       "      <td>Hypertrophy</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>4</td>\n",
       "      <td>45595</td>\n",
       "      <td>80.636254</td>\n",
       "      <td>917.205220</td>\n",
       "      <td>0.705256</td>\n",
       "      <td>0</td>\n",
       "      <td>760</td>\n",
       "      <td>210</td>\n",
       "      <td>1102</td>\n",
       "      <td>[[False False False ... False False False]\\n [...</td>\n",
       "      <td>951.595021</td>\n",
       "      <td>342.527371</td>\n",
       "      <td>106.868540</td>\n",
       "      <td>Hypertrophy</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>5</td>\n",
       "      <td>17997</td>\n",
       "      <td>69.825138</td>\n",
       "      <td>1241.320720</td>\n",
       "      <td>0.798332</td>\n",
       "      <td>0</td>\n",
       "      <td>1143</td>\n",
       "      <td>180</td>\n",
       "      <td>1300</td>\n",
       "      <td>[[False False False ... False False False]\\n [...</td>\n",
       "      <td>592.132034</td>\n",
       "      <td>223.600089</td>\n",
       "      <td>69.763228</td>\n",
       "      <td>Normal</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>6</td>\n",
       "      <td>61886</td>\n",
       "      <td>186.388682</td>\n",
       "      <td>1119.213877</td>\n",
       "      <td>0.568769</td>\n",
       "      <td>11</td>\n",
       "      <td>983</td>\n",
       "      <td>334</td>\n",
       "      <td>1255</td>\n",
       "      <td>[[False False False ... False False False]\\n [...</td>\n",
       "      <td>983.986940</td>\n",
       "      <td>326.167135</td>\n",
       "      <td>101.764146</td>\n",
       "      <td>Hypertrophy</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>7</td>\n",
       "      <td>8656</td>\n",
       "      <td>132.348082</td>\n",
       "      <td>20.894177</td>\n",
       "      <td>0.976646</td>\n",
       "      <td>13</td>\n",
       "      <td>0</td>\n",
       "      <td>235</td>\n",
       "      <td>51</td>\n",
       "      <td>[[False False False ... False False False]\\n [...</td>\n",
       "      <td>499.787843</td>\n",
       "      <td>222.324088</td>\n",
       "      <td>69.365115</td>\n",
       "      <td>Normal</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>8</td>\n",
       "      <td>40028</td>\n",
       "      <td>161.908689</td>\n",
       "      <td>702.735685</td>\n",
       "      <td>0.598231</td>\n",
       "      <td>29</td>\n",
       "      <td>602</td>\n",
       "      <td>291</td>\n",
       "      <td>819</td>\n",
       "      <td>[[False False False ... False False False]\\n [...</td>\n",
       "      <td>802.358477</td>\n",
       "      <td>264.850901</td>\n",
       "      <td>82.633481</td>\n",
       "      <td>Hypertrophy</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>9</td>\n",
       "      <td>48578</td>\n",
       "      <td>276.923628</td>\n",
       "      <td>340.470563</td>\n",
       "      <td>0.698555</td>\n",
       "      <td>135</td>\n",
       "      <td>219</td>\n",
       "      <td>443</td>\n",
       "      <td>454</td>\n",
       "      <td>[[False False False ... False False False]\\n [...</td>\n",
       "      <td>888.246825</td>\n",
       "      <td>309.657876</td>\n",
       "      <td>96.613257</td>\n",
       "      <td>Hypertrophy</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>10</td>\n",
       "      <td>17792</td>\n",
       "      <td>326.442952</td>\n",
       "      <td>1264.944357</td>\n",
       "      <td>0.949231</td>\n",
       "      <td>184</td>\n",
       "      <td>1209</td>\n",
       "      <td>468</td>\n",
       "      <td>1300</td>\n",
       "      <td>[[False False False ... False False False]\\n [...</td>\n",
       "      <td>668.132034</td>\n",
       "      <td>284.112654</td>\n",
       "      <td>88.643148</td>\n",
       "      <td>Hypertrophy</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>10</th>\n",
       "      <td>11</td>\n",
       "      <td>43025</td>\n",
       "      <td>319.591331</td>\n",
       "      <td>906.064730</td>\n",
       "      <td>0.710462</td>\n",
       "      <td>194</td>\n",
       "      <td>789</td>\n",
       "      <td>467</td>\n",
       "      <td>1017</td>\n",
       "      <td>[[False False False ... False False False]\\n [...</td>\n",
       "      <td>843.293506</td>\n",
       "      <td>293.552380</td>\n",
       "      <td>91.588343</td>\n",
       "      <td>Hypertrophy</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>11</th>\n",
       "      <td>12</td>\n",
       "      <td>47271</td>\n",
       "      <td>387.986355</td>\n",
       "      <td>226.346238</td>\n",
       "      <td>0.927667</td>\n",
       "      <td>233</td>\n",
       "      <td>89</td>\n",
       "      <td>557</td>\n",
       "      <td>398</td>\n",
       "      <td>[[False False False ... False False False]\\n [...</td>\n",
       "      <td>1041.241774</td>\n",
       "      <td>413.175508</td>\n",
       "      <td>128.910758</td>\n",
       "      <td>Hypertrophy</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>12</th>\n",
       "      <td>13</td>\n",
       "      <td>23430</td>\n",
       "      <td>375.474904</td>\n",
       "      <td>40.805036</td>\n",
       "      <td>0.951484</td>\n",
       "      <td>235</td>\n",
       "      <td>0</td>\n",
       "      <td>534</td>\n",
       "      <td>92</td>\n",
       "      <td>[[False False False ... False False False]\\n [...</td>\n",
       "      <td>722.735065</td>\n",
       "      <td>299.376018</td>\n",
       "      <td>93.405318</td>\n",
       "      <td>Hypertrophy</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>13</th>\n",
       "      <td>14</td>\n",
       "      <td>52692</td>\n",
       "      <td>385.633758</td>\n",
       "      <td>527.460241</td>\n",
       "      <td>0.713008</td>\n",
       "      <td>236</td>\n",
       "      <td>411</td>\n",
       "      <td>530</td>\n",
       "      <td>631</td>\n",
       "      <td>[[False False False ... False False False]\\n [...</td>\n",
       "      <td>903.990945</td>\n",
       "      <td>307.358097</td>\n",
       "      <td>95.895726</td>\n",
       "      <td>Hypertrophy</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>14</th>\n",
       "      <td>15</td>\n",
       "      <td>53905</td>\n",
       "      <td>410.831593</td>\n",
       "      <td>745.444300</td>\n",
       "      <td>0.620854</td>\n",
       "      <td>262</td>\n",
       "      <td>622</td>\n",
       "      <td>540</td>\n",
       "      <td>890</td>\n",
       "      <td>[[False False False ... False False False]\\n [...</td>\n",
       "      <td>938.536147</td>\n",
       "      <td>313.178863</td>\n",
       "      <td>97.711805</td>\n",
       "      <td>Hypertrophy</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>15</th>\n",
       "      <td>16</td>\n",
       "      <td>60554</td>\n",
       "      <td>453.870776</td>\n",
       "      <td>1116.579466</td>\n",
       "      <td>0.506663</td>\n",
       "      <td>314</td>\n",
       "      <td>976</td>\n",
       "      <td>593</td>\n",
       "      <td>1273</td>\n",
       "      <td>[[False False False ... False False False]\\n [...</td>\n",
       "      <td>961.116882</td>\n",
       "      <td>308.768522</td>\n",
       "      <td>96.335779</td>\n",
       "      <td>Hypertrophy</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>16</th>\n",
       "      <td>17</td>\n",
       "      <td>45889</td>\n",
       "      <td>543.939136</td>\n",
       "      <td>195.414152</td>\n",
       "      <td>0.802051</td>\n",
       "      <td>405</td>\n",
       "      <td>64</td>\n",
       "      <td>663</td>\n",
       "      <td>372</td>\n",
       "      <td>[[False False False ... False False False]\\n [...</td>\n",
       "      <td>907.993037</td>\n",
       "      <td>323.358934</td>\n",
       "      <td>100.887987</td>\n",
       "      <td>Hypertrophy</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>17</th>\n",
       "      <td>18</td>\n",
       "      <td>96953</td>\n",
       "      <td>684.202160</td>\n",
       "      <td>1000.089342</td>\n",
       "      <td>0.700270</td>\n",
       "      <td>487</td>\n",
       "      <td>822</td>\n",
       "      <td>844</td>\n",
       "      <td>1210</td>\n",
       "      <td>[[False False False ... False False False]\\n [...</td>\n",
       "      <td>1256.283405</td>\n",
       "      <td>427.488012</td>\n",
       "      <td>133.376260</td>\n",
       "      <td>Hypertrophy</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>18</th>\n",
       "      <td>19</td>\n",
       "      <td>27706</td>\n",
       "      <td>640.809428</td>\n",
       "      <td>1242.168483</td>\n",
       "      <td>0.843306</td>\n",
       "      <td>499</td>\n",
       "      <td>1162</td>\n",
       "      <td>765</td>\n",
       "      <td>1300</td>\n",
       "      <td>[[False False False ... False False False]\\n [...</td>\n",
       "      <td>703.730014</td>\n",
       "      <td>268.881015</td>\n",
       "      <td>83.890877</td>\n",
       "      <td>Hypertrophy</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>19</th>\n",
       "      <td>20</td>\n",
       "      <td>37523</td>\n",
       "      <td>614.828692</td>\n",
       "      <td>731.495030</td>\n",
       "      <td>0.621346</td>\n",
       "      <td>511</td>\n",
       "      <td>610</td>\n",
       "      <td>727</td>\n",
       "      <td>839</td>\n",
       "      <td>[[False False False ... False False False]\\n [...</td>\n",
       "      <td>765.369624</td>\n",
       "      <td>261.137895</td>\n",
       "      <td>81.475023</td>\n",
       "      <td>Hypertrophy</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>20</th>\n",
       "      <td>21</td>\n",
       "      <td>38726</td>\n",
       "      <td>652.313045</td>\n",
       "      <td>530.632392</td>\n",
       "      <td>0.778509</td>\n",
       "      <td>527</td>\n",
       "      <td>439</td>\n",
       "      <td>807</td>\n",
       "      <td>623</td>\n",
       "      <td>[[False False False ... False False False]\\n [...</td>\n",
       "      <td>801.062013</td>\n",
       "      <td>284.606746</td>\n",
       "      <td>88.797305</td>\n",
       "      <td>Hypertrophy</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>21</th>\n",
       "      <td>22</td>\n",
       "      <td>55983</td>\n",
       "      <td>717.541164</td>\n",
       "      <td>360.989229</td>\n",
       "      <td>0.463724</td>\n",
       "      <td>540</td>\n",
       "      <td>215</td>\n",
       "      <td>853</td>\n",
       "      <td>487</td>\n",
       "      <td>[[False False False ... False False False]\\n [...</td>\n",
       "      <td>988.063059</td>\n",
       "      <td>313.996815</td>\n",
       "      <td>97.967006</td>\n",
       "      <td>Hypertrophy</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>22</th>\n",
       "      <td>23</td>\n",
       "      <td>46852</td>\n",
       "      <td>704.595023</td>\n",
       "      <td>90.721762</td>\n",
       "      <td>0.734250</td>\n",
       "      <td>545</td>\n",
       "      <td>0</td>\n",
       "      <td>830</td>\n",
       "      <td>213</td>\n",
       "      <td>[[False False False ... False False False]\\n [...</td>\n",
       "      <td>886.191955</td>\n",
       "      <td>322.931881</td>\n",
       "      <td>100.754747</td>\n",
       "      <td>Hypertrophy</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>23</th>\n",
       "      <td>24</td>\n",
       "      <td>21303</td>\n",
       "      <td>793.924987</td>\n",
       "      <td>649.218326</td>\n",
       "      <td>0.722032</td>\n",
       "      <td>696</td>\n",
       "      <td>567</td>\n",
       "      <td>889</td>\n",
       "      <td>731</td>\n",
       "      <td>[[False False False ... False False False]\\n [...</td>\n",
       "      <td>591.813275</td>\n",
       "      <td>207.337888</td>\n",
       "      <td>64.689421</td>\n",
       "      <td>Normal</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>24</th>\n",
       "      <td>25</td>\n",
       "      <td>17162</td>\n",
       "      <td>798.689430</td>\n",
       "      <td>770.005186</td>\n",
       "      <td>0.693853</td>\n",
       "      <td>720</td>\n",
       "      <td>701</td>\n",
       "      <td>886</td>\n",
       "      <td>840</td>\n",
       "      <td>[[False False False ... False False False]\\n [...</td>\n",
       "      <td>522.617316</td>\n",
       "      <td>182.060430</td>\n",
       "      <td>56.802854</td>\n",
       "      <td>Normal</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>25</th>\n",
       "      <td>26</td>\n",
       "      <td>7606</td>\n",
       "      <td>870.608598</td>\n",
       "      <td>1274.302787</td>\n",
       "      <td>0.929803</td>\n",
       "      <td>786</td>\n",
       "      <td>1240</td>\n",
       "      <td>952</td>\n",
       "      <td>1300</td>\n",
       "      <td>[[False False False ... False False False]\\n [...</td>\n",
       "      <td>395.279221</td>\n",
       "      <td>166.508258</td>\n",
       "      <td>51.950577</td>\n",
       "      <td>Normal</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>26</th>\n",
       "      <td>27</td>\n",
       "      <td>55287</td>\n",
       "      <td>929.110966</td>\n",
       "      <td>962.369544</td>\n",
       "      <td>0.751346</td>\n",
       "      <td>811</td>\n",
       "      <td>814</td>\n",
       "      <td>1030</td>\n",
       "      <td>1119</td>\n",
       "      <td>[[False False False ... False False False]\\n [...</td>\n",
       "      <td>934.564538</td>\n",
       "      <td>325.098447</td>\n",
       "      <td>101.430715</td>\n",
       "      <td>Hypertrophy</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>27</th>\n",
       "      <td>28</td>\n",
       "      <td>25621</td>\n",
       "      <td>929.749541</td>\n",
       "      <td>63.038250</td>\n",
       "      <td>0.769402</td>\n",
       "      <td>818</td>\n",
       "      <td>0</td>\n",
       "      <td>1030</td>\n",
       "      <td>136</td>\n",
       "      <td>[[False False False ... False False False]\\n [...</td>\n",
       "      <td>663.693434</td>\n",
       "      <td>240.707291</td>\n",
       "      <td>75.100675</td>\n",
       "      <td>Normal</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>28</th>\n",
       "      <td>29</td>\n",
       "      <td>51991</td>\n",
       "      <td>929.556943</td>\n",
       "      <td>269.469274</td>\n",
       "      <td>0.674596</td>\n",
       "      <td>819</td>\n",
       "      <td>130</td>\n",
       "      <td>1030</td>\n",
       "      <td>418</td>\n",
       "      <td>[[False False False ... False False False]\\n [...</td>\n",
       "      <td>892.943218</td>\n",
       "      <td>308.609786</td>\n",
       "      <td>96.286253</td>\n",
       "      <td>Hypertrophy</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>29</th>\n",
       "      <td>30</td>\n",
       "      <td>42666</td>\n",
       "      <td>941.917921</td>\n",
       "      <td>648.577486</td>\n",
       "      <td>0.905643</td>\n",
       "      <td>841</td>\n",
       "      <td>477</td>\n",
       "      <td>1030</td>\n",
       "      <td>815</td>\n",
       "      <td>[[False False False ... False False False]\\n [...</td>\n",
       "      <td>907.488419</td>\n",
       "      <td>358.436884</td>\n",
       "      <td>111.832308</td>\n",
       "      <td>Hypertrophy</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>30</th>\n",
       "      <td>31</td>\n",
       "      <td>17846</td>\n",
       "      <td>979.530315</td>\n",
       "      <td>479.090104</td>\n",
       "      <td>0.771451</td>\n",
       "      <td>901</td>\n",
       "      <td>385</td>\n",
       "      <td>1030</td>\n",
       "      <td>597</td>\n",
       "      <td>[[False False False ... False False False]\\n [...</td>\n",
       "      <td>575.593975</td>\n",
       "      <td>212.461761</td>\n",
       "      <td>66.288070</td>\n",
       "      <td>Normal</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "    label   area  centroid-0   centroid-1  eccentricity  bbox-0  bbox-1  \\\n",
       "0       1  42573  114.372584   134.664435      0.590280       0      26   \n",
       "1       2  24120   63.611774   308.462935      0.641193       0     209   \n",
       "2       3  49842  116.046547   510.143514      0.359108       0     388   \n",
       "3       4  45595   80.636254   917.205220      0.705256       0     760   \n",
       "4       5  17997   69.825138  1241.320720      0.798332       0    1143   \n",
       "5       6  61886  186.388682  1119.213877      0.568769      11     983   \n",
       "6       7   8656  132.348082    20.894177      0.976646      13       0   \n",
       "7       8  40028  161.908689   702.735685      0.598231      29     602   \n",
       "8       9  48578  276.923628   340.470563      0.698555     135     219   \n",
       "9      10  17792  326.442952  1264.944357      0.949231     184    1209   \n",
       "10     11  43025  319.591331   906.064730      0.710462     194     789   \n",
       "11     12  47271  387.986355   226.346238      0.927667     233      89   \n",
       "12     13  23430  375.474904    40.805036      0.951484     235       0   \n",
       "13     14  52692  385.633758   527.460241      0.713008     236     411   \n",
       "14     15  53905  410.831593   745.444300      0.620854     262     622   \n",
       "15     16  60554  453.870776  1116.579466      0.506663     314     976   \n",
       "16     17  45889  543.939136   195.414152      0.802051     405      64   \n",
       "17     18  96953  684.202160  1000.089342      0.700270     487     822   \n",
       "18     19  27706  640.809428  1242.168483      0.843306     499    1162   \n",
       "19     20  37523  614.828692   731.495030      0.621346     511     610   \n",
       "20     21  38726  652.313045   530.632392      0.778509     527     439   \n",
       "21     22  55983  717.541164   360.989229      0.463724     540     215   \n",
       "22     23  46852  704.595023    90.721762      0.734250     545       0   \n",
       "23     24  21303  793.924987   649.218326      0.722032     696     567   \n",
       "24     25  17162  798.689430   770.005186      0.693853     720     701   \n",
       "25     26   7606  870.608598  1274.302787      0.929803     786    1240   \n",
       "26     27  55287  929.110966   962.369544      0.751346     811     814   \n",
       "27     28  25621  929.749541    63.038250      0.769402     818       0   \n",
       "28     29  51991  929.556943   269.469274      0.674596     819     130   \n",
       "29     30  42666  941.917921   648.577486      0.905643     841     477   \n",
       "30     31  17846  979.530315   479.090104      0.771451     901     385   \n",
       "\n",
       "    bbox-2  bbox-3                                              image  \\\n",
       "0      240     253  [[False False False ... False False False]\\n [...   \n",
       "1      154     422  [[False False False ... False False False]\\n [...   \n",
       "2      249     631  [[False False False ... False False False]\\n [...   \n",
       "3      210    1102  [[False False False ... False False False]\\n [...   \n",
       "4      180    1300  [[False False False ... False False False]\\n [...   \n",
       "5      334    1255  [[False False False ... False False False]\\n [...   \n",
       "6      235      51  [[False False False ... False False False]\\n [...   \n",
       "7      291     819  [[False False False ... False False False]\\n [...   \n",
       "8      443     454  [[False False False ... False False False]\\n [...   \n",
       "9      468    1300  [[False False False ... False False False]\\n [...   \n",
       "10     467    1017  [[False False False ... False False False]\\n [...   \n",
       "11     557     398  [[False False False ... False False False]\\n [...   \n",
       "12     534      92  [[False False False ... False False False]\\n [...   \n",
       "13     530     631  [[False False False ... False False False]\\n [...   \n",
       "14     540     890  [[False False False ... False False False]\\n [...   \n",
       "15     593    1273  [[False False False ... False False False]\\n [...   \n",
       "16     663     372  [[False False False ... False False False]\\n [...   \n",
       "17     844    1210  [[False False False ... False False False]\\n [...   \n",
       "18     765    1300  [[False False False ... False False False]\\n [...   \n",
       "19     727     839  [[False False False ... False False False]\\n [...   \n",
       "20     807     623  [[False False False ... False False False]\\n [...   \n",
       "21     853     487  [[False False False ... False False False]\\n [...   \n",
       "22     830     213  [[False False False ... False False False]\\n [...   \n",
       "23     889     731  [[False False False ... False False False]\\n [...   \n",
       "24     886     840  [[False False False ... False False False]\\n [...   \n",
       "25     952    1300  [[False False False ... False False False]\\n [...   \n",
       "26    1030    1119  [[False False False ... False False False]\\n [...   \n",
       "27    1030     136  [[False False False ... False False False]\\n [...   \n",
       "28    1030     418  [[False False False ... False False False]\\n [...   \n",
       "29    1030     815  [[False False False ... False False False]\\n [...   \n",
       "30    1030     597  [[False False False ... False False False]\\n [...   \n",
       "\n",
       "      perimeter  feret_diameter_max  diameter_µm   State_cell  \n",
       "0    832.315801          274.417565    85.618280  Hypertrophy  \n",
       "1    644.238636          214.200840    66.830662       Normal  \n",
       "2    866.748304          277.650860    86.627068  Hypertrophy  \n",
       "3    951.595021          342.527371   106.868540  Hypertrophy  \n",
       "4    592.132034          223.600089    69.763228       Normal  \n",
       "5    983.986940          326.167135   101.764146  Hypertrophy  \n",
       "6    499.787843          222.324088    69.365115       Normal  \n",
       "7    802.358477          264.850901    82.633481  Hypertrophy  \n",
       "8    888.246825          309.657876    96.613257  Hypertrophy  \n",
       "9    668.132034          284.112654    88.643148  Hypertrophy  \n",
       "10   843.293506          293.552380    91.588343  Hypertrophy  \n",
       "11  1041.241774          413.175508   128.910758  Hypertrophy  \n",
       "12   722.735065          299.376018    93.405318  Hypertrophy  \n",
       "13   903.990945          307.358097    95.895726  Hypertrophy  \n",
       "14   938.536147          313.178863    97.711805  Hypertrophy  \n",
       "15   961.116882          308.768522    96.335779  Hypertrophy  \n",
       "16   907.993037          323.358934   100.887987  Hypertrophy  \n",
       "17  1256.283405          427.488012   133.376260  Hypertrophy  \n",
       "18   703.730014          268.881015    83.890877  Hypertrophy  \n",
       "19   765.369624          261.137895    81.475023  Hypertrophy  \n",
       "20   801.062013          284.606746    88.797305  Hypertrophy  \n",
       "21   988.063059          313.996815    97.967006  Hypertrophy  \n",
       "22   886.191955          322.931881   100.754747  Hypertrophy  \n",
       "23   591.813275          207.337888    64.689421       Normal  \n",
       "24   522.617316          182.060430    56.802854       Normal  \n",
       "25   395.279221          166.508258    51.950577       Normal  \n",
       "26   934.564538          325.098447   101.430715  Hypertrophy  \n",
       "27   663.693434          240.707291    75.100675       Normal  \n",
       "28   892.943218          308.609786    96.286253  Hypertrophy  \n",
       "29   907.488419          358.436884   111.832308  Hypertrophy  \n",
       "30   575.593975          212.461761    66.288070       Normal  "
      ]
     },
     "execution_count": 32,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "import pandas as pd \n",
    "#on importe les fichiers csv nécessaire \n",
    "df=pd.read_csv('muscle_atlas_clean.csv') #atlas du muscle\n",
    "df_cell=pd.read_csv('data_5_jpg.csv') # fichier info image 5 (taille, diamètre, centre...)\n",
    "\n",
    "\n",
    "\n",
    "def conversion_pix_µm(im, data_frame,muscle_atlas):\n",
    "    'Convertion du diamètre en µm'\n",
    "    barre_echelle= muscle_atlas.loc[(df['Number']== im), 'Calibration (um/px)']\n",
    "    \n",
    "    data_frame['diameter_µm']=(data_frame['feret_diameter_max'])*barre_echelle.values\n",
    "\n",
    "conversion_pix_µm('5.jpg',df_cell,df )\n",
    "\n",
    "def count_atrophic_cells (data_frame,min_size, max_size):\n",
    "    hyper='Hypertrophy'\n",
    "    hypo= 'Hypotrophy'\n",
    "    norm= 'Normal'\n",
    "    data_frame[\"State_cell\"] = ''\n",
    "    for index in data_frame.index:\n",
    "        a=data_frame['diameter_µm'][index]\n",
    "        if a > max_size:\n",
    "            data_frame[\"State_cell\"][index]=hyper\n",
    "        elif a < min_size:\n",
    "            data_frame[\"State_cell\"][index]=hypo\n",
    "        else: \n",
    "            data_frame[\"State_cell\"][index]= norm\n",
    "\n",
    "\n",
    "count_atrophic_cells (df_cell, 30, 80)\n",
    "\n",
    "df_cell\n",
    "    "
   ]
  }
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