cell-cycle/Compound_Images_List.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Compound Analysis"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "import pandas as pd\n",
    "import numpy"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "# path to the .csv file from BBBC022 (Warning : the one from the website may contain some errors)\n",
    "df = pd.read_csv('./BBBC022_v1_image.csv')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## List of the compounds with their number of replicates"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "CYCLOPIAZONIC ACID                                                                  72\n",
       "Gabazine                                                                            72\n",
       "ESTRADIOL                                                                           72\n",
       "OSAJIN                                                                              36\n",
       "Dizocilpine maleate                                                                 36\n",
       "Amiloride hydrochloride dihydrate                                                   36\n",
       "ESTRADIOL DIACETATE                                                                 36\n",
       "m-CHLOROPHENYLBIGUANIDE                                                             36\n",
       "OXFENDAZOLE                                                                         36\n",
       "Calycanthine                                                                        36\n",
       "2,4-DICHLOROPHENOXYACETIC ACID                                                      36\n",
       "METACETAMOL                                                                         36\n",
       "Huperzine A [(-)-Huperzine A]                                                       36\n",
       "OSELTAMIVIR TARTRATE                                                                36\n",
       "DIMETHOATE                                                                          36\n",
       "HOMATROPINE METHYLBROMIDE                                                           36\n",
       "MEGESTROL ACETATE                                                                   36\n",
       "Harpagoside                                                                         36\n",
       "ATENOLOL                                                                            36\n",
       "Diphenylpyraline hydrochloride                                                      36\n",
       "Thyroxine (L)                                                                       36\n",
       "TOLMETIN SODIUM                                                                     36\n",
       "PHENAMIL                                                                            36\n",
       "PARTHENOLIDE                                                                        36\n",
       "(S)-(-)-Atenolol                                                                    36\n",
       "4'-HYDROXYCHALCONE                                                                  36\n",
       "Homochlorcyclizine dihydrochloride                                                  36\n",
       "ANIRACETAM                                                                          36\n",
       "PENITREM A                                                                          36\n",
       "PHLORIDZIN                                                                          36\n",
       "                                                                                    ..\n",
       "ESTRIOL METHYL ETHER                                                                36\n",
       "ESTRADIOL ACETATE                                                                   36\n",
       "MDL-72222                                                                           36\n",
       "NEOHESPERIDIN DIHYDROCHALCONE                                                       36\n",
       "Lomefloxacin hydrochloride                                                          36\n",
       "PSEUDOEPHEDRINE HYDROCHLORIDE                                                       36\n",
       "MCI-186                                                                             36\n",
       "Famprofazone                                                                        36\n",
       "EPICATECHIN PENTAACETATE                                                            36\n",
       "AUSTRICINE                                                                          36\n",
       "S(-)-RACLOPRIDE                                                                     36\n",
       "Repaglinide                                                                         36\n",
       "SULFAMETHAZINE                                                                      36\n",
       "BENTAZON                                                                            36\n",
       "MICONAZOLE NITRATE                                                                  36\n",
       "LEVULINIC ACID,  3-BENZYLIDENYL-                                                    36\n",
       "Cefaclor                                                                            36\n",
       "Gelsemine                                                                           36\n",
       "METHYLERGOMETRINE                                                                   36\n",
       "Diflunisal                                                                          36\n",
       "Flumequine                                                                          36\n",
       "Dilazep dihydrochloride                                                             36\n",
       "SDZ SER 082                                                                         36\n",
       "FENAMISAL                                                                           36\n",
       "Atovaquone                                                                          36\n",
       "7-[2-TRIFLUOROMETHYL-4-(2-HYDROXYPHENYL)-1,3-DIOXAN-cis-5-YL]-HEPT-5Z-ENOIC ACID    36\n",
       "FUREGRELATE SODIUM                                                                  36\n",
       "DEACETOXY-7-OXOGEDUNIN                                                              36\n",
       "ETHYL 1-BENZYL-3-HYDROXY- 2-OXO[5H]PYRROLE-4-CARBOXYLATE                            36\n",
       "4,7-DIMETHOXYFLAVONE                                                                36\n",
       "Name: Image_Metadata_SOURCE_COMPOUND_NAME, Length: 1597, dtype: int64"
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df2 = df[['ImageNumber', 'Image_Metadata_SOURCE_COMPOUND_NAME']]\n",
    "df2['Image_Metadata_SOURCE_COMPOUND_NAME'].value_counts()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "etoposide                                                                108\n",
       "medrysone                                                                 72\n",
       "yohimbine hydrochloride                                                   72\n",
       "picrotoxinin                                                              72\n",
       "estropipate                                                               72\n",
       "digoxin                                                                   72\n",
       "estrone                                                                   72\n",
       "chloramphenicol                                                           72\n",
       "lincomycin hydrochloride                                                  72\n",
       "estradiol                                                                 72\n",
       "isoxsuprine hydrochloride                                                 72\n",
       "gabazine                                                                  72\n",
       "clobetasol propionate                                                     72\n",
       "ketoconazole                                                              72\n",
       "cyproterone acetate                                                       72\n",
       "norethindrone                                                             72\n",
       "cortisone                                                                 72\n",
       "cinchonine                                                                72\n",
       "minoxidil                                                                 72\n",
       "prednisone                                                                72\n",
       "nalbuphine hydrochloride                                                  72\n",
       "naloxone hydrochloride                                                    72\n",
       "fluocinonide                                                              72\n",
       "molsidomine                                                               72\n",
       "aconitine                                                                 72\n",
       "cyclopiazonic acid                                                        72\n",
       "flunixin meglumine                                                        72\n",
       "lycorine                                                                  72\n",
       "chelidonine (+)                                                           72\n",
       "levamisole hydrochloride                                                  72\n",
       "                                                                        ... \n",
       "phenothrin                                                                36\n",
       "clomiphene citrate                                                        36\n",
       "2'-methoxyformonetin                                                      36\n",
       "hydrochlorothiazide                                                       36\n",
       "hydroxytoluic acid                                                        36\n",
       "beta-dihydrorotenone                                                      36\n",
       "cycloveratrylene                                                          36\n",
       "coumarin                                                                  36\n",
       "digitoxigenin                                                             36\n",
       "chlorthalidone                                                            36\n",
       "methazolamide                                                             36\n",
       "loxapine succinate                                                        36\n",
       "quinine                                                                   36\n",
       "tetrahydropalmatine                                                       36\n",
       "desoxypeganine hydrochloride                                              36\n",
       "5-[(dimethylamino)methyl]-3-(1-methyl-1h-indol-3-yl)-1,2,4-oxadiazole     36\n",
       "dantrolene sodium salt                                                    36\n",
       "my-5445                                                                   36\n",
       "chlorogenic acid                                                          36\n",
       "pronethalol hydrochloride                                                 36\n",
       "verapamil                                                                 36\n",
       "naringin                                                                  36\n",
       "u-74389g                                                                  36\n",
       "retrorsine                                                                36\n",
       "dicumarol                                                                 36\n",
       "cerulenin                                                                 36\n",
       "tropisetron                                                               36\n",
       "fendiline hydrochloride                                                   36\n",
       "dl-pdmp                                                                   36\n",
       "deoxyandirobin lactone                                                    36\n",
       "Name: Image_Metadata_SOURCE_COMPOUND_NAME, Length: 1546, dtype: int64"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "dftemp = df2['Image_Metadata_SOURCE_COMPOUND_NAME']\n",
    "dftemp = dftemp.str.lower()\n",
    "dftemp = dftemp.value_counts()\n",
    "dftemp.to_csv('compounds.csv')\n",
    "dftemp"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "array(['20585/', '20586/', '20589/', '20590/', '20591/', '20592/',\n",
       "       '20593/', '20594/', '20595/', '20596/', '20607/', '20608/',\n",
       "       '20625/', '20626/', '20630/', '20633/', '20639/', '20640/',\n",
       "       '20641/', '20646/'], dtype=object)"
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "plates = numpy.unique(df.Image_PathName_OrigHoechst.values)\n",
    "# plates = [plates[0]]\n",
    "plates"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Compound selection and creation of the list of the corresponding images"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "data": {
      "text/html": [
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       "    }\n",
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       "    .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>ImageNumber</th>\n",
       "      <th>Image_FileName_OrigER</th>\n",
       "      <th>Image_FileName_OrigHoechst</th>\n",
       "      <th>Image_FileName_OrigMito</th>\n",
       "      <th>Image_FileName_OrigPh_golgi</th>\n",
       "      <th>Image_FileName_OrigSyto</th>\n",
       "      <th>Image_Metadata_ASSAY_WELL_ROLE</th>\n",
       "      <th>Image_Metadata_BROAD_ID</th>\n",
       "      <th>Image_Metadata_CPD_MMOL_CONC</th>\n",
       "      <th>Image_Metadata_CPD_PLATE_MAP_NAME</th>\n",
       "      <th>...</th>\n",
       "      <th>Image_Metadata_SOURCE_COMPOUND_NAME</th>\n",
       "      <th>Image_Metadata_SOURCE_NAME</th>\n",
       "      <th>Image_Metadata_Site</th>\n",
       "      <th>Image_Metadata_Time</th>\n",
       "      <th>Image_PathName_OrigER</th>\n",
       "      <th>Image_PathName_OrigHoechst</th>\n",
       "      <th>Image_PathName_OrigMito</th>\n",
       "      <th>Image_PathName_OrigPh_golgi</th>\n",
       "      <th>Image_PathName_OrigSyto</th>\n",
       "      <th>IXMtest</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>4194</th>\n",
       "      <td>4195</td>\n",
       "      <td>IXMtest_D14_s1_w205B05914-92D1-4E66-BF35-812B3...</td>\n",
       "      <td>IXMtest_D14_s1_w12F978460-B7F4-4A65-AD72-44C9D...</td>\n",
       "      <td>IXMtest_D14_s1_w5886B65E8-9B26-4BEA-98DD-F1534...</td>\n",
       "      <td>IXMtest_D14_s1_w4A581954E-41BB-42C2-999D-91231...</td>\n",
       "      <td>IXMtest_D14_s1_w32366353B-7500-4A39-8756-39EAD...</td>\n",
       "      <td>compound</td>\n",
       "      <td>BRD-K79905821-001-01-6</td>\n",
       "      <td>5.000000</td>\n",
       "      <td>H-BIOA-003-1</td>\n",
       "      <td>...</td>\n",
       "      <td>Gabazine</td>\n",
       "      <td>Biomol International Inc.</td>\n",
       "      <td>1</td>\n",
       "      <td>1.267570e+12</td>\n",
       "      <td>20586/</td>\n",
       "      <td>20586/</td>\n",
       "      <td>20586/</td>\n",
       "      <td>20586/</td>\n",
       "      <td>20586/</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4195</th>\n",
       "      <td>4196</td>\n",
       "      <td>IXMtest_D14_s2_w236194DAE-70DA-4769-8A35-04199...</td>\n",
       "      <td>IXMtest_D14_s2_w141CECDA9-5A06-42CF-9DF6-CC5A8...</td>\n",
       "      <td>IXMtest_D14_s2_w555A0CE74-2554-41FD-8F09-97892...</td>\n",
       "      <td>IXMtest_D14_s2_w414ECB73E-8AA0-41FE-9FEA-D9AC1...</td>\n",
       "      <td>IXMtest_D14_s2_w387508B7F-F087-4186-AB8B-9E493...</td>\n",
       "      <td>compound</td>\n",
       "      <td>BRD-K79905821-001-01-6</td>\n",
       "      <td>5.000000</td>\n",
       "      <td>H-BIOA-003-1</td>\n",
       "      <td>...</td>\n",
       "      <td>Gabazine</td>\n",
       "      <td>Biomol International Inc.</td>\n",
       "      <td>2</td>\n",
       "      <td>1.267570e+12</td>\n",
       "      <td>20586/</td>\n",
       "      <td>20586/</td>\n",
       "      <td>20586/</td>\n",
       "      <td>20586/</td>\n",
       "      <td>20586/</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4196</th>\n",
       "      <td>4197</td>\n",
       "      <td>IXMtest_D14_s3_w2F44F7D4D-8FA3-4A2B-AA66-DD476...</td>\n",
       "      <td>IXMtest_D14_s3_w191EE929D-654B-4C99-8A0F-3F324...</td>\n",
       "      <td>IXMtest_D14_s3_w539399806-E7F8-4A29-B604-04AF2...</td>\n",
       "      <td>IXMtest_D14_s3_w4A1B5B202-7323-490B-8074-277FE...</td>\n",
       "      <td>IXMtest_D14_s3_w3345CAD66-B1FE-4D98-A6F7-1CEFD...</td>\n",
       "      <td>compound</td>\n",
       "      <td>BRD-K79905821-001-01-6</td>\n",
       "      <td>5.000000</td>\n",
       "      <td>H-BIOA-003-1</td>\n",
       "      <td>...</td>\n",
       "      <td>Gabazine</td>\n",
       "      <td>Biomol International Inc.</td>\n",
       "      <td>3</td>\n",
       "      <td>1.267570e+12</td>\n",
       "      <td>20586/</td>\n",
       "      <td>20586/</td>\n",
       "      <td>20586/</td>\n",
       "      <td>20586/</td>\n",
       "      <td>20586/</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4197</th>\n",
       "      <td>4198</td>\n",
       "      <td>IXMtest_D14_s4_w255BC67E4-B89E-4491-B11E-FCCEA...</td>\n",
       "      <td>IXMtest_D14_s4_w1CE02AEAB-E014-4033-9F97-EF3D4...</td>\n",
       "      <td>IXMtest_D14_s4_w532D34840-81B1-4B6C-AC5F-86A4C...</td>\n",
       "      <td>IXMtest_D14_s4_w4703401C2-49D5-4ACE-B185-4C058...</td>\n",
       "      <td>IXMtest_D14_s4_w3807D770C-80F0-4A17-9310-B7176...</td>\n",
       "      <td>compound</td>\n",
       "      <td>BRD-K79905821-001-01-6</td>\n",
       "      <td>5.000000</td>\n",
       "      <td>H-BIOA-003-1</td>\n",
       "      <td>...</td>\n",
       "      <td>Gabazine</td>\n",
       "      <td>Biomol International Inc.</td>\n",
       "      <td>4</td>\n",
       "      <td>1.267570e+12</td>\n",
       "      <td>20586/</td>\n",
       "      <td>20586/</td>\n",
       "      <td>20586/</td>\n",
       "      <td>20586/</td>\n",
       "      <td>20586/</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4198</th>\n",
       "      <td>4199</td>\n",
       "      <td>IXMtest_D14_s5_w2C6CB5AD0-FABD-4AF0-8B60-F0B3B...</td>\n",
       "      <td>IXMtest_D14_s5_w110875F57-3FD2-4F97-8A15-EEC9E...</td>\n",
       "      <td>IXMtest_D14_s5_w5ADC816D6-656A-42B7-B6C0-0DFFC...</td>\n",
       "      <td>IXMtest_D14_s5_w4D38124D8-DA3E-43F9-AFA3-2BE59...</td>\n",
       "      <td>IXMtest_D14_s5_w3EE367BFF-AE68-4FAC-A6E6-46FAA...</td>\n",
       "      <td>compound</td>\n",
       "      <td>BRD-K79905821-001-01-6</td>\n",
       "      <td>5.000000</td>\n",
       "      <td>H-BIOA-003-1</td>\n",
       "      <td>...</td>\n",
       "      <td>Gabazine</td>\n",
       "      <td>Biomol International Inc.</td>\n",
       "      <td>5</td>\n",
       "      <td>1.267570e+12</td>\n",
       "      <td>20586/</td>\n",
       "      <td>20586/</td>\n",
       "      <td>20586/</td>\n",
       "      <td>20586/</td>\n",
       "      <td>20586/</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4199</th>\n",
       "      <td>4200</td>\n",
       "      <td>IXMtest_D14_s6_w2065C6DE4-7737-4271-B77F-BF1D5...</td>\n",
       "      <td>IXMtest_D14_s6_w11E8295C2-6FB1-4F2B-97AE-A22A7...</td>\n",
       "      <td>IXMtest_D14_s6_w5E627B00C-54A0-4611-B7F7-ACA10...</td>\n",
       "      <td>IXMtest_D14_s6_w4B39BBA41-9CDC-4508-A16E-B0429...</td>\n",
       "      <td>IXMtest_D14_s6_w3EAE55115-EC24-408E-9255-FB4A6...</td>\n",
       "      <td>compound</td>\n",
       "      <td>BRD-K79905821-001-01-6</td>\n",
       "      <td>5.000000</td>\n",
       "      <td>H-BIOA-003-1</td>\n",
       "      <td>...</td>\n",
       "      <td>Gabazine</td>\n",
       "      <td>Biomol International Inc.</td>\n",
       "      <td>6</td>\n",
       "      <td>1.267570e+12</td>\n",
       "      <td>20586/</td>\n",
       "      <td>20586/</td>\n",
       "      <td>20586/</td>\n",
       "      <td>20586/</td>\n",
       "      <td>20586/</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4200</th>\n",
       "      <td>4201</td>\n",
       "      <td>IXMtest_D14_s7_w2616EE522-D61A-4773-B5F8-A678F...</td>\n",
       "      <td>IXMtest_D14_s7_w1A6716324-AE58-4585-975F-CF587...</td>\n",
       "      <td>IXMtest_D14_s7_w505211AC8-5229-46DB-9067-D6943...</td>\n",
       "      <td>IXMtest_D14_s7_w41A25E2FE-975B-4204-9172-4BF00...</td>\n",
       "      <td>IXMtest_D14_s7_w36C760DDA-0715-4243-93DB-53BCD...</td>\n",
       "      <td>compound</td>\n",
       "      <td>BRD-K79905821-001-01-6</td>\n",
       "      <td>5.000000</td>\n",
       "      <td>H-BIOA-003-1</td>\n",
       "      <td>...</td>\n",
       "      <td>Gabazine</td>\n",
       "      <td>Biomol International Inc.</td>\n",
       "      <td>7</td>\n",
       "      <td>1.267570e+12</td>\n",
       "      <td>20586/</td>\n",
       "      <td>20586/</td>\n",
       "      <td>20586/</td>\n",
       "      <td>20586/</td>\n",
       "      <td>20586/</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4201</th>\n",
       "      <td>4202</td>\n",
       "      <td>IXMtest_D14_s8_w270BA2267-733E-45D5-A0CB-61017...</td>\n",
       "      <td>IXMtest_D14_s8_w1FC44A4B1-35C8-4F5F-B46D-6055C...</td>\n",
       "      <td>IXMtest_D14_s8_w514B8B702-D565-4763-8F60-A0684...</td>\n",
       "      <td>IXMtest_D14_s8_w400FC1631-F57E-4EE9-9E54-F9242...</td>\n",
       "      <td>IXMtest_D14_s8_w3ADE3A78D-D781-42C0-A49C-C3BE8...</td>\n",
       "      <td>compound</td>\n",
       "      <td>BRD-K79905821-001-01-6</td>\n",
       "      <td>5.000000</td>\n",
       "      <td>H-BIOA-003-1</td>\n",
       "      <td>...</td>\n",
       "      <td>Gabazine</td>\n",
       "      <td>Biomol International Inc.</td>\n",
       "      <td>8</td>\n",
       "      <td>1.267570e+12</td>\n",
       "      <td>20586/</td>\n",
       "      <td>20586/</td>\n",
       "      <td>20586/</td>\n",
       "      <td>20586/</td>\n",
       "      <td>20586/</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4202</th>\n",
       "      <td>4203</td>\n",
       "      <td>IXMtest_D14_s9_w2E0E9C5BF-9541-44BA-B7AF-389E4...</td>\n",
       "      <td>IXMtest_D14_s9_w1461E6B60-1BE6-4105-880A-93FAD...</td>\n",
       "      <td>IXMtest_D14_s9_w58C8EAED5-325B-43A0-AF9E-EF8C6...</td>\n",
       "      <td>IXMtest_D14_s9_w47F0DF5C9-8F57-4F71-B113-6A05D...</td>\n",
       "      <td>IXMtest_D14_s9_w3C175E6A6-2A41-494A-B82F-AD3E2...</td>\n",
       "      <td>compound</td>\n",
       "      <td>BRD-K79905821-001-01-6</td>\n",
       "      <td>5.000000</td>\n",
       "      <td>H-BIOA-003-1</td>\n",
       "      <td>...</td>\n",
       "      <td>Gabazine</td>\n",
       "      <td>Biomol International Inc.</td>\n",
       "      <td>9</td>\n",
       "      <td>1.267570e+12</td>\n",
       "      <td>20586/</td>\n",
       "      <td>20586/</td>\n",
       "      <td>20586/</td>\n",
       "      <td>20586/</td>\n",
       "      <td>20586/</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8019</th>\n",
       "      <td>8020</td>\n",
       "      <td>IXMtest_F04_s1_w28B0CE185-B4FE-475A-B5D1-67509...</td>\n",
       "      <td>IXMtest_F04_s1_w1747DA47C-A8D7-4435-A17B-3B936...</td>\n",
       "      <td>IXMtest_F04_s1_w52D3352E9-FC10-4072-AD9B-49018...</td>\n",
       "      <td>IXMtest_F04_s1_w4ACCAED6B-7D92-49CD-846C-C8D0E...</td>\n",
       "      <td>IXMtest_F04_s1_w321AF6479-6747-4B0D-91BB-5F47E...</td>\n",
       "      <td>compound</td>\n",
       "      <td>BRD-K93280214-004-02-3</td>\n",
       "      <td>2.708312</td>\n",
       "      <td>H-BIOA-004-1</td>\n",
       "      <td>...</td>\n",
       "      <td>Gabazine</td>\n",
       "      <td>Prestwick Chemical Inc.</td>\n",
       "      <td>1</td>\n",
       "      <td>1.267580e+12</td>\n",
       "      <td>20589/</td>\n",
       "      <td>20589/</td>\n",
       "      <td>20589/</td>\n",
       "      <td>20589/</td>\n",
       "      <td>20589/</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>10 rows × 23 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "      ImageNumber                              Image_FileName_OrigER  \\\n",
       "4194         4195  IXMtest_D14_s1_w205B05914-92D1-4E66-BF35-812B3...   \n",
       "4195         4196  IXMtest_D14_s2_w236194DAE-70DA-4769-8A35-04199...   \n",
       "4196         4197  IXMtest_D14_s3_w2F44F7D4D-8FA3-4A2B-AA66-DD476...   \n",
       "4197         4198  IXMtest_D14_s4_w255BC67E4-B89E-4491-B11E-FCCEA...   \n",
       "4198         4199  IXMtest_D14_s5_w2C6CB5AD0-FABD-4AF0-8B60-F0B3B...   \n",
       "4199         4200  IXMtest_D14_s6_w2065C6DE4-7737-4271-B77F-BF1D5...   \n",
       "4200         4201  IXMtest_D14_s7_w2616EE522-D61A-4773-B5F8-A678F...   \n",
       "4201         4202  IXMtest_D14_s8_w270BA2267-733E-45D5-A0CB-61017...   \n",
       "4202         4203  IXMtest_D14_s9_w2E0E9C5BF-9541-44BA-B7AF-389E4...   \n",
       "8019         8020  IXMtest_F04_s1_w28B0CE185-B4FE-475A-B5D1-67509...   \n",
       "\n",
       "                             Image_FileName_OrigHoechst  \\\n",
       "4194  IXMtest_D14_s1_w12F978460-B7F4-4A65-AD72-44C9D...   \n",
       "4195  IXMtest_D14_s2_w141CECDA9-5A06-42CF-9DF6-CC5A8...   \n",
       "4196  IXMtest_D14_s3_w191EE929D-654B-4C99-8A0F-3F324...   \n",
       "4197  IXMtest_D14_s4_w1CE02AEAB-E014-4033-9F97-EF3D4...   \n",
       "4198  IXMtest_D14_s5_w110875F57-3FD2-4F97-8A15-EEC9E...   \n",
       "4199  IXMtest_D14_s6_w11E8295C2-6FB1-4F2B-97AE-A22A7...   \n",
       "4200  IXMtest_D14_s7_w1A6716324-AE58-4585-975F-CF587...   \n",
       "4201  IXMtest_D14_s8_w1FC44A4B1-35C8-4F5F-B46D-6055C...   \n",
       "4202  IXMtest_D14_s9_w1461E6B60-1BE6-4105-880A-93FAD...   \n",
       "8019  IXMtest_F04_s1_w1747DA47C-A8D7-4435-A17B-3B936...   \n",
       "\n",
       "                                Image_FileName_OrigMito  \\\n",
       "4194  IXMtest_D14_s1_w5886B65E8-9B26-4BEA-98DD-F1534...   \n",
       "4195  IXMtest_D14_s2_w555A0CE74-2554-41FD-8F09-97892...   \n",
       "4196  IXMtest_D14_s3_w539399806-E7F8-4A29-B604-04AF2...   \n",
       "4197  IXMtest_D14_s4_w532D34840-81B1-4B6C-AC5F-86A4C...   \n",
       "4198  IXMtest_D14_s5_w5ADC816D6-656A-42B7-B6C0-0DFFC...   \n",
       "4199  IXMtest_D14_s6_w5E627B00C-54A0-4611-B7F7-ACA10...   \n",
       "4200  IXMtest_D14_s7_w505211AC8-5229-46DB-9067-D6943...   \n",
       "4201  IXMtest_D14_s8_w514B8B702-D565-4763-8F60-A0684...   \n",
       "4202  IXMtest_D14_s9_w58C8EAED5-325B-43A0-AF9E-EF8C6...   \n",
       "8019  IXMtest_F04_s1_w52D3352E9-FC10-4072-AD9B-49018...   \n",
       "\n",
       "                            Image_FileName_OrigPh_golgi  \\\n",
       "4194  IXMtest_D14_s1_w4A581954E-41BB-42C2-999D-91231...   \n",
       "4195  IXMtest_D14_s2_w414ECB73E-8AA0-41FE-9FEA-D9AC1...   \n",
       "4196  IXMtest_D14_s3_w4A1B5B202-7323-490B-8074-277FE...   \n",
       "4197  IXMtest_D14_s4_w4703401C2-49D5-4ACE-B185-4C058...   \n",
       "4198  IXMtest_D14_s5_w4D38124D8-DA3E-43F9-AFA3-2BE59...   \n",
       "4199  IXMtest_D14_s6_w4B39BBA41-9CDC-4508-A16E-B0429...   \n",
       "4200  IXMtest_D14_s7_w41A25E2FE-975B-4204-9172-4BF00...   \n",
       "4201  IXMtest_D14_s8_w400FC1631-F57E-4EE9-9E54-F9242...   \n",
       "4202  IXMtest_D14_s9_w47F0DF5C9-8F57-4F71-B113-6A05D...   \n",
       "8019  IXMtest_F04_s1_w4ACCAED6B-7D92-49CD-846C-C8D0E...   \n",
       "\n",
       "                                Image_FileName_OrigSyto  \\\n",
       "4194  IXMtest_D14_s1_w32366353B-7500-4A39-8756-39EAD...   \n",
       "4195  IXMtest_D14_s2_w387508B7F-F087-4186-AB8B-9E493...   \n",
       "4196  IXMtest_D14_s3_w3345CAD66-B1FE-4D98-A6F7-1CEFD...   \n",
       "4197  IXMtest_D14_s4_w3807D770C-80F0-4A17-9310-B7176...   \n",
       "4198  IXMtest_D14_s5_w3EE367BFF-AE68-4FAC-A6E6-46FAA...   \n",
       "4199  IXMtest_D14_s6_w3EAE55115-EC24-408E-9255-FB4A6...   \n",
       "4200  IXMtest_D14_s7_w36C760DDA-0715-4243-93DB-53BCD...   \n",
       "4201  IXMtest_D14_s8_w3ADE3A78D-D781-42C0-A49C-C3BE8...   \n",
       "4202  IXMtest_D14_s9_w3C175E6A6-2A41-494A-B82F-AD3E2...   \n",
       "8019  IXMtest_F04_s1_w321AF6479-6747-4B0D-91BB-5F47E...   \n",
       "\n",
       "     Image_Metadata_ASSAY_WELL_ROLE Image_Metadata_BROAD_ID  \\\n",
       "4194                       compound  BRD-K79905821-001-01-6   \n",
       "4195                       compound  BRD-K79905821-001-01-6   \n",
       "4196                       compound  BRD-K79905821-001-01-6   \n",
       "4197                       compound  BRD-K79905821-001-01-6   \n",
       "4198                       compound  BRD-K79905821-001-01-6   \n",
       "4199                       compound  BRD-K79905821-001-01-6   \n",
       "4200                       compound  BRD-K79905821-001-01-6   \n",
       "4201                       compound  BRD-K79905821-001-01-6   \n",
       "4202                       compound  BRD-K79905821-001-01-6   \n",
       "8019                       compound  BRD-K93280214-004-02-3   \n",
       "\n",
       "      Image_Metadata_CPD_MMOL_CONC Image_Metadata_CPD_PLATE_MAP_NAME   ...    \\\n",
       "4194                      5.000000                      H-BIOA-003-1   ...     \n",
       "4195                      5.000000                      H-BIOA-003-1   ...     \n",
       "4196                      5.000000                      H-BIOA-003-1   ...     \n",
       "4197                      5.000000                      H-BIOA-003-1   ...     \n",
       "4198                      5.000000                      H-BIOA-003-1   ...     \n",
       "4199                      5.000000                      H-BIOA-003-1   ...     \n",
       "4200                      5.000000                      H-BIOA-003-1   ...     \n",
       "4201                      5.000000                      H-BIOA-003-1   ...     \n",
       "4202                      5.000000                      H-BIOA-003-1   ...     \n",
       "8019                      2.708312                      H-BIOA-004-1   ...     \n",
       "\n",
       "     Image_Metadata_SOURCE_COMPOUND_NAME Image_Metadata_SOURCE_NAME  \\\n",
       "4194                            Gabazine  Biomol International Inc.   \n",
       "4195                            Gabazine  Biomol International Inc.   \n",
       "4196                            Gabazine  Biomol International Inc.   \n",
       "4197                            Gabazine  Biomol International Inc.   \n",
       "4198                            Gabazine  Biomol International Inc.   \n",
       "4199                            Gabazine  Biomol International Inc.   \n",
       "4200                            Gabazine  Biomol International Inc.   \n",
       "4201                            Gabazine  Biomol International Inc.   \n",
       "4202                            Gabazine  Biomol International Inc.   \n",
       "8019                            Gabazine    Prestwick Chemical Inc.   \n",
       "\n",
       "      Image_Metadata_Site Image_Metadata_Time Image_PathName_OrigER  \\\n",
       "4194                    1        1.267570e+12                20586/   \n",
       "4195                    2        1.267570e+12                20586/   \n",
       "4196                    3        1.267570e+12                20586/   \n",
       "4197                    4        1.267570e+12                20586/   \n",
       "4198                    5        1.267570e+12                20586/   \n",
       "4199                    6        1.267570e+12                20586/   \n",
       "4200                    7        1.267570e+12                20586/   \n",
       "4201                    8        1.267570e+12                20586/   \n",
       "4202                    9        1.267570e+12                20586/   \n",
       "8019                    1        1.267580e+12                20589/   \n",
       "\n",
       "     Image_PathName_OrigHoechst  Image_PathName_OrigMito  \\\n",
       "4194                     20586/                   20586/   \n",
       "4195                     20586/                   20586/   \n",
       "4196                     20586/                   20586/   \n",
       "4197                     20586/                   20586/   \n",
       "4198                     20586/                   20586/   \n",
       "4199                     20586/                   20586/   \n",
       "4200                     20586/                   20586/   \n",
       "4201                     20586/                   20586/   \n",
       "4202                     20586/                   20586/   \n",
       "8019                     20589/                   20589/   \n",
       "\n",
       "     Image_PathName_OrigPh_golgi Image_PathName_OrigSyto IXMtest  \n",
       "4194                      20586/                  20586/     NaN  \n",
       "4195                      20586/                  20586/     NaN  \n",
       "4196                      20586/                  20586/     NaN  \n",
       "4197                      20586/                  20586/     NaN  \n",
       "4198                      20586/                  20586/     NaN  \n",
       "4199                      20586/                  20586/     NaN  \n",
       "4200                      20586/                  20586/     NaN  \n",
       "4201                      20586/                  20586/     NaN  \n",
       "4202                      20586/                  20586/     NaN  \n",
       "8019                      20589/                  20589/     NaN  \n",
       "\n",
       "[10 rows x 23 columns]"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "compounds = ['Gabazine', 'CYCLOPIAZONIC ACID', \n",
    "             'ESTRADIOL', 'DMSO', \n",
    "             'Proglumide', 'PIZOTIFEN', \n",
    "             'CATECHIN PENTABENZOATE', 'TRIADIMEFON',\n",
    "             '3-HYDROXYCOUMARIN', 'Etoposide',\n",
    "             'DACTINOMYCIN', 'Colchicine',\n",
    "             'Blebbistatin']\n",
    "\n",
    "\n",
    "compound = compounds[0]\n",
    "if compound == 'DMSO':\n",
    "    codf1 = df[df.Image_Metadata_ASSAY_WELL_ROLE == 'mock']\n",
    "    \n",
    "    for ind, plate in enumerate(plates) :\n",
    "        codf2 = codf1[codf1.Image_PathName_OrigHoechst == plate]\n",
    "        l = len(codf2)\n",
    "        rows = range(50)\n",
    "        codf2 = codf2.iloc[rows]\n",
    "        \n",
    "        if ind == 0:\n",
    "            indicies = list(codf2.index)\n",
    "            continue\n",
    "            \n",
    "        indicies += list(codf2.index)\n",
    "        codf = codf1.loc[indicies]\n",
    "    \n",
    "else:\n",
    "    codf = df[df.Image_Metadata_SOURCE_COMPOUND_NAME.str.lower() == compound.lower()]\n",
    "\n",
    "codf.head(10)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "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>Image_FileName_OrigHoechst</th>\n",
       "      <th>Image_PathName_OrigHoechst</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>4194</th>\n",
       "      <td>IXMtest_D14_s1_w12F978460-B7F4-4A65-AD72-44C9D...</td>\n",
       "      <td>20586/</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4195</th>\n",
       "      <td>IXMtest_D14_s2_w141CECDA9-5A06-42CF-9DF6-CC5A8...</td>\n",
       "      <td>20586/</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4196</th>\n",
       "      <td>IXMtest_D14_s3_w191EE929D-654B-4C99-8A0F-3F324...</td>\n",
       "      <td>20586/</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4197</th>\n",
       "      <td>IXMtest_D14_s4_w1CE02AEAB-E014-4033-9F97-EF3D4...</td>\n",
       "      <td>20586/</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4198</th>\n",
       "      <td>IXMtest_D14_s5_w110875F57-3FD2-4F97-8A15-EEC9E...</td>\n",
       "      <td>20586/</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4199</th>\n",
       "      <td>IXMtest_D14_s6_w11E8295C2-6FB1-4F2B-97AE-A22A7...</td>\n",
       "      <td>20586/</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4200</th>\n",
       "      <td>IXMtest_D14_s7_w1A6716324-AE58-4585-975F-CF587...</td>\n",
       "      <td>20586/</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4201</th>\n",
       "      <td>IXMtest_D14_s8_w1FC44A4B1-35C8-4F5F-B46D-6055C...</td>\n",
       "      <td>20586/</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4202</th>\n",
       "      <td>IXMtest_D14_s9_w1461E6B60-1BE6-4105-880A-93FAD...</td>\n",
       "      <td>20586/</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8019</th>\n",
       "      <td>IXMtest_F04_s1_w1747DA47C-A8D7-4435-A17B-3B936...</td>\n",
       "      <td>20589/</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8020</th>\n",
       "      <td>IXMtest_F04_s2_w10201BAB2-89E5-4FE0-83D3-BD7EA...</td>\n",
       "      <td>20589/</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8021</th>\n",
       "      <td>IXMtest_F04_s3_w1A8B037B6-C37D-427D-978F-AF8D9...</td>\n",
       "      <td>20589/</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8022</th>\n",
       "      <td>IXMtest_F04_s4_w14DAC099F-1F8D-47C7-AD97-38B47...</td>\n",
       "      <td>20589/</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8023</th>\n",
       "      <td>IXMtest_F04_s5_w1F60F68FA-DAB0-4E4C-A49F-30C7B...</td>\n",
       "      <td>20589/</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8024</th>\n",
       "      <td>IXMtest_F04_s6_w1CE907BF9-ACB4-4DB5-BBDF-79E82...</td>\n",
       "      <td>20589/</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8025</th>\n",
       "      <td>IXMtest_F04_s7_w17263C8F1-274A-4EDF-959C-6A404...</td>\n",
       "      <td>20589/</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8026</th>\n",
       "      <td>IXMtest_F04_s8_w16B1736BC-5BBD-4397-AE94-B8375...</td>\n",
       "      <td>20589/</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8027</th>\n",
       "      <td>IXMtest_F04_s9_w1D32670CD-6ED3-4A0C-AA76-40F36...</td>\n",
       "      <td>20589/</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>21501</th>\n",
       "      <td>IXMtest_D14_s1_w1512BAD45-1E60-4AE4-AD14-A27A2...</td>\n",
       "      <td>20593/</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>21502</th>\n",
       "      <td>IXMtest_D14_s2_w14E73B4BE-D4CF-4F69-91CD-01978...</td>\n",
       "      <td>20593/</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>21503</th>\n",
       "      <td>IXMtest_D14_s3_w15F807DA3-AB87-4CEB-91D2-07E64...</td>\n",
       "      <td>20593/</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>21504</th>\n",
       "      <td>IXMtest_D14_s4_w1C25029E2-F686-4163-80CE-B7940...</td>\n",
       "      <td>20593/</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>21505</th>\n",
       "      <td>IXMtest_D14_s5_w1A23530B9-3754-43AB-8029-61B38...</td>\n",
       "      <td>20593/</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>21506</th>\n",
       "      <td>IXMtest_D14_s6_w1E23656D9-2F4B-4193-AF3F-F3515...</td>\n",
       "      <td>20593/</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>21507</th>\n",
       "      <td>IXMtest_D14_s7_w11689E8B9-379D-4AC0-B9D1-F9333...</td>\n",
       "      <td>20593/</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>21508</th>\n",
       "      <td>IXMtest_D14_s8_w19C44A265-8EAA-4168-AE76-77606...</td>\n",
       "      <td>20593/</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>21509</th>\n",
       "      <td>IXMtest_D14_s9_w1C4B83189-2CA7-452C-B6B6-86187...</td>\n",
       "      <td>20593/</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>25299</th>\n",
       "      <td>IXMtest_F04_s1_w10CC3FCE3-A91B-4584-8A26-6C24F...</td>\n",
       "      <td>20594/</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>25300</th>\n",
       "      <td>IXMtest_F04_s2_w128C6F48B-3320-46DB-986C-37286...</td>\n",
       "      <td>20594/</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>25301</th>\n",
       "      <td>IXMtest_F04_s3_w1C0CD7839-DD8E-4167-82BC-723C4...</td>\n",
       "      <td>20594/</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>38787</th>\n",
       "      <td>IXMtest_D14_s7_w14C4C854C-B04B-4A99-8874-63FB0...</td>\n",
       "      <td>20608/</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>38788</th>\n",
       "      <td>IXMtest_D14_s8_w1BB7A43F1-8A71-4886-A2EB-BC05F...</td>\n",
       "      <td>20608/</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>38789</th>\n",
       "      <td>IXMtest_D14_s9_w11ECFCC74-1B6C-4D02-9761-17D94...</td>\n",
       "      <td>20608/</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>42579</th>\n",
       "      <td>IXMtest_F04_s1_w1FF3BA401-17ED-4855-A3AD-E8800...</td>\n",
       "      <td>20625/</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>42580</th>\n",
       "      <td>IXMtest_F04_s2_w1EF21FB51-3E40-413D-8585-4CDCF...</td>\n",
       "      <td>20625/</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>42581</th>\n",
       "      <td>IXMtest_F04_s3_w14A32D190-3130-460E-B08E-A127B...</td>\n",
       "      <td>20625/</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>42582</th>\n",
       "      <td>IXMtest_F04_s4_w152D1755D-6E2A-4F88-9A8B-346EF...</td>\n",
       "      <td>20625/</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>42583</th>\n",
       "      <td>IXMtest_F04_s5_w1C80828CC-724B-459D-8A5F-7BE11...</td>\n",
       "      <td>20625/</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>42584</th>\n",
       "      <td>IXMtest_F04_s6_w13EB649CA-087E-4594-83A8-A4303...</td>\n",
       "      <td>20625/</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>42585</th>\n",
       "      <td>IXMtest_F04_s7_w187D0B42F-7C48-4D5F-8B73-4AD01...</td>\n",
       "      <td>20625/</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>42586</th>\n",
       "      <td>IXMtest_F04_s8_w101040FE6-96BA-4CC0-9658-C45E0...</td>\n",
       "      <td>20625/</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>42587</th>\n",
       "      <td>IXMtest_F04_s9_w1F881EC09-D70A-4DC8-B073-F9120...</td>\n",
       "      <td>20625/</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>56061</th>\n",
       "      <td>IXMtest_D14_s1_w170277CB7-5995-4B29-AF9C-23D4B...</td>\n",
       "      <td>20639/</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>56062</th>\n",
       "      <td>IXMtest_D14_s2_w18F649829-D379-448C-AAC2-9191A...</td>\n",
       "      <td>20639/</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>56063</th>\n",
       "      <td>IXMtest_D14_s3_w1EF5FF1B5-A888-47CD-A16A-EAE16...</td>\n",
       "      <td>20639/</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>56064</th>\n",
       "      <td>IXMtest_D14_s4_w169755FB9-D420-495D-BA81-A7B54...</td>\n",
       "      <td>20639/</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>56065</th>\n",
       "      <td>IXMtest_D14_s5_w11D5DDA76-D483-492B-8B65-737B9...</td>\n",
       "      <td>20639/</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>56066</th>\n",
       "      <td>IXMtest_D14_s6_w1CE504357-84F2-4EF4-9D47-F21CC...</td>\n",
       "      <td>20639/</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>56067</th>\n",
       "      <td>IXMtest_D14_s7_w164F9AA05-8319-4316-B1E8-CE30A...</td>\n",
       "      <td>20639/</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>56068</th>\n",
       "      <td>IXMtest_D14_s8_w152EBED23-2A88-4615-A63E-398F4...</td>\n",
       "      <td>20639/</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>56069</th>\n",
       "      <td>IXMtest_D14_s9_w19B0D3466-1016-4A8E-8BC6-BE8BB...</td>\n",
       "      <td>20639/</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>59859</th>\n",
       "      <td>IXMtest_F04_s1_w1CD13792A-F9DD-4245-A516-BC9CF...</td>\n",
       "      <td>20640/</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>59860</th>\n",
       "      <td>IXMtest_F04_s2_w1D3E8F619-8497-415D-9B8C-FDF34...</td>\n",
       "      <td>20640/</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>59861</th>\n",
       "      <td>IXMtest_F04_s3_w1D06D063D-9688-45C8-849B-8BBE4...</td>\n",
       "      <td>20640/</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>59862</th>\n",
       "      <td>IXMtest_F04_s4_w1EDA551E9-F578-479F-9AD6-4B6C2...</td>\n",
       "      <td>20640/</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>59863</th>\n",
       "      <td>IXMtest_F04_s5_w1E3AFFCB3-6CC1-45C3-99E1-6FD8E...</td>\n",
       "      <td>20640/</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>59864</th>\n",
       "      <td>IXMtest_F04_s6_w12BAD78F1-225C-481C-80F8-6679C...</td>\n",
       "      <td>20640/</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>59865</th>\n",
       "      <td>IXMtest_F04_s7_w1DB8167FA-93EA-41DE-9B2E-D34B8...</td>\n",
       "      <td>20640/</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>59866</th>\n",
       "      <td>IXMtest_F04_s8_w172FC34A8-E906-4B33-948E-EF895...</td>\n",
       "      <td>20640/</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>59867</th>\n",
       "      <td>IXMtest_F04_s9_w18F72FCBC-56B7-4DD5-B5A4-5788A...</td>\n",
       "      <td>20640/</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>72 rows × 2 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                              Image_FileName_OrigHoechst  \\\n",
       "4194   IXMtest_D14_s1_w12F978460-B7F4-4A65-AD72-44C9D...   \n",
       "4195   IXMtest_D14_s2_w141CECDA9-5A06-42CF-9DF6-CC5A8...   \n",
       "4196   IXMtest_D14_s3_w191EE929D-654B-4C99-8A0F-3F324...   \n",
       "4197   IXMtest_D14_s4_w1CE02AEAB-E014-4033-9F97-EF3D4...   \n",
       "4198   IXMtest_D14_s5_w110875F57-3FD2-4F97-8A15-EEC9E...   \n",
       "4199   IXMtest_D14_s6_w11E8295C2-6FB1-4F2B-97AE-A22A7...   \n",
       "4200   IXMtest_D14_s7_w1A6716324-AE58-4585-975F-CF587...   \n",
       "4201   IXMtest_D14_s8_w1FC44A4B1-35C8-4F5F-B46D-6055C...   \n",
       "4202   IXMtest_D14_s9_w1461E6B60-1BE6-4105-880A-93FAD...   \n",
       "8019   IXMtest_F04_s1_w1747DA47C-A8D7-4435-A17B-3B936...   \n",
       "8020   IXMtest_F04_s2_w10201BAB2-89E5-4FE0-83D3-BD7EA...   \n",
       "8021   IXMtest_F04_s3_w1A8B037B6-C37D-427D-978F-AF8D9...   \n",
       "8022   IXMtest_F04_s4_w14DAC099F-1F8D-47C7-AD97-38B47...   \n",
       "8023   IXMtest_F04_s5_w1F60F68FA-DAB0-4E4C-A49F-30C7B...   \n",
       "8024   IXMtest_F04_s6_w1CE907BF9-ACB4-4DB5-BBDF-79E82...   \n",
       "8025   IXMtest_F04_s7_w17263C8F1-274A-4EDF-959C-6A404...   \n",
       "8026   IXMtest_F04_s8_w16B1736BC-5BBD-4397-AE94-B8375...   \n",
       "8027   IXMtest_F04_s9_w1D32670CD-6ED3-4A0C-AA76-40F36...   \n",
       "21501  IXMtest_D14_s1_w1512BAD45-1E60-4AE4-AD14-A27A2...   \n",
       "21502  IXMtest_D14_s2_w14E73B4BE-D4CF-4F69-91CD-01978...   \n",
       "21503  IXMtest_D14_s3_w15F807DA3-AB87-4CEB-91D2-07E64...   \n",
       "21504  IXMtest_D14_s4_w1C25029E2-F686-4163-80CE-B7940...   \n",
       "21505  IXMtest_D14_s5_w1A23530B9-3754-43AB-8029-61B38...   \n",
       "21506  IXMtest_D14_s6_w1E23656D9-2F4B-4193-AF3F-F3515...   \n",
       "21507  IXMtest_D14_s7_w11689E8B9-379D-4AC0-B9D1-F9333...   \n",
       "21508  IXMtest_D14_s8_w19C44A265-8EAA-4168-AE76-77606...   \n",
       "21509  IXMtest_D14_s9_w1C4B83189-2CA7-452C-B6B6-86187...   \n",
       "25299  IXMtest_F04_s1_w10CC3FCE3-A91B-4584-8A26-6C24F...   \n",
       "25300  IXMtest_F04_s2_w128C6F48B-3320-46DB-986C-37286...   \n",
       "25301  IXMtest_F04_s3_w1C0CD7839-DD8E-4167-82BC-723C4...   \n",
       "...                                                  ...   \n",
       "38787  IXMtest_D14_s7_w14C4C854C-B04B-4A99-8874-63FB0...   \n",
       "38788  IXMtest_D14_s8_w1BB7A43F1-8A71-4886-A2EB-BC05F...   \n",
       "38789  IXMtest_D14_s9_w11ECFCC74-1B6C-4D02-9761-17D94...   \n",
       "42579  IXMtest_F04_s1_w1FF3BA401-17ED-4855-A3AD-E8800...   \n",
       "42580  IXMtest_F04_s2_w1EF21FB51-3E40-413D-8585-4CDCF...   \n",
       "42581  IXMtest_F04_s3_w14A32D190-3130-460E-B08E-A127B...   \n",
       "42582  IXMtest_F04_s4_w152D1755D-6E2A-4F88-9A8B-346EF...   \n",
       "42583  IXMtest_F04_s5_w1C80828CC-724B-459D-8A5F-7BE11...   \n",
       "42584  IXMtest_F04_s6_w13EB649CA-087E-4594-83A8-A4303...   \n",
       "42585  IXMtest_F04_s7_w187D0B42F-7C48-4D5F-8B73-4AD01...   \n",
       "42586  IXMtest_F04_s8_w101040FE6-96BA-4CC0-9658-C45E0...   \n",
       "42587  IXMtest_F04_s9_w1F881EC09-D70A-4DC8-B073-F9120...   \n",
       "56061  IXMtest_D14_s1_w170277CB7-5995-4B29-AF9C-23D4B...   \n",
       "56062  IXMtest_D14_s2_w18F649829-D379-448C-AAC2-9191A...   \n",
       "56063  IXMtest_D14_s3_w1EF5FF1B5-A888-47CD-A16A-EAE16...   \n",
       "56064  IXMtest_D14_s4_w169755FB9-D420-495D-BA81-A7B54...   \n",
       "56065  IXMtest_D14_s5_w11D5DDA76-D483-492B-8B65-737B9...   \n",
       "56066  IXMtest_D14_s6_w1CE504357-84F2-4EF4-9D47-F21CC...   \n",
       "56067  IXMtest_D14_s7_w164F9AA05-8319-4316-B1E8-CE30A...   \n",
       "56068  IXMtest_D14_s8_w152EBED23-2A88-4615-A63E-398F4...   \n",
       "56069  IXMtest_D14_s9_w19B0D3466-1016-4A8E-8BC6-BE8BB...   \n",
       "59859  IXMtest_F04_s1_w1CD13792A-F9DD-4245-A516-BC9CF...   \n",
       "59860  IXMtest_F04_s2_w1D3E8F619-8497-415D-9B8C-FDF34...   \n",
       "59861  IXMtest_F04_s3_w1D06D063D-9688-45C8-849B-8BBE4...   \n",
       "59862  IXMtest_F04_s4_w1EDA551E9-F578-479F-9AD6-4B6C2...   \n",
       "59863  IXMtest_F04_s5_w1E3AFFCB3-6CC1-45C3-99E1-6FD8E...   \n",
       "59864  IXMtest_F04_s6_w12BAD78F1-225C-481C-80F8-6679C...   \n",
       "59865  IXMtest_F04_s7_w1DB8167FA-93EA-41DE-9B2E-D34B8...   \n",
       "59866  IXMtest_F04_s8_w172FC34A8-E906-4B33-948E-EF895...   \n",
       "59867  IXMtest_F04_s9_w18F72FCBC-56B7-4DD5-B5A4-5788A...   \n",
       "\n",
       "      Image_PathName_OrigHoechst  \n",
       "4194                      20586/  \n",
       "4195                      20586/  \n",
       "4196                      20586/  \n",
       "4197                      20586/  \n",
       "4198                      20586/  \n",
       "4199                      20586/  \n",
       "4200                      20586/  \n",
       "4201                      20586/  \n",
       "4202                      20586/  \n",
       "8019                      20589/  \n",
       "8020                      20589/  \n",
       "8021                      20589/  \n",
       "8022                      20589/  \n",
       "8023                      20589/  \n",
       "8024                      20589/  \n",
       "8025                      20589/  \n",
       "8026                      20589/  \n",
       "8027                      20589/  \n",
       "21501                     20593/  \n",
       "21502                     20593/  \n",
       "21503                     20593/  \n",
       "21504                     20593/  \n",
       "21505                     20593/  \n",
       "21506                     20593/  \n",
       "21507                     20593/  \n",
       "21508                     20593/  \n",
       "21509                     20593/  \n",
       "25299                     20594/  \n",
       "25300                     20594/  \n",
       "25301                     20594/  \n",
       "...                          ...  \n",
       "38787                     20608/  \n",
       "38788                     20608/  \n",
       "38789                     20608/  \n",
       "42579                     20625/  \n",
       "42580                     20625/  \n",
       "42581                     20625/  \n",
       "42582                     20625/  \n",
       "42583                     20625/  \n",
       "42584                     20625/  \n",
       "42585                     20625/  \n",
       "42586                     20625/  \n",
       "42587                     20625/  \n",
       "56061                     20639/  \n",
       "56062                     20639/  \n",
       "56063                     20639/  \n",
       "56064                     20639/  \n",
       "56065                     20639/  \n",
       "56066                     20639/  \n",
       "56067                     20639/  \n",
       "56068                     20639/  \n",
       "56069                     20639/  \n",
       "59859                     20640/  \n",
       "59860                     20640/  \n",
       "59861                     20640/  \n",
       "59862                     20640/  \n",
       "59863                     20640/  \n",
       "59864                     20640/  \n",
       "59865                     20640/  \n",
       "59866                     20640/  \n",
       "59867                     20640/  \n",
       "\n",
       "[72 rows x 2 columns]"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "coimages = codf[['Image_FileName_OrigHoechst',\n",
    "               'Image_PathName_OrigHoechst']]\n",
    "\n",
    "coimages"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "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>DNA</th>\n",
       "      <th>Done</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "Empty DataFrame\n",
       "Columns: [DNA, Done]\n",
       "Index: []"
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "image_list = pd.DataFrame(columns = ['DNA', 'Done'])\n",
    "\n",
    "image_list"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "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>DNA</th>\n",
       "      <th>Done</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>BBBC022_v1_images_20586w1/IXMtest_D14_s1_w12F9...</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>BBBC022_v1_images_20586w1/IXMtest_D14_s2_w141C...</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>BBBC022_v1_images_20586w1/IXMtest_D14_s3_w191E...</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>BBBC022_v1_images_20586w1/IXMtest_D14_s4_w1CE0...</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>BBBC022_v1_images_20586w1/IXMtest_D14_s5_w1108...</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>BBBC022_v1_images_20586w1/IXMtest_D14_s6_w11E8...</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>BBBC022_v1_images_20586w1/IXMtest_D14_s7_w1A67...</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>BBBC022_v1_images_20586w1/IXMtest_D14_s8_w1FC4...</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>BBBC022_v1_images_20586w1/IXMtest_D14_s9_w1461...</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>BBBC022_v1_images_20589w1/IXMtest_F04_s1_w1747...</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>10</th>\n",
       "      <td>BBBC022_v1_images_20589w1/IXMtest_F04_s2_w1020...</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>11</th>\n",
       "      <td>BBBC022_v1_images_20589w1/IXMtest_F04_s3_w1A8B...</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>12</th>\n",
       "      <td>BBBC022_v1_images_20589w1/IXMtest_F04_s4_w14DA...</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>13</th>\n",
       "      <td>BBBC022_v1_images_20589w1/IXMtest_F04_s5_w1F60...</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>14</th>\n",
       "      <td>BBBC022_v1_images_20589w1/IXMtest_F04_s6_w1CE9...</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>15</th>\n",
       "      <td>BBBC022_v1_images_20589w1/IXMtest_F04_s7_w1726...</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>16</th>\n",
       "      <td>BBBC022_v1_images_20589w1/IXMtest_F04_s8_w16B1...</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>17</th>\n",
       "      <td>BBBC022_v1_images_20589w1/IXMtest_F04_s9_w1D32...</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>18</th>\n",
       "      <td>BBBC022_v1_images_20593w1/IXMtest_D14_s1_w1512...</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>19</th>\n",
       "      <td>BBBC022_v1_images_20593w1/IXMtest_D14_s2_w14E7...</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>20</th>\n",
       "      <td>BBBC022_v1_images_20593w1/IXMtest_D14_s3_w15F8...</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>21</th>\n",
       "      <td>BBBC022_v1_images_20593w1/IXMtest_D14_s4_w1C25...</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>22</th>\n",
       "      <td>BBBC022_v1_images_20593w1/IXMtest_D14_s5_w1A23...</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>23</th>\n",
       "      <td>BBBC022_v1_images_20593w1/IXMtest_D14_s6_w1E23...</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>24</th>\n",
       "      <td>BBBC022_v1_images_20593w1/IXMtest_D14_s7_w1168...</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>25</th>\n",
       "      <td>BBBC022_v1_images_20593w1/IXMtest_D14_s8_w19C4...</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>26</th>\n",
       "      <td>BBBC022_v1_images_20593w1/IXMtest_D14_s9_w1C4B...</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>27</th>\n",
       "      <td>BBBC022_v1_images_20594w1/IXMtest_F04_s1_w10CC...</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>28</th>\n",
       "      <td>BBBC022_v1_images_20594w1/IXMtest_F04_s2_w128C...</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>29</th>\n",
       "      <td>BBBC022_v1_images_20594w1/IXMtest_F04_s3_w1C0C...</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>42</th>\n",
       "      <td>BBBC022_v1_images_20608w1/IXMtest_D14_s7_w14C4...</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>43</th>\n",
       "      <td>BBBC022_v1_images_20608w1/IXMtest_D14_s8_w1BB7...</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>44</th>\n",
       "      <td>BBBC022_v1_images_20608w1/IXMtest_D14_s9_w11EC...</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>45</th>\n",
       "      <td>BBBC022_v1_images_20625w1/IXMtest_F04_s1_w1FF3...</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>46</th>\n",
       "      <td>BBBC022_v1_images_20625w1/IXMtest_F04_s2_w1EF2...</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>47</th>\n",
       "      <td>BBBC022_v1_images_20625w1/IXMtest_F04_s3_w14A3...</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>48</th>\n",
       "      <td>BBBC022_v1_images_20625w1/IXMtest_F04_s4_w152D...</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>49</th>\n",
       "      <td>BBBC022_v1_images_20625w1/IXMtest_F04_s5_w1C80...</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>50</th>\n",
       "      <td>BBBC022_v1_images_20625w1/IXMtest_F04_s6_w13EB...</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>51</th>\n",
       "      <td>BBBC022_v1_images_20625w1/IXMtest_F04_s7_w187D...</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>52</th>\n",
       "      <td>BBBC022_v1_images_20625w1/IXMtest_F04_s8_w1010...</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>53</th>\n",
       "      <td>BBBC022_v1_images_20625w1/IXMtest_F04_s9_w1F88...</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>54</th>\n",
       "      <td>BBBC022_v1_images_20639w1/IXMtest_D14_s1_w1702...</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>55</th>\n",
       "      <td>BBBC022_v1_images_20639w1/IXMtest_D14_s2_w18F6...</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>56</th>\n",
       "      <td>BBBC022_v1_images_20639w1/IXMtest_D14_s3_w1EF5...</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>57</th>\n",
       "      <td>BBBC022_v1_images_20639w1/IXMtest_D14_s4_w1697...</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>58</th>\n",
       "      <td>BBBC022_v1_images_20639w1/IXMtest_D14_s5_w11D5...</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>59</th>\n",
       "      <td>BBBC022_v1_images_20639w1/IXMtest_D14_s6_w1CE5...</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>60</th>\n",
       "      <td>BBBC022_v1_images_20639w1/IXMtest_D14_s7_w164F...</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>61</th>\n",
       "      <td>BBBC022_v1_images_20639w1/IXMtest_D14_s8_w152E...</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>62</th>\n",
       "      <td>BBBC022_v1_images_20639w1/IXMtest_D14_s9_w19B0...</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>63</th>\n",
       "      <td>BBBC022_v1_images_20640w1/IXMtest_F04_s1_w1CD1...</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>64</th>\n",
       "      <td>BBBC022_v1_images_20640w1/IXMtest_F04_s2_w1D3E...</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>65</th>\n",
       "      <td>BBBC022_v1_images_20640w1/IXMtest_F04_s3_w1D06...</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>66</th>\n",
       "      <td>BBBC022_v1_images_20640w1/IXMtest_F04_s4_w1EDA...</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>67</th>\n",
       "      <td>BBBC022_v1_images_20640w1/IXMtest_F04_s5_w1E3A...</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>68</th>\n",
       "      <td>BBBC022_v1_images_20640w1/IXMtest_F04_s6_w12BA...</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>69</th>\n",
       "      <td>BBBC022_v1_images_20640w1/IXMtest_F04_s7_w1DB8...</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>70</th>\n",
       "      <td>BBBC022_v1_images_20640w1/IXMtest_F04_s8_w172F...</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>71</th>\n",
       "      <td>BBBC022_v1_images_20640w1/IXMtest_F04_s9_w18F7...</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>72 rows × 2 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                                                  DNA   Done\n",
       "0   BBBC022_v1_images_20586w1/IXMtest_D14_s1_w12F9...  False\n",
       "1   BBBC022_v1_images_20586w1/IXMtest_D14_s2_w141C...  False\n",
       "2   BBBC022_v1_images_20586w1/IXMtest_D14_s3_w191E...  False\n",
       "3   BBBC022_v1_images_20586w1/IXMtest_D14_s4_w1CE0...  False\n",
       "4   BBBC022_v1_images_20586w1/IXMtest_D14_s5_w1108...  False\n",
       "5   BBBC022_v1_images_20586w1/IXMtest_D14_s6_w11E8...  False\n",
       "6   BBBC022_v1_images_20586w1/IXMtest_D14_s7_w1A67...  False\n",
       "7   BBBC022_v1_images_20586w1/IXMtest_D14_s8_w1FC4...  False\n",
       "8   BBBC022_v1_images_20586w1/IXMtest_D14_s9_w1461...  False\n",
       "9   BBBC022_v1_images_20589w1/IXMtest_F04_s1_w1747...  False\n",
       "10  BBBC022_v1_images_20589w1/IXMtest_F04_s2_w1020...  False\n",
       "11  BBBC022_v1_images_20589w1/IXMtest_F04_s3_w1A8B...  False\n",
       "12  BBBC022_v1_images_20589w1/IXMtest_F04_s4_w14DA...  False\n",
       "13  BBBC022_v1_images_20589w1/IXMtest_F04_s5_w1F60...  False\n",
       "14  BBBC022_v1_images_20589w1/IXMtest_F04_s6_w1CE9...  False\n",
       "15  BBBC022_v1_images_20589w1/IXMtest_F04_s7_w1726...  False\n",
       "16  BBBC022_v1_images_20589w1/IXMtest_F04_s8_w16B1...  False\n",
       "17  BBBC022_v1_images_20589w1/IXMtest_F04_s9_w1D32...  False\n",
       "18  BBBC022_v1_images_20593w1/IXMtest_D14_s1_w1512...  False\n",
       "19  BBBC022_v1_images_20593w1/IXMtest_D14_s2_w14E7...  False\n",
       "20  BBBC022_v1_images_20593w1/IXMtest_D14_s3_w15F8...  False\n",
       "21  BBBC022_v1_images_20593w1/IXMtest_D14_s4_w1C25...  False\n",
       "22  BBBC022_v1_images_20593w1/IXMtest_D14_s5_w1A23...  False\n",
       "23  BBBC022_v1_images_20593w1/IXMtest_D14_s6_w1E23...  False\n",
       "24  BBBC022_v1_images_20593w1/IXMtest_D14_s7_w1168...  False\n",
       "25  BBBC022_v1_images_20593w1/IXMtest_D14_s8_w19C4...  False\n",
       "26  BBBC022_v1_images_20593w1/IXMtest_D14_s9_w1C4B...  False\n",
       "27  BBBC022_v1_images_20594w1/IXMtest_F04_s1_w10CC...  False\n",
       "28  BBBC022_v1_images_20594w1/IXMtest_F04_s2_w128C...  False\n",
       "29  BBBC022_v1_images_20594w1/IXMtest_F04_s3_w1C0C...  False\n",
       "..                                                ...    ...\n",
       "42  BBBC022_v1_images_20608w1/IXMtest_D14_s7_w14C4...  False\n",
       "43  BBBC022_v1_images_20608w1/IXMtest_D14_s8_w1BB7...  False\n",
       "44  BBBC022_v1_images_20608w1/IXMtest_D14_s9_w11EC...  False\n",
       "45  BBBC022_v1_images_20625w1/IXMtest_F04_s1_w1FF3...  False\n",
       "46  BBBC022_v1_images_20625w1/IXMtest_F04_s2_w1EF2...  False\n",
       "47  BBBC022_v1_images_20625w1/IXMtest_F04_s3_w14A3...  False\n",
       "48  BBBC022_v1_images_20625w1/IXMtest_F04_s4_w152D...  False\n",
       "49  BBBC022_v1_images_20625w1/IXMtest_F04_s5_w1C80...  False\n",
       "50  BBBC022_v1_images_20625w1/IXMtest_F04_s6_w13EB...  False\n",
       "51  BBBC022_v1_images_20625w1/IXMtest_F04_s7_w187D...  False\n",
       "52  BBBC022_v1_images_20625w1/IXMtest_F04_s8_w1010...  False\n",
       "53  BBBC022_v1_images_20625w1/IXMtest_F04_s9_w1F88...  False\n",
       "54  BBBC022_v1_images_20639w1/IXMtest_D14_s1_w1702...  False\n",
       "55  BBBC022_v1_images_20639w1/IXMtest_D14_s2_w18F6...  False\n",
       "56  BBBC022_v1_images_20639w1/IXMtest_D14_s3_w1EF5...  False\n",
       "57  BBBC022_v1_images_20639w1/IXMtest_D14_s4_w1697...  False\n",
       "58  BBBC022_v1_images_20639w1/IXMtest_D14_s5_w11D5...  False\n",
       "59  BBBC022_v1_images_20639w1/IXMtest_D14_s6_w1CE5...  False\n",
       "60  BBBC022_v1_images_20639w1/IXMtest_D14_s7_w164F...  False\n",
       "61  BBBC022_v1_images_20639w1/IXMtest_D14_s8_w152E...  False\n",
       "62  BBBC022_v1_images_20639w1/IXMtest_D14_s9_w19B0...  False\n",
       "63  BBBC022_v1_images_20640w1/IXMtest_F04_s1_w1CD1...  False\n",
       "64  BBBC022_v1_images_20640w1/IXMtest_F04_s2_w1D3E...  False\n",
       "65  BBBC022_v1_images_20640w1/IXMtest_F04_s3_w1D06...  False\n",
       "66  BBBC022_v1_images_20640w1/IXMtest_F04_s4_w1EDA...  False\n",
       "67  BBBC022_v1_images_20640w1/IXMtest_F04_s5_w1E3A...  False\n",
       "68  BBBC022_v1_images_20640w1/IXMtest_F04_s6_w12BA...  False\n",
       "69  BBBC022_v1_images_20640w1/IXMtest_F04_s7_w1DB8...  False\n",
       "70  BBBC022_v1_images_20640w1/IXMtest_F04_s8_w172F...  False\n",
       "71  BBBC022_v1_images_20640w1/IXMtest_F04_s9_w18F7...  False\n",
       "\n",
       "[72 rows x 2 columns]"
      ]
     },
     "execution_count": 9,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "for i in range(0, len(coimages.index)):\n",
    "    row = coimages.index[i]\n",
    "#     print('\"{}\"'.format(coimages.iloc[i].Image_FileName_OrigHoechst))\n",
    "    ipath = 'BBBC022_v1_images_' \n",
    "    ipath += coimages.iloc[i].Image_PathName_OrigHoechst[:-1] \n",
    "    ipath += 'w' \n",
    "    ipath += coimages.iloc[i].Image_FileName_OrigHoechst[16]\n",
    "    ipath += '/'\n",
    "    ipath += coimages.iloc[i].Image_FileName_OrigHoechst\n",
    "#     print(\"Path of index {} : {}\".format(row, ipath))\n",
    "    image_list.loc[i] = [ipath, 'False']\n",
    "    \n",
    "image_list"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Separating the images from the rest"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [],
   "source": [
    "import os\n",
    "from shutil import copyfile\n",
    "import os.path"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Directory  ./../UNET/Gabazine  already exists\n",
      "Directory  ./../UNET/Gabazine/masks  Created \n",
      "Directory  ./../UNET/Gabazine/cp  Created \n",
      "Directory  ./../CP/Gabazine  already exists\n",
      "Directory  ./../UNET/Gabazine/images  Created \n"
     ]
    }
   ],
   "source": [
    "dirName = './../UNET/' + compound\n",
    "try:\n",
    "    # Create target Directory\n",
    "    os.mkdir(dirName)\n",
    "    print(\"Directory \" , dirName ,  \" Created \") \n",
    "except FileExistsError:\n",
    "    print(\"Directory \" , dirName ,  \" already exists\")\n",
    "\n",
    "\n",
    "dirName = './../UNET/' + compound + '/masks'\n",
    "try:\n",
    "    # Create target Directory\n",
    "    os.mkdir(dirName)\n",
    "    print(\"Directory \" , dirName ,  \" Created \") \n",
    "except FileExistsError:\n",
    "    print(\"Directory \" , dirName ,  \" already exists\")\n",
    "\n",
    "dirName = './../UNET/' + compound + '/cp'\n",
    "try:\n",
    "    # Create target Directory\n",
    "    os.mkdir(dirName)\n",
    "    print(\"Directory \" , dirName ,  \" Created \") \n",
    "except FileExistsError:\n",
    "    print(\"Directory \" , dirName ,  \" already exists\")\n",
    "    \n",
    "    \n",
    "dirName = './../CP/' + compound\n",
    "try:\n",
    "    # Create target Directory\n",
    "    os.mkdir(dirName)\n",
    "    print(\"Directory \" , dirName ,  \" Created \") \n",
    "except FileExistsError:\n",
    "    print(\"Directory \" , dirName ,  \" already exists\")\n",
    "\n",
    "\n",
    "dirName = './../UNET/' + compound + '/images'\n",
    "try:\n",
    "    # Create target Directory\n",
    "    os.mkdir(dirName)\n",
    "    print(\"Directory \" , dirName ,  \" Created \") \n",
    "except FileExistsError:\n",
    "    print(\"Directory \" , dirName ,  \" already exists\")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Need to change the path below : enter the source of your images !"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "outputs": [],
   "source": [
    "for i in range(0, len(image_list)):\n",
    "    \n",
    "    # This path should be the source of the BBBC dataset (not the images, the different folders)\n",
    "    src = './../../DSBPaper/code/unet4nuclei/data/' + image_list.DNA.iloc[i]\n",
    "    \n",
    "    \n",
    "    dst = dirName + '/' + image_list.DNA.iloc[i][:25] + image_list.DNA.iloc[i][26:]\n",
    "    if not(os.path.isfile(dst)):\n",
    "        copyfile(src, dst)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "                                                  DNA   Done\n",
      "0   /BBBC022_v1_images_20586w1IXMtest_D14_s1_w12F9...  False\n",
      "1   /BBBC022_v1_images_20586w1IXMtest_D14_s2_w141C...  False\n",
      "2   /BBBC022_v1_images_20586w1IXMtest_D14_s3_w191E...  False\n",
      "3   /BBBC022_v1_images_20586w1IXMtest_D14_s4_w1CE0...  False\n",
      "4   /BBBC022_v1_images_20586w1IXMtest_D14_s5_w1108...  False\n",
      "5   /BBBC022_v1_images_20586w1IXMtest_D14_s6_w11E8...  False\n",
      "6   /BBBC022_v1_images_20586w1IXMtest_D14_s7_w1A67...  False\n",
      "7   /BBBC022_v1_images_20586w1IXMtest_D14_s8_w1FC4...  False\n",
      "8   /BBBC022_v1_images_20586w1IXMtest_D14_s9_w1461...  False\n",
      "9   /BBBC022_v1_images_20589w1IXMtest_F04_s1_w1747...  False\n",
      "10  /BBBC022_v1_images_20589w1IXMtest_F04_s2_w1020...  False\n",
      "11  /BBBC022_v1_images_20589w1IXMtest_F04_s3_w1A8B...  False\n",
      "12  /BBBC022_v1_images_20589w1IXMtest_F04_s4_w14DA...  False\n",
      "13  /BBBC022_v1_images_20589w1IXMtest_F04_s5_w1F60...  False\n",
      "14  /BBBC022_v1_images_20589w1IXMtest_F04_s6_w1CE9...  False\n",
      "15  /BBBC022_v1_images_20589w1IXMtest_F04_s7_w1726...  False\n",
      "16  /BBBC022_v1_images_20589w1IXMtest_F04_s8_w16B1...  False\n",
      "17  /BBBC022_v1_images_20589w1IXMtest_F04_s9_w1D32...  False\n",
      "18  /BBBC022_v1_images_20593w1IXMtest_D14_s1_w1512...  False\n",
      "19  /BBBC022_v1_images_20593w1IXMtest_D14_s2_w14E7...  False\n",
      "20  /BBBC022_v1_images_20593w1IXMtest_D14_s3_w15F8...  False\n",
      "21  /BBBC022_v1_images_20593w1IXMtest_D14_s4_w1C25...  False\n",
      "22  /BBBC022_v1_images_20593w1IXMtest_D14_s5_w1A23...  False\n",
      "23  /BBBC022_v1_images_20593w1IXMtest_D14_s6_w1E23...  False\n",
      "24  /BBBC022_v1_images_20593w1IXMtest_D14_s7_w1168...  False\n",
      "25  /BBBC022_v1_images_20593w1IXMtest_D14_s8_w19C4...  False\n",
      "26  /BBBC022_v1_images_20593w1IXMtest_D14_s9_w1C4B...  False\n",
      "27  /BBBC022_v1_images_20594w1IXMtest_F04_s1_w10CC...  False\n",
      "28  /BBBC022_v1_images_20594w1IXMtest_F04_s2_w128C...  False\n",
      "29  /BBBC022_v1_images_20594w1IXMtest_F04_s3_w1C0C...  False\n",
      "..                                                ...    ...\n",
      "42  /BBBC022_v1_images_20608w1IXMtest_D14_s7_w14C4...  False\n",
      "43  /BBBC022_v1_images_20608w1IXMtest_D14_s8_w1BB7...  False\n",
      "44  /BBBC022_v1_images_20608w1IXMtest_D14_s9_w11EC...  False\n",
      "45  /BBBC022_v1_images_20625w1IXMtest_F04_s1_w1FF3...  False\n",
      "46  /BBBC022_v1_images_20625w1IXMtest_F04_s2_w1EF2...  False\n",
      "47  /BBBC022_v1_images_20625w1IXMtest_F04_s3_w14A3...  False\n",
      "48  /BBBC022_v1_images_20625w1IXMtest_F04_s4_w152D...  False\n",
      "49  /BBBC022_v1_images_20625w1IXMtest_F04_s5_w1C80...  False\n",
      "50  /BBBC022_v1_images_20625w1IXMtest_F04_s6_w13EB...  False\n",
      "51  /BBBC022_v1_images_20625w1IXMtest_F04_s7_w187D...  False\n",
      "52  /BBBC022_v1_images_20625w1IXMtest_F04_s8_w1010...  False\n",
      "53  /BBBC022_v1_images_20625w1IXMtest_F04_s9_w1F88...  False\n",
      "54  /BBBC022_v1_images_20639w1IXMtest_D14_s1_w1702...  False\n",
      "55  /BBBC022_v1_images_20639w1IXMtest_D14_s2_w18F6...  False\n",
      "56  /BBBC022_v1_images_20639w1IXMtest_D14_s3_w1EF5...  False\n",
      "57  /BBBC022_v1_images_20639w1IXMtest_D14_s4_w1697...  False\n",
      "58  /BBBC022_v1_images_20639w1IXMtest_D14_s5_w11D5...  False\n",
      "59  /BBBC022_v1_images_20639w1IXMtest_D14_s6_w1CE5...  False\n",
      "60  /BBBC022_v1_images_20639w1IXMtest_D14_s7_w164F...  False\n",
      "61  /BBBC022_v1_images_20639w1IXMtest_D14_s8_w152E...  False\n",
      "62  /BBBC022_v1_images_20639w1IXMtest_D14_s9_w19B0...  False\n",
      "63  /BBBC022_v1_images_20640w1IXMtest_F04_s1_w1CD1...  False\n",
      "64  /BBBC022_v1_images_20640w1IXMtest_F04_s2_w1D3E...  False\n",
      "65  /BBBC022_v1_images_20640w1IXMtest_F04_s3_w1D06...  False\n",
      "66  /BBBC022_v1_images_20640w1IXMtest_F04_s4_w1EDA...  False\n",
      "67  /BBBC022_v1_images_20640w1IXMtest_F04_s5_w1E3A...  False\n",
      "68  /BBBC022_v1_images_20640w1IXMtest_F04_s6_w12BA...  False\n",
      "69  /BBBC022_v1_images_20640w1IXMtest_F04_s7_w1DB8...  False\n",
      "70  /BBBC022_v1_images_20640w1IXMtest_F04_s8_w172F...  False\n",
      "71  /BBBC022_v1_images_20640w1IXMtest_F04_s9_w18F7...  False\n",
      "\n",
      "[72 rows x 2 columns]\n"
     ]
    }
   ],
   "source": [
    "for i in range(0, len(image_list)):\n",
    "    image_list.DNA.iloc[i] = '/' + image_list.DNA.iloc[i][:25] + image_list.DNA.iloc[i][26:]\n",
    "\n",
    "fname = compound + '_image_list.csv'\n",
    "image_list.to_csv(fname)\n",
    "print(image_list)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "array(['False'], dtype=object)"
      ]
     },
     "execution_count": 15,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "numpy.unique(image_list.Done.values)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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