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jmuhlich/screen data processing.ipynb

Last active May 26, 2017 19:08
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Explore some snippets of code from the ramm_screening_data_processing project.
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screen data processing.ipynb
{
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Exploring the screening data processing script\n",
"This notebook explores some snippets of code from the ramm_screening_data_processing project."
]
},
{
"cell_type": "code",
"execution_count": 1,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"import pathlib\n",
"from collections import OrderedDict\n",
"import itertools\n",
"import pandas as pd"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Set up input and output paths"
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {
"collapsed": false
},
"outputs": [],
"source": [
"PROJECT_NAME = '20170516_hptec_oat1_two_panel'\n",
"project_path = pathlib.Path('/Users/jmuhlich/development/ramm_screening_data_processing')"
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {
"collapsed": false
},
"outputs": [],
"source": [
"input_path = project_path.joinpath('input', PROJECT_NAME)\n",
"output_path = project_path.joinpath('output', PROJECT_NAME)\n",
"assert input_path.exists(), \"input path doesn't exist\"\n",
"output_path.mkdir(exist_ok=True)\n"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Synthesize plate-level experimental design"
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"exp_meta_table_1 = OrderedDict((\n",
" ('CellType', ('HPTEC', 'OAT1')),\n",
" ('BiologicalReplicate', (1, 2, 3)),\n",
" ('TimePointHours', (0, 6, 12, 24, 48, 72)),\n",
"))\n"
]
},
{
"cell_type": "code",
"execution_count": 5,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"exp_meta_table_2 = OrderedDict((\n",
" ('CellType', ('OAT1',)),\n",
" ('BiologicalReplicate', exp_meta_table_1['BiologicalReplicate']),\n",
" ('TimePointHours', (18,)),\n",
"))\n"
]
},
{
"cell_type": "code",
"execution_count": 6,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/plain": [
"odict_values([('HPTEC', 'OAT1'), (1, 2, 3), (0, 6, 12, 24, 48, 72)])"
]
},
"execution_count": 6,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"exp_meta_table_1.values()"
]
},
{
"cell_type": "code",
"execution_count": 7,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"exp_metadata = sorted(\n",
" list(itertools.product(*exp_meta_table_1.values()))\n",
" + list(itertools.product(*exp_meta_table_2.values()))\n",
")"
]
},
{
"cell_type": "code",
"execution_count": 8,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/plain": [
"[('HPTEC', 1, 0),\n",
" ('HPTEC', 1, 6),\n",
" ('HPTEC', 1, 12),\n",
" ('HPTEC', 1, 24),\n",
" ('HPTEC', 1, 48),\n",
" ('HPTEC', 1, 72),\n",
" ('HPTEC', 2, 0),\n",
" ('HPTEC', 2, 6),\n",
" ('HPTEC', 2, 12),\n",
" ('HPTEC', 2, 24),\n",
" ('HPTEC', 2, 48),\n",
" ('HPTEC', 2, 72),\n",
" ('HPTEC', 3, 0),\n",
" ('HPTEC', 3, 6),\n",
" ('HPTEC', 3, 12),\n",
" ('HPTEC', 3, 24),\n",
" ('HPTEC', 3, 48),\n",
" ('HPTEC', 3, 72),\n",
" ('OAT1', 1, 0),\n",
" ('OAT1', 1, 6),\n",
" ('OAT1', 1, 12),\n",
" ('OAT1', 1, 18),\n",
" ('OAT1', 1, 24),\n",
" ('OAT1', 1, 48),\n",
" ('OAT1', 1, 72),\n",
" ('OAT1', 2, 0),\n",
" ('OAT1', 2, 6),\n",
" ('OAT1', 2, 12),\n",
" ('OAT1', 2, 18),\n",
" ('OAT1', 2, 24),\n",
" ('OAT1', 2, 48),\n",
" ('OAT1', 2, 72),\n",
" ('OAT1', 3, 0),\n",
" ('OAT1', 3, 6),\n",
" ('OAT1', 3, 12),\n",
" ('OAT1', 3, 18),\n",
" ('OAT1', 3, 24),\n",
" ('OAT1', 3, 48),\n",
" ('OAT1', 3, 72)]"
]
},
"execution_count": 8,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"exp_metadata"
]
},
{
"cell_type": "code",
"execution_count": 9,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/html": [
"<div>\n",
"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
" <th>CellType</th>\n",
" <th>BiologicalReplicate</th>\n",
" <th>TimePointHours</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
" <td>HPTEC</td>\n",
" <td>1</td>\n",
" <td>0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
" <td>HPTEC</td>\n",
" <td>1</td>\n",
" <td>6</td>\n",
" </tr>\n",
" <tr>\n",
" <th>2</th>\n",
" <td>HPTEC</td>\n",
" <td>1</td>\n",
" <td>12</td>\n",
" </tr>\n",
" <tr>\n",
" <th>3</th>\n",
" <td>HPTEC</td>\n",
" <td>1</td>\n",
" <td>24</td>\n",
" </tr>\n",
" <tr>\n",
" <th>4</th>\n",
" <td>HPTEC</td>\n",
" <td>1</td>\n",
" <td>48</td>\n",
" </tr>\n",
" <tr>\n",
" <th>5</th>\n",
" <td>HPTEC</td>\n",
" <td>1</td>\n",
" <td>72</td>\n",
" </tr>\n",
" <tr>\n",
" <th>6</th>\n",
" <td>HPTEC</td>\n",
" <td>2</td>\n",
" <td>0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>7</th>\n",
" <td>HPTEC</td>\n",
" <td>2</td>\n",
" <td>6</td>\n",
" </tr>\n",
" <tr>\n",
" <th>8</th>\n",
" <td>HPTEC</td>\n",
" <td>2</td>\n",
" <td>12</td>\n",
" </tr>\n",
" <tr>\n",
" <th>9</th>\n",
" <td>HPTEC</td>\n",
" <td>2</td>\n",
" <td>24</td>\n",
" </tr>\n",
" <tr>\n",
" <th>10</th>\n",
" <td>HPTEC</td>\n",
" <td>2</td>\n",
" <td>48</td>\n",
" </tr>\n",
" <tr>\n",
" <th>11</th>\n",
" <td>HPTEC</td>\n",
" <td>2</td>\n",
" <td>72</td>\n",
" </tr>\n",
" <tr>\n",
" <th>12</th>\n",
" <td>HPTEC</td>\n",
" <td>3</td>\n",
" <td>0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>13</th>\n",
" <td>HPTEC</td>\n",
" <td>3</td>\n",
" <td>6</td>\n",
" </tr>\n",
" <tr>\n",
" <th>14</th>\n",
" <td>HPTEC</td>\n",
" <td>3</td>\n",
" <td>12</td>\n",
" </tr>\n",
" <tr>\n",
" <th>15</th>\n",
" <td>HPTEC</td>\n",
" <td>3</td>\n",
" <td>24</td>\n",
" </tr>\n",
" <tr>\n",
" <th>16</th>\n",
" <td>HPTEC</td>\n",
" <td>3</td>\n",
" <td>48</td>\n",
" </tr>\n",
" <tr>\n",
" <th>17</th>\n",
" <td>HPTEC</td>\n",
" <td>3</td>\n",
" <td>72</td>\n",
" </tr>\n",
" <tr>\n",
" <th>18</th>\n",
" <td>OAT1</td>\n",
" <td>1</td>\n",
" <td>0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>19</th>\n",
" <td>OAT1</td>\n",
" <td>1</td>\n",
" <td>6</td>\n",
" </tr>\n",
" <tr>\n",
" <th>20</th>\n",
" <td>OAT1</td>\n",
" <td>1</td>\n",
" <td>12</td>\n",
" </tr>\n",
" <tr>\n",
" <th>21</th>\n",
" <td>OAT1</td>\n",
" <td>1</td>\n",
" <td>18</td>\n",
" </tr>\n",
" <tr>\n",
" <th>22</th>\n",
" <td>OAT1</td>\n",
" <td>1</td>\n",
" <td>24</td>\n",
" </tr>\n",
" <tr>\n",
" <th>23</th>\n",
" <td>OAT1</td>\n",
" <td>1</td>\n",
" <td>48</td>\n",
" </tr>\n",
" <tr>\n",
" <th>24</th>\n",
" <td>OAT1</td>\n",
" <td>1</td>\n",
" <td>72</td>\n",
" </tr>\n",
" <tr>\n",
" <th>25</th>\n",
" <td>OAT1</td>\n",
" <td>2</td>\n",
" <td>0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>26</th>\n",
" <td>OAT1</td>\n",
" <td>2</td>\n",
" <td>6</td>\n",
" </tr>\n",
" <tr>\n",
" <th>27</th>\n",
" <td>OAT1</td>\n",
" <td>2</td>\n",
" <td>12</td>\n",
" </tr>\n",
" <tr>\n",
" <th>28</th>\n",
" <td>OAT1</td>\n",
" <td>2</td>\n",
" <td>18</td>\n",
" </tr>\n",
" <tr>\n",
" <th>29</th>\n",
" <td>OAT1</td>\n",
" <td>2</td>\n",
" <td>24</td>\n",
" </tr>\n",
" <tr>\n",
" <th>30</th>\n",
" <td>OAT1</td>\n",
" <td>2</td>\n",
" <td>48</td>\n",
" </tr>\n",
" <tr>\n",
" <th>31</th>\n",
" <td>OAT1</td>\n",
" <td>2</td>\n",
" <td>72</td>\n",
" </tr>\n",
" <tr>\n",
" <th>32</th>\n",
" <td>OAT1</td>\n",
" <td>3</td>\n",
" <td>0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>33</th>\n",
" <td>OAT1</td>\n",
" <td>3</td>\n",
" <td>6</td>\n",
" </tr>\n",
" <tr>\n",
" <th>34</th>\n",
" <td>OAT1</td>\n",
" <td>3</td>\n",
" <td>12</td>\n",
" </tr>\n",
" <tr>\n",
" <th>35</th>\n",
" <td>OAT1</td>\n",
" <td>3</td>\n",
" <td>18</td>\n",
" </tr>\n",
" <tr>\n",
" <th>36</th>\n",
" <td>OAT1</td>\n",
" <td>3</td>\n",
" <td>24</td>\n",
" </tr>\n",
" <tr>\n",
" <th>37</th>\n",
" <td>OAT1</td>\n",
" <td>3</td>\n",
" <td>48</td>\n",
" </tr>\n",
" <tr>\n",
" <th>38</th>\n",
" <td>OAT1</td>\n",
" <td>3</td>\n",
" <td>72</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"</div>"
],
"text/plain": [
" CellType BiologicalReplicate TimePointHours\n",
"0 HPTEC 1 0\n",
"1 HPTEC 1 6\n",
"2 HPTEC 1 12\n",
"3 HPTEC 1 24\n",
"4 HPTEC 1 48\n",
"5 HPTEC 1 72\n",
"6 HPTEC 2 0\n",
"7 HPTEC 2 6\n",
"8 HPTEC 2 12\n",
"9 HPTEC 2 24\n",
"10 HPTEC 2 48\n",
"11 HPTEC 2 72\n",
"12 HPTEC 3 0\n",
"13 HPTEC 3 6\n",
"14 HPTEC 3 12\n",
"15 HPTEC 3 24\n",
"16 HPTEC 3 48\n",
"17 HPTEC 3 72\n",
"18 OAT1 1 0\n",
"19 OAT1 1 6\n",
"20 OAT1 1 12\n",
"21 OAT1 1 18\n",
"22 OAT1 1 24\n",
"23 OAT1 1 48\n",
"24 OAT1 1 72\n",
"25 OAT1 2 0\n",
"26 OAT1 2 6\n",
"27 OAT1 2 12\n",
"28 OAT1 2 18\n",
"29 OAT1 2 24\n",
"30 OAT1 2 48\n",
"31 OAT1 2 72\n",
"32 OAT1 3 0\n",
"33 OAT1 3 6\n",
"34 OAT1 3 12\n",
"35 OAT1 3 18\n",
"36 OAT1 3 24\n",
"37 OAT1 3 48\n",
"38 OAT1 3 72"
]
},
"execution_count": 9,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"exp_design = pd.DataFrame(exp_metadata,\n",
" columns=exp_meta_table_1.keys())\n",
"exp_design"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Read in well-level design (plate map)"
]
},
{
"cell_type": "code",
"execution_count": 10,
"metadata": {
"collapsed": false
},
"outputs": [],
"source": [
"plate_design_path = input_path.joinpath('1705015_4batch_Layout_Plates.xlsx')\n",
"plate_design = pd.read_excel(str(plate_design_path))"
]
},
{
"cell_type": "code",
"execution_count": 11,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/html": [
"<div>\n",
"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
" <th>WellName</th>\n",
" <th>Column</th>\n",
" <th>Row</th>\n",
" <th>pert_iname</th>\n",
" <th>pert_dose</th>\n",
" <th>pert_dose_unit</th>\n",
" <th>pert_replicate</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
" <td>I3</td>\n",
" <td>3</td>\n",
" <td>9</td>\n",
" <td>Aspirin</td>\n",
" <td>3.173691</td>\n",
" <td>um</td>\n",
" <td>1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
" <td>J3</td>\n",
" <td>3</td>\n",
" <td>10</td>\n",
" <td>Aspirin</td>\n",
" <td>10.028862</td>\n",
" <td>um</td>\n",
" <td>1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>2</th>\n",
" <td>K3</td>\n",
" <td>3</td>\n",
" <td>11</td>\n",
" <td>Aspirin</td>\n",
" <td>31.691205</td>\n",
" <td>um</td>\n",
" <td>1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>3</th>\n",
" <td>L3</td>\n",
" <td>3</td>\n",
" <td>12</td>\n",
" <td>Aspirin</td>\n",
" <td>100.144208</td>\n",
" <td>um</td>\n",
" <td>1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>4</th>\n",
" <td>M3</td>\n",
" <td>3</td>\n",
" <td>13</td>\n",
" <td>Aspirin</td>\n",
" <td>316.455696</td>\n",
" <td>um</td>\n",
" <td>1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>5</th>\n",
" <td>N3</td>\n",
" <td>3</td>\n",
" <td>14</td>\n",
" <td>Aspirin</td>\n",
" <td>1000.000000</td>\n",
" <td>um</td>\n",
" <td>1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>6</th>\n",
" <td>I4</td>\n",
" <td>4</td>\n",
" <td>9</td>\n",
" <td>Aspirin</td>\n",
" <td>3.173691</td>\n",
" <td>um</td>\n",
" <td>2</td>\n",
" </tr>\n",
" <tr>\n",
" <th>7</th>\n",
" <td>J4</td>\n",
" <td>4</td>\n",
" <td>10</td>\n",
" <td>Aspirin</td>\n",
" <td>10.028862</td>\n",
" <td>um</td>\n",
" <td>2</td>\n",
" </tr>\n",
" <tr>\n",
" <th>8</th>\n",
" <td>K4</td>\n",
" <td>4</td>\n",
" <td>11</td>\n",
" <td>Aspirin</td>\n",
" <td>31.691205</td>\n",
" <td>um</td>\n",
" <td>2</td>\n",
" </tr>\n",
" <tr>\n",
" <th>9</th>\n",
" <td>L4</td>\n",
" <td>4</td>\n",
" <td>12</td>\n",
" <td>Aspirin</td>\n",
" <td>100.144208</td>\n",
" <td>um</td>\n",
" <td>2</td>\n",
" </tr>\n",
" <tr>\n",
" <th>10</th>\n",
" <td>M4</td>\n",
" <td>4</td>\n",
" <td>13</td>\n",
" <td>Aspirin</td>\n",
" <td>316.455696</td>\n",
" <td>um</td>\n",
" <td>2</td>\n",
" </tr>\n",
" <tr>\n",
" <th>11</th>\n",
" <td>N4</td>\n",
" <td>4</td>\n",
" <td>14</td>\n",
" <td>Aspirin</td>\n",
" <td>1000.000000</td>\n",
" <td>um</td>\n",
" <td>2</td>\n",
" </tr>\n",
" <tr>\n",
" <th>12</th>\n",
" <td>I5</td>\n",
" <td>5</td>\n",
" <td>9</td>\n",
" <td>Sorbitol</td>\n",
" <td>3.173691</td>\n",
" <td>um</td>\n",
" <td>1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>13</th>\n",
" <td>J5</td>\n",
" <td>5</td>\n",
" <td>10</td>\n",
" <td>Sorbitol</td>\n",
" <td>10.028862</td>\n",
" <td>um</td>\n",
" <td>1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>14</th>\n",
" <td>K5</td>\n",
" <td>5</td>\n",
" <td>11</td>\n",
" <td>Sorbitol</td>\n",
" <td>31.691205</td>\n",
" <td>um</td>\n",
" <td>1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>15</th>\n",
" <td>L5</td>\n",
" <td>5</td>\n",
" <td>12</td>\n",
" <td>Sorbitol</td>\n",
" <td>100.144208</td>\n",
" <td>um</td>\n",
" <td>1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>16</th>\n",
" <td>M5</td>\n",
" <td>5</td>\n",
" <td>13</td>\n",
" <td>Sorbitol</td>\n",
" <td>316.455696</td>\n",
" <td>um</td>\n",
" <td>1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>17</th>\n",
" <td>N5</td>\n",
" <td>5</td>\n",
" <td>14</td>\n",
" <td>Sorbitol</td>\n",
" <td>1000.000000</td>\n",
" <td>um</td>\n",
" <td>1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>18</th>\n",
" <td>I6</td>\n",
" <td>6</td>\n",
" <td>9</td>\n",
" <td>Sorbitol</td>\n",
" <td>3.173691</td>\n",
" <td>um</td>\n",
" <td>2</td>\n",
" </tr>\n",
" <tr>\n",
" <th>19</th>\n",
" <td>J6</td>\n",
" <td>6</td>\n",
" <td>10</td>\n",
" <td>Sorbitol</td>\n",
" <td>10.028862</td>\n",
" <td>um</td>\n",
" <td>2</td>\n",
" </tr>\n",
" <tr>\n",
" <th>20</th>\n",
" <td>K6</td>\n",
" <td>6</td>\n",
" <td>11</td>\n",
" <td>Sorbitol</td>\n",
" <td>31.691205</td>\n",
" <td>um</td>\n",
" <td>2</td>\n",
" </tr>\n",
" <tr>\n",
" <th>21</th>\n",
" <td>L6</td>\n",
" <td>6</td>\n",
" <td>12</td>\n",
" <td>Sorbitol</td>\n",
" <td>100.144208</td>\n",
" <td>um</td>\n",
" <td>2</td>\n",
" </tr>\n",
" <tr>\n",
" <th>22</th>\n",
" <td>M6</td>\n",
" <td>6</td>\n",
" <td>13</td>\n",
" <td>Sorbitol</td>\n",
" <td>316.455696</td>\n",
" <td>um</td>\n",
" <td>2</td>\n",
" </tr>\n",
" <tr>\n",
" <th>23</th>\n",
" <td>N6</td>\n",
" <td>6</td>\n",
" <td>14</td>\n",
" <td>Sorbitol</td>\n",
" <td>1000.000000</td>\n",
" <td>um</td>\n",
" <td>2</td>\n",
" </tr>\n",
" <tr>\n",
" <th>24</th>\n",
" <td>I7</td>\n",
" <td>7</td>\n",
" <td>9</td>\n",
" <td>Acyclovir</td>\n",
" <td>3.173691</td>\n",
" <td>um</td>\n",
" <td>1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>25</th>\n",
" <td>J7</td>\n",
" <td>7</td>\n",
" <td>10</td>\n",
" <td>Acyclovir</td>\n",
" <td>10.028862</td>\n",
" <td>um</td>\n",
" <td>1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>26</th>\n",
" <td>K7</td>\n",
" <td>7</td>\n",
" <td>11</td>\n",
" <td>Acyclovir</td>\n",
" <td>31.691205</td>\n",
" <td>um</td>\n",
" <td>1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>27</th>\n",
" <td>L7</td>\n",
" <td>7</td>\n",
" <td>12</td>\n",
" <td>Acyclovir</td>\n",
" <td>100.144208</td>\n",
" <td>um</td>\n",
" <td>1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>28</th>\n",
" <td>M7</td>\n",
" <td>7</td>\n",
" <td>13</td>\n",
" <td>Acyclovir</td>\n",
" <td>316.455696</td>\n",
" <td>um</td>\n",
" <td>1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>29</th>\n",
" <td>N7</td>\n",
" <td>7</td>\n",
" <td>14</td>\n",
" <td>Acyclovir</td>\n",
" <td>1000.000000</td>\n",
" <td>um</td>\n",
" <td>1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>...</th>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>210</th>\n",
" <td>C18</td>\n",
" <td>18</td>\n",
" <td>3</td>\n",
" <td>PF-05279870</td>\n",
" <td>1.586845</td>\n",
" <td>um</td>\n",
" <td>2</td>\n",
" </tr>\n",
" <tr>\n",
" <th>211</th>\n",
" <td>D18</td>\n",
" <td>18</td>\n",
" <td>4</td>\n",
" <td>PF-05279870</td>\n",
" <td>5.014431</td>\n",
" <td>um</td>\n",
" <td>2</td>\n",
" </tr>\n",
" <tr>\n",
" <th>212</th>\n",
" <td>E18</td>\n",
" <td>18</td>\n",
" <td>5</td>\n",
" <td>PF-05279870</td>\n",
" <td>15.845602</td>\n",
" <td>um</td>\n",
" <td>2</td>\n",
" </tr>\n",
" <tr>\n",
" <th>213</th>\n",
" <td>F18</td>\n",
" <td>18</td>\n",
" <td>6</td>\n",
" <td>PF-05279870</td>\n",
" <td>50.072104</td>\n",
" <td>um</td>\n",
" <td>2</td>\n",
" </tr>\n",
" <tr>\n",
" <th>214</th>\n",
" <td>G18</td>\n",
" <td>18</td>\n",
" <td>7</td>\n",
" <td>PF-05279870</td>\n",
" <td>158.227848</td>\n",
" <td>um</td>\n",
" <td>2</td>\n",
" </tr>\n",
" <tr>\n",
" <th>215</th>\n",
" <td>H18</td>\n",
" <td>18</td>\n",
" <td>8</td>\n",
" <td>PF-05279870</td>\n",
" <td>500.000000</td>\n",
" <td>um</td>\n",
" <td>2</td>\n",
" </tr>\n",
" <tr>\n",
" <th>216</th>\n",
" <td>C19</td>\n",
" <td>19</td>\n",
" <td>3</td>\n",
" <td>PF-06260618</td>\n",
" <td>1.586845</td>\n",
" <td>um</td>\n",
" <td>1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>217</th>\n",
" <td>D19</td>\n",
" <td>19</td>\n",
" <td>4</td>\n",
" <td>PF-06260618</td>\n",
" <td>5.014431</td>\n",
" <td>um</td>\n",
" <td>1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>218</th>\n",
" <td>E19</td>\n",
" <td>19</td>\n",
" <td>5</td>\n",
" <td>PF-06260618</td>\n",
" <td>15.845602</td>\n",
" <td>um</td>\n",
" <td>1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>219</th>\n",
" <td>F19</td>\n",
" <td>19</td>\n",
" <td>6</td>\n",
" <td>PF-06260618</td>\n",
" <td>50.072104</td>\n",
" <td>um</td>\n",
" <td>1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>220</th>\n",
" <td>G19</td>\n",
" <td>19</td>\n",
" <td>7</td>\n",
" <td>PF-06260618</td>\n",
" <td>158.227848</td>\n",
" <td>um</td>\n",
" <td>1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>221</th>\n",
" <td>H19</td>\n",
" <td>19</td>\n",
" <td>8</td>\n",
" <td>PF-06260618</td>\n",
" <td>500.000000</td>\n",
" <td>um</td>\n",
" <td>1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>222</th>\n",
" <td>C20</td>\n",
" <td>20</td>\n",
" <td>3</td>\n",
" <td>PF-06260618</td>\n",
" <td>1.586845</td>\n",
" <td>um</td>\n",
" <td>2</td>\n",
" </tr>\n",
" <tr>\n",
" <th>223</th>\n",
" <td>D20</td>\n",
" <td>20</td>\n",
" <td>4</td>\n",
" <td>PF-06260618</td>\n",
" <td>5.014431</td>\n",
" <td>um</td>\n",
" <td>2</td>\n",
" </tr>\n",
" <tr>\n",
" <th>224</th>\n",
" <td>E20</td>\n",
" <td>20</td>\n",
" <td>5</td>\n",
" <td>PF-06260618</td>\n",
" <td>15.845602</td>\n",
" <td>um</td>\n",
" <td>2</td>\n",
" </tr>\n",
" <tr>\n",
" <th>225</th>\n",
" <td>F20</td>\n",
" <td>20</td>\n",
" <td>6</td>\n",
" <td>PF-06260618</td>\n",
" <td>50.072104</td>\n",
" <td>um</td>\n",
" <td>2</td>\n",
" </tr>\n",
" <tr>\n",
" <th>226</th>\n",
" <td>G20</td>\n",
" <td>20</td>\n",
" <td>7</td>\n",
" <td>PF-06260618</td>\n",
" <td>158.227848</td>\n",
" <td>um</td>\n",
" <td>2</td>\n",
" </tr>\n",
" <tr>\n",
" <th>227</th>\n",
" <td>H20</td>\n",
" <td>20</td>\n",
" <td>8</td>\n",
" <td>PF-06260618</td>\n",
" <td>500.000000</td>\n",
" <td>um</td>\n",
" <td>2</td>\n",
" </tr>\n",
" <tr>\n",
" <th>228</th>\n",
" <td>C21</td>\n",
" <td>21</td>\n",
" <td>3</td>\n",
" <td>PF-06740120</td>\n",
" <td>3.173691</td>\n",
" <td>um</td>\n",
" <td>1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>229</th>\n",
" <td>D21</td>\n",
" <td>21</td>\n",
" <td>4</td>\n",
" <td>PF-06740120</td>\n",
" <td>10.028862</td>\n",
" <td>um</td>\n",
" <td>1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>230</th>\n",
" <td>E21</td>\n",
" <td>21</td>\n",
" <td>5</td>\n",
" <td>PF-06740120</td>\n",
" <td>31.691205</td>\n",
" <td>um</td>\n",
" <td>1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>231</th>\n",
" <td>F21</td>\n",
" <td>21</td>\n",
" <td>6</td>\n",
" <td>PF-06740120</td>\n",
" <td>100.144208</td>\n",
" <td>um</td>\n",
" <td>1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>232</th>\n",
" <td>G21</td>\n",
" <td>21</td>\n",
" <td>7</td>\n",
" <td>PF-06740120</td>\n",
" <td>316.455696</td>\n",
" <td>um</td>\n",
" <td>1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>233</th>\n",
" <td>H21</td>\n",
" <td>21</td>\n",
" <td>8</td>\n",
" <td>PF-06740120</td>\n",
" <td>1000.000000</td>\n",
" <td>um</td>\n",
" <td>1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>234</th>\n",
" <td>C22</td>\n",
" <td>22</td>\n",
" <td>3</td>\n",
" <td>PF-06740120</td>\n",
" <td>3.173691</td>\n",
" <td>um</td>\n",
" <td>2</td>\n",
" </tr>\n",
" <tr>\n",
" <th>235</th>\n",
" <td>D22</td>\n",
" <td>22</td>\n",
" <td>4</td>\n",
" <td>PF-06740120</td>\n",
" <td>10.028862</td>\n",
" <td>um</td>\n",
" <td>2</td>\n",
" </tr>\n",
" <tr>\n",
" <th>236</th>\n",
" <td>E22</td>\n",
" <td>22</td>\n",
" <td>5</td>\n",
" <td>PF-06740120</td>\n",
" <td>31.691205</td>\n",
" <td>um</td>\n",
" <td>2</td>\n",
" </tr>\n",
" <tr>\n",
" <th>237</th>\n",
" <td>F22</td>\n",
" <td>22</td>\n",
" <td>6</td>\n",
" <td>PF-06740120</td>\n",
" <td>100.144208</td>\n",
" <td>um</td>\n",
" <td>2</td>\n",
" </tr>\n",
" <tr>\n",
" <th>238</th>\n",
" <td>G22</td>\n",
" <td>22</td>\n",
" <td>7</td>\n",
" <td>PF-06740120</td>\n",
" <td>316.455696</td>\n",
" <td>um</td>\n",
" <td>2</td>\n",
" </tr>\n",
" <tr>\n",
" <th>239</th>\n",
" <td>H22</td>\n",
" <td>22</td>\n",
" <td>8</td>\n",
" <td>PF-06740120</td>\n",
" <td>1000.000000</td>\n",
" <td>um</td>\n",
" <td>2</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"<p>240 rows × 7 columns</p>\n",
"</div>"
],
"text/plain": [
" WellName Column Row pert_iname pert_dose pert_dose_unit \\\n",
"0 I3 3 9 Aspirin 3.173691 um \n",
"1 J3 3 10 Aspirin 10.028862 um \n",
"2 K3 3 11 Aspirin 31.691205 um \n",
"3 L3 3 12 Aspirin 100.144208 um \n",
"4 M3 3 13 Aspirin 316.455696 um \n",
"5 N3 3 14 Aspirin 1000.000000 um \n",
"6 I4 4 9 Aspirin 3.173691 um \n",
"7 J4 4 10 Aspirin 10.028862 um \n",
"8 K4 4 11 Aspirin 31.691205 um \n",
"9 L4 4 12 Aspirin 100.144208 um \n",
"10 M4 4 13 Aspirin 316.455696 um \n",
"11 N4 4 14 Aspirin 1000.000000 um \n",
"12 I5 5 9 Sorbitol 3.173691 um \n",
"13 J5 5 10 Sorbitol 10.028862 um \n",
"14 K5 5 11 Sorbitol 31.691205 um \n",
"15 L5 5 12 Sorbitol 100.144208 um \n",
"16 M5 5 13 Sorbitol 316.455696 um \n",
"17 N5 5 14 Sorbitol 1000.000000 um \n",
"18 I6 6 9 Sorbitol 3.173691 um \n",
"19 J6 6 10 Sorbitol 10.028862 um \n",
"20 K6 6 11 Sorbitol 31.691205 um \n",
"21 L6 6 12 Sorbitol 100.144208 um \n",
"22 M6 6 13 Sorbitol 316.455696 um \n",
"23 N6 6 14 Sorbitol 1000.000000 um \n",
"24 I7 7 9 Acyclovir 3.173691 um \n",
"25 J7 7 10 Acyclovir 10.028862 um \n",
"26 K7 7 11 Acyclovir 31.691205 um \n",
"27 L7 7 12 Acyclovir 100.144208 um \n",
"28 M7 7 13 Acyclovir 316.455696 um \n",
"29 N7 7 14 Acyclovir 1000.000000 um \n",
".. ... ... ... ... ... ... \n",
"210 C18 18 3 PF-05279870 1.586845 um \n",
"211 D18 18 4 PF-05279870 5.014431 um \n",
"212 E18 18 5 PF-05279870 15.845602 um \n",
"213 F18 18 6 PF-05279870 50.072104 um \n",
"214 G18 18 7 PF-05279870 158.227848 um \n",
"215 H18 18 8 PF-05279870 500.000000 um \n",
"216 C19 19 3 PF-06260618 1.586845 um \n",
"217 D19 19 4 PF-06260618 5.014431 um \n",
"218 E19 19 5 PF-06260618 15.845602 um \n",
"219 F19 19 6 PF-06260618 50.072104 um \n",
"220 G19 19 7 PF-06260618 158.227848 um \n",
"221 H19 19 8 PF-06260618 500.000000 um \n",
"222 C20 20 3 PF-06260618 1.586845 um \n",
"223 D20 20 4 PF-06260618 5.014431 um \n",
"224 E20 20 5 PF-06260618 15.845602 um \n",
"225 F20 20 6 PF-06260618 50.072104 um \n",
"226 G20 20 7 PF-06260618 158.227848 um \n",
"227 H20 20 8 PF-06260618 500.000000 um \n",
"228 C21 21 3 PF-06740120 3.173691 um \n",
"229 D21 21 4 PF-06740120 10.028862 um \n",
"230 E21 21 5 PF-06740120 31.691205 um \n",
"231 F21 21 6 PF-06740120 100.144208 um \n",
"232 G21 21 7 PF-06740120 316.455696 um \n",
"233 H21 21 8 PF-06740120 1000.000000 um \n",
"234 C22 22 3 PF-06740120 3.173691 um \n",
"235 D22 22 4 PF-06740120 10.028862 um \n",
"236 E22 22 5 PF-06740120 31.691205 um \n",
"237 F22 22 6 PF-06740120 100.144208 um \n",
"238 G22 22 7 PF-06740120 316.455696 um \n",
"239 H22 22 8 PF-06740120 1000.000000 um \n",
"\n",
" pert_replicate \n",
"0 1 \n",
"1 1 \n",
"2 1 \n",
"3 1 \n",
"4 1 \n",
"5 1 \n",
"6 2 \n",
"7 2 \n",
"8 2 \n",
"9 2 \n",
"10 2 \n",
"11 2 \n",
"12 1 \n",
"13 1 \n",
"14 1 \n",
"15 1 \n",
"16 1 \n",
"17 1 \n",
"18 2 \n",
"19 2 \n",
"20 2 \n",
"21 2 \n",
"22 2 \n",
"23 2 \n",
"24 1 \n",
"25 1 \n",
"26 1 \n",
"27 1 \n",
"28 1 \n",
"29 1 \n",
".. ... \n",
"210 2 \n",
"211 2 \n",
"212 2 \n",
"213 2 \n",
"214 2 \n",
"215 2 \n",
"216 1 \n",
"217 1 \n",
"218 1 \n",
"219 1 \n",
"220 1 \n",
"221 1 \n",
"222 2 \n",
"223 2 \n",
"224 2 \n",
"225 2 \n",
"226 2 \n",
"227 2 \n",
"228 1 \n",
"229 1 \n",
"230 1 \n",
"231 1 \n",
"232 1 \n",
"233 1 \n",
"234 2 \n",
"235 2 \n",
"236 2 \n",
"237 2 \n",
"238 2 \n",
"239 2 \n",
"\n",
"[240 rows x 7 columns]"
]
},
"execution_count": 11,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"plate_design"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Generate cartesian product of plate- and well-level design\n",
"This uses the \"trick\" of adding a dummy column with a single value to both dataframes and then merging."
]
},
{
"cell_type": "code",
"execution_count": 12,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"exp_design['_temp'] = 0\n",
"plate_design['_temp'] = 0\n",
"design = pd.merge(exp_design, plate_design, on='_temp').drop('_temp', axis=1)\n"
]
},
{
"cell_type": "code",
"execution_count": 13,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/plain": [
"(9360, 10)"
]
},
"execution_count": 13,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"design.shape"
]
},
{
"cell_type": "code",
"execution_count": 14,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/html": [
"<div>\n",
"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
" <th>CellType</th>\n",
" <th>BiologicalReplicate</th>\n",
" <th>TimePointHours</th>\n",
" <th>WellName</th>\n",
" <th>Column</th>\n",
" <th>Row</th>\n",
" <th>pert_iname</th>\n",
" <th>pert_dose</th>\n",
" <th>pert_dose_unit</th>\n",
" <th>pert_replicate</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
" <td>HPTEC</td>\n",
" <td>1</td>\n",
" <td>0</td>\n",
" <td>I3</td>\n",
" <td>3</td>\n",
" <td>9</td>\n",
" <td>Aspirin</td>\n",
" <td>3.173691</td>\n",
" <td>um</td>\n",
" <td>1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
" <td>HPTEC</td>\n",
" <td>1</td>\n",
" <td>0</td>\n",
" <td>J3</td>\n",
" <td>3</td>\n",
" <td>10</td>\n",
" <td>Aspirin</td>\n",
" <td>10.028862</td>\n",
" <td>um</td>\n",
" <td>1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>2</th>\n",
" <td>HPTEC</td>\n",
" <td>1</td>\n",
" <td>0</td>\n",
" <td>K3</td>\n",
" <td>3</td>\n",
" <td>11</td>\n",
" <td>Aspirin</td>\n",
" <td>31.691205</td>\n",
" <td>um</td>\n",
" <td>1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>3</th>\n",
" <td>HPTEC</td>\n",
" <td>1</td>\n",
" <td>0</td>\n",
" <td>L3</td>\n",
" <td>3</td>\n",
" <td>12</td>\n",
" <td>Aspirin</td>\n",
" <td>100.144208</td>\n",
" <td>um</td>\n",
" <td>1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>4</th>\n",
" <td>HPTEC</td>\n",
" <td>1</td>\n",
" <td>0</td>\n",
" <td>M3</td>\n",
" <td>3</td>\n",
" <td>13</td>\n",
" <td>Aspirin</td>\n",
" <td>316.455696</td>\n",
" <td>um</td>\n",
" <td>1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>5</th>\n",
" <td>HPTEC</td>\n",
" <td>1</td>\n",
" <td>0</td>\n",
" <td>N3</td>\n",
" <td>3</td>\n",
" <td>14</td>\n",
" <td>Aspirin</td>\n",
" <td>1000.000000</td>\n",
" <td>um</td>\n",
" <td>1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>6</th>\n",
" <td>HPTEC</td>\n",
" <td>1</td>\n",
" <td>0</td>\n",
" <td>I4</td>\n",
" <td>4</td>\n",
" <td>9</td>\n",
" <td>Aspirin</td>\n",
" <td>3.173691</td>\n",
" <td>um</td>\n",
" <td>2</td>\n",
" </tr>\n",
" <tr>\n",
" <th>7</th>\n",
" <td>HPTEC</td>\n",
" <td>1</td>\n",
" <td>0</td>\n",
" <td>J4</td>\n",
" <td>4</td>\n",
" <td>10</td>\n",
" <td>Aspirin</td>\n",
" <td>10.028862</td>\n",
" <td>um</td>\n",
" <td>2</td>\n",
" </tr>\n",
" <tr>\n",
" <th>8</th>\n",
" <td>HPTEC</td>\n",
" <td>1</td>\n",
" <td>0</td>\n",
" <td>K4</td>\n",
" <td>4</td>\n",
" <td>11</td>\n",
" <td>Aspirin</td>\n",
" <td>31.691205</td>\n",
" <td>um</td>\n",
" <td>2</td>\n",
" </tr>\n",
" <tr>\n",
" <th>9</th>\n",
" <td>HPTEC</td>\n",
" <td>1</td>\n",
" <td>0</td>\n",
" <td>L4</td>\n",
" <td>4</td>\n",
" <td>12</td>\n",
" <td>Aspirin</td>\n",
" <td>100.144208</td>\n",
" <td>um</td>\n",
" <td>2</td>\n",
" </tr>\n",
" <tr>\n",
" <th>10</th>\n",
" <td>HPTEC</td>\n",
" <td>1</td>\n",
" <td>0</td>\n",
" <td>M4</td>\n",
" <td>4</td>\n",
" <td>13</td>\n",
" <td>Aspirin</td>\n",
" <td>316.455696</td>\n",
" <td>um</td>\n",
" <td>2</td>\n",
" </tr>\n",
" <tr>\n",
" <th>11</th>\n",
" <td>HPTEC</td>\n",
" <td>1</td>\n",
" <td>0</td>\n",
" <td>N4</td>\n",
" <td>4</td>\n",
" <td>14</td>\n",
" <td>Aspirin</td>\n",
" <td>1000.000000</td>\n",
" <td>um</td>\n",
" <td>2</td>\n",
" </tr>\n",
" <tr>\n",
" <th>12</th>\n",
" <td>HPTEC</td>\n",
" <td>1</td>\n",
" <td>0</td>\n",
" <td>I5</td>\n",
" <td>5</td>\n",
" <td>9</td>\n",
" <td>Sorbitol</td>\n",
" <td>3.173691</td>\n",
" <td>um</td>\n",
" <td>1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>13</th>\n",
" <td>HPTEC</td>\n",
" <td>1</td>\n",
" <td>0</td>\n",
" <td>J5</td>\n",
" <td>5</td>\n",
" <td>10</td>\n",
" <td>Sorbitol</td>\n",
" <td>10.028862</td>\n",
" <td>um</td>\n",
" <td>1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>14</th>\n",
" <td>HPTEC</td>\n",
" <td>1</td>\n",
" <td>0</td>\n",
" <td>K5</td>\n",
" <td>5</td>\n",
" <td>11</td>\n",
" <td>Sorbitol</td>\n",
" <td>31.691205</td>\n",
" <td>um</td>\n",
" <td>1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>15</th>\n",
" <td>HPTEC</td>\n",
" <td>1</td>\n",
" <td>0</td>\n",
" <td>L5</td>\n",
" <td>5</td>\n",
" <td>12</td>\n",
" <td>Sorbitol</td>\n",
" <td>100.144208</td>\n",
" <td>um</td>\n",
" <td>1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>16</th>\n",
" <td>HPTEC</td>\n",
" <td>1</td>\n",
" <td>0</td>\n",
" <td>M5</td>\n",
" <td>5</td>\n",
" <td>13</td>\n",
" <td>Sorbitol</td>\n",
" <td>316.455696</td>\n",
" <td>um</td>\n",
" <td>1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>17</th>\n",
" <td>HPTEC</td>\n",
" <td>1</td>\n",
" <td>0</td>\n",
" <td>N5</td>\n",
" <td>5</td>\n",
" <td>14</td>\n",
" <td>Sorbitol</td>\n",
" <td>1000.000000</td>\n",
" <td>um</td>\n",
" <td>1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>18</th>\n",
" <td>HPTEC</td>\n",
" <td>1</td>\n",
" <td>0</td>\n",
" <td>I6</td>\n",
" <td>6</td>\n",
" <td>9</td>\n",
" <td>Sorbitol</td>\n",
" <td>3.173691</td>\n",
" <td>um</td>\n",
" <td>2</td>\n",
" </tr>\n",
" <tr>\n",
" <th>19</th>\n",
" <td>HPTEC</td>\n",
" <td>1</td>\n",
" <td>0</td>\n",
" <td>J6</td>\n",
" <td>6</td>\n",
" <td>10</td>\n",
" <td>Sorbitol</td>\n",
" <td>10.028862</td>\n",
" <td>um</td>\n",
" <td>2</td>\n",
" </tr>\n",
" <tr>\n",
" <th>20</th>\n",
" <td>HPTEC</td>\n",
" <td>1</td>\n",
" <td>0</td>\n",
" <td>K6</td>\n",
" <td>6</td>\n",
" <td>11</td>\n",
" <td>Sorbitol</td>\n",
" <td>31.691205</td>\n",
" <td>um</td>\n",
" <td>2</td>\n",
" </tr>\n",
" <tr>\n",
" <th>21</th>\n",
" <td>HPTEC</td>\n",
" <td>1</td>\n",
" <td>0</td>\n",
" <td>L6</td>\n",
" <td>6</td>\n",
" <td>12</td>\n",
" <td>Sorbitol</td>\n",
" <td>100.144208</td>\n",
" <td>um</td>\n",
" <td>2</td>\n",
" </tr>\n",
" <tr>\n",
" <th>22</th>\n",
" <td>HPTEC</td>\n",
" <td>1</td>\n",
" <td>0</td>\n",
" <td>M6</td>\n",
" <td>6</td>\n",
" <td>13</td>\n",
" <td>Sorbitol</td>\n",
" <td>316.455696</td>\n",
" <td>um</td>\n",
" <td>2</td>\n",
" </tr>\n",
" <tr>\n",
" <th>23</th>\n",
" <td>HPTEC</td>\n",
" <td>1</td>\n",
" <td>0</td>\n",
" <td>N6</td>\n",
" <td>6</td>\n",
" <td>14</td>\n",
" <td>Sorbitol</td>\n",
" <td>1000.000000</td>\n",
" <td>um</td>\n",
" <td>2</td>\n",
" </tr>\n",
" <tr>\n",
" <th>24</th>\n",
" <td>HPTEC</td>\n",
" <td>1</td>\n",
" <td>0</td>\n",
" <td>I7</td>\n",
" <td>7</td>\n",
" <td>9</td>\n",
" <td>Acyclovir</td>\n",
" <td>3.173691</td>\n",
" <td>um</td>\n",
" <td>1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>25</th>\n",
" <td>HPTEC</td>\n",
" <td>1</td>\n",
" <td>0</td>\n",
" <td>J7</td>\n",
" <td>7</td>\n",
" <td>10</td>\n",
" <td>Acyclovir</td>\n",
" <td>10.028862</td>\n",
" <td>um</td>\n",
" <td>1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>26</th>\n",
" <td>HPTEC</td>\n",
" <td>1</td>\n",
" <td>0</td>\n",
" <td>K7</td>\n",
" <td>7</td>\n",
" <td>11</td>\n",
" <td>Acyclovir</td>\n",
" <td>31.691205</td>\n",
" <td>um</td>\n",
" <td>1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>27</th>\n",
" <td>HPTEC</td>\n",
" <td>1</td>\n",
" <td>0</td>\n",
" <td>L7</td>\n",
" <td>7</td>\n",
" <td>12</td>\n",
" <td>Acyclovir</td>\n",
" <td>100.144208</td>\n",
" <td>um</td>\n",
" <td>1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>28</th>\n",
" <td>HPTEC</td>\n",
" <td>1</td>\n",
" <td>0</td>\n",
" <td>M7</td>\n",
" <td>7</td>\n",
" <td>13</td>\n",
" <td>Acyclovir</td>\n",
" <td>316.455696</td>\n",
" <td>um</td>\n",
" <td>1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>29</th>\n",
" <td>HPTEC</td>\n",
" <td>1</td>\n",
" <td>0</td>\n",
" <td>N7</td>\n",
" <td>7</td>\n",
" <td>14</td>\n",
" <td>Acyclovir</td>\n",
" <td>1000.000000</td>\n",
" <td>um</td>\n",
" <td>1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>...</th>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>9330</th>\n",
" <td>OAT1</td>\n",
" <td>3</td>\n",
" <td>72</td>\n",
" <td>C18</td>\n",
" <td>18</td>\n",
" <td>3</td>\n",
" <td>PF-05279870</td>\n",
" <td>1.586845</td>\n",
" <td>um</td>\n",
" <td>2</td>\n",
" </tr>\n",
" <tr>\n",
" <th>9331</th>\n",
" <td>OAT1</td>\n",
" <td>3</td>\n",
" <td>72</td>\n",
" <td>D18</td>\n",
" <td>18</td>\n",
" <td>4</td>\n",
" <td>PF-05279870</td>\n",
" <td>5.014431</td>\n",
" <td>um</td>\n",
" <td>2</td>\n",
" </tr>\n",
" <tr>\n",
" <th>9332</th>\n",
" <td>OAT1</td>\n",
" <td>3</td>\n",
" <td>72</td>\n",
" <td>E18</td>\n",
" <td>18</td>\n",
" <td>5</td>\n",
" <td>PF-05279870</td>\n",
" <td>15.845602</td>\n",
" <td>um</td>\n",
" <td>2</td>\n",
" </tr>\n",
" <tr>\n",
" <th>9333</th>\n",
" <td>OAT1</td>\n",
" <td>3</td>\n",
" <td>72</td>\n",
" <td>F18</td>\n",
" <td>18</td>\n",
" <td>6</td>\n",
" <td>PF-05279870</td>\n",
" <td>50.072104</td>\n",
" <td>um</td>\n",
" <td>2</td>\n",
" </tr>\n",
" <tr>\n",
" <th>9334</th>\n",
" <td>OAT1</td>\n",
" <td>3</td>\n",
" <td>72</td>\n",
" <td>G18</td>\n",
" <td>18</td>\n",
" <td>7</td>\n",
" <td>PF-05279870</td>\n",
" <td>158.227848</td>\n",
" <td>um</td>\n",
" <td>2</td>\n",
" </tr>\n",
" <tr>\n",
" <th>9335</th>\n",
" <td>OAT1</td>\n",
" <td>3</td>\n",
" <td>72</td>\n",
" <td>H18</td>\n",
" <td>18</td>\n",
" <td>8</td>\n",
" <td>PF-05279870</td>\n",
" <td>500.000000</td>\n",
" <td>um</td>\n",
" <td>2</td>\n",
" </tr>\n",
" <tr>\n",
" <th>9336</th>\n",
" <td>OAT1</td>\n",
" <td>3</td>\n",
" <td>72</td>\n",
" <td>C19</td>\n",
" <td>19</td>\n",
" <td>3</td>\n",
" <td>PF-06260618</td>\n",
" <td>1.586845</td>\n",
" <td>um</td>\n",
" <td>1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>9337</th>\n",
" <td>OAT1</td>\n",
" <td>3</td>\n",
" <td>72</td>\n",
" <td>D19</td>\n",
" <td>19</td>\n",
" <td>4</td>\n",
" <td>PF-06260618</td>\n",
" <td>5.014431</td>\n",
" <td>um</td>\n",
" <td>1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>9338</th>\n",
" <td>OAT1</td>\n",
" <td>3</td>\n",
" <td>72</td>\n",
" <td>E19</td>\n",
" <td>19</td>\n",
" <td>5</td>\n",
" <td>PF-06260618</td>\n",
" <td>15.845602</td>\n",
" <td>um</td>\n",
" <td>1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>9339</th>\n",
" <td>OAT1</td>\n",
" <td>3</td>\n",
" <td>72</td>\n",
" <td>F19</td>\n",
" <td>19</td>\n",
" <td>6</td>\n",
" <td>PF-06260618</td>\n",
" <td>50.072104</td>\n",
" <td>um</td>\n",
" <td>1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>9340</th>\n",
" <td>OAT1</td>\n",
" <td>3</td>\n",
" <td>72</td>\n",
" <td>G19</td>\n",
" <td>19</td>\n",
" <td>7</td>\n",
" <td>PF-06260618</td>\n",
" <td>158.227848</td>\n",
" <td>um</td>\n",
" <td>1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>9341</th>\n",
" <td>OAT1</td>\n",
" <td>3</td>\n",
" <td>72</td>\n",
" <td>H19</td>\n",
" <td>19</td>\n",
" <td>8</td>\n",
" <td>PF-06260618</td>\n",
" <td>500.000000</td>\n",
" <td>um</td>\n",
" <td>1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>9342</th>\n",
" <td>OAT1</td>\n",
" <td>3</td>\n",
" <td>72</td>\n",
" <td>C20</td>\n",
" <td>20</td>\n",
" <td>3</td>\n",
" <td>PF-06260618</td>\n",
" <td>1.586845</td>\n",
" <td>um</td>\n",
" <td>2</td>\n",
" </tr>\n",
" <tr>\n",
" <th>9343</th>\n",
" <td>OAT1</td>\n",
" <td>3</td>\n",
" <td>72</td>\n",
" <td>D20</td>\n",
" <td>20</td>\n",
" <td>4</td>\n",
" <td>PF-06260618</td>\n",
" <td>5.014431</td>\n",
" <td>um</td>\n",
" <td>2</td>\n",
" </tr>\n",
" <tr>\n",
" <th>9344</th>\n",
" <td>OAT1</td>\n",
" <td>3</td>\n",
" <td>72</td>\n",
" <td>E20</td>\n",
" <td>20</td>\n",
" <td>5</td>\n",
" <td>PF-06260618</td>\n",
" <td>15.845602</td>\n",
" <td>um</td>\n",
" <td>2</td>\n",
" </tr>\n",
" <tr>\n",
" <th>9345</th>\n",
" <td>OAT1</td>\n",
" <td>3</td>\n",
" <td>72</td>\n",
" <td>F20</td>\n",
" <td>20</td>\n",
" <td>6</td>\n",
" <td>PF-06260618</td>\n",
" <td>50.072104</td>\n",
" <td>um</td>\n",
" <td>2</td>\n",
" </tr>\n",
" <tr>\n",
" <th>9346</th>\n",
" <td>OAT1</td>\n",
" <td>3</td>\n",
" <td>72</td>\n",
" <td>G20</td>\n",
" <td>20</td>\n",
" <td>7</td>\n",
" <td>PF-06260618</td>\n",
" <td>158.227848</td>\n",
" <td>um</td>\n",
" <td>2</td>\n",
" </tr>\n",
" <tr>\n",
" <th>9347</th>\n",
" <td>OAT1</td>\n",
" <td>3</td>\n",
" <td>72</td>\n",
" <td>H20</td>\n",
" <td>20</td>\n",
" <td>8</td>\n",
" <td>PF-06260618</td>\n",
" <td>500.000000</td>\n",
" <td>um</td>\n",
" <td>2</td>\n",
" </tr>\n",
" <tr>\n",
" <th>9348</th>\n",
" <td>OAT1</td>\n",
" <td>3</td>\n",
" <td>72</td>\n",
" <td>C21</td>\n",
" <td>21</td>\n",
" <td>3</td>\n",
" <td>PF-06740120</td>\n",
" <td>3.173691</td>\n",
" <td>um</td>\n",
" <td>1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>9349</th>\n",
" <td>OAT1</td>\n",
" <td>3</td>\n",
" <td>72</td>\n",
" <td>D21</td>\n",
" <td>21</td>\n",
" <td>4</td>\n",
" <td>PF-06740120</td>\n",
" <td>10.028862</td>\n",
" <td>um</td>\n",
" <td>1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>9350</th>\n",
" <td>OAT1</td>\n",
" <td>3</td>\n",
" <td>72</td>\n",
" <td>E21</td>\n",
" <td>21</td>\n",
" <td>5</td>\n",
" <td>PF-06740120</td>\n",
" <td>31.691205</td>\n",
" <td>um</td>\n",
" <td>1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>9351</th>\n",
" <td>OAT1</td>\n",
" <td>3</td>\n",
" <td>72</td>\n",
" <td>F21</td>\n",
" <td>21</td>\n",
" <td>6</td>\n",
" <td>PF-06740120</td>\n",
" <td>100.144208</td>\n",
" <td>um</td>\n",
" <td>1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>9352</th>\n",
" <td>OAT1</td>\n",
" <td>3</td>\n",
" <td>72</td>\n",
" <td>G21</td>\n",
" <td>21</td>\n",
" <td>7</td>\n",
" <td>PF-06740120</td>\n",
" <td>316.455696</td>\n",
" <td>um</td>\n",
" <td>1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>9353</th>\n",
" <td>OAT1</td>\n",
" <td>3</td>\n",
" <td>72</td>\n",
" <td>H21</td>\n",
" <td>21</td>\n",
" <td>8</td>\n",
" <td>PF-06740120</td>\n",
" <td>1000.000000</td>\n",
" <td>um</td>\n",
" <td>1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>9354</th>\n",
" <td>OAT1</td>\n",
" <td>3</td>\n",
" <td>72</td>\n",
" <td>C22</td>\n",
" <td>22</td>\n",
" <td>3</td>\n",
" <td>PF-06740120</td>\n",
" <td>3.173691</td>\n",
" <td>um</td>\n",
" <td>2</td>\n",
" </tr>\n",
" <tr>\n",
" <th>9355</th>\n",
" <td>OAT1</td>\n",
" <td>3</td>\n",
" <td>72</td>\n",
" <td>D22</td>\n",
" <td>22</td>\n",
" <td>4</td>\n",
" <td>PF-06740120</td>\n",
" <td>10.028862</td>\n",
" <td>um</td>\n",
" <td>2</td>\n",
" </tr>\n",
" <tr>\n",
" <th>9356</th>\n",
" <td>OAT1</td>\n",
" <td>3</td>\n",
" <td>72</td>\n",
" <td>E22</td>\n",
" <td>22</td>\n",
" <td>5</td>\n",
" <td>PF-06740120</td>\n",
" <td>31.691205</td>\n",
" <td>um</td>\n",
" <td>2</td>\n",
" </tr>\n",
" <tr>\n",
" <th>9357</th>\n",
" <td>OAT1</td>\n",
" <td>3</td>\n",
" <td>72</td>\n",
" <td>F22</td>\n",
" <td>22</td>\n",
" <td>6</td>\n",
" <td>PF-06740120</td>\n",
" <td>100.144208</td>\n",
" <td>um</td>\n",
" <td>2</td>\n",
" </tr>\n",
" <tr>\n",
" <th>9358</th>\n",
" <td>OAT1</td>\n",
" <td>3</td>\n",
" <td>72</td>\n",
" <td>G22</td>\n",
" <td>22</td>\n",
" <td>7</td>\n",
" <td>PF-06740120</td>\n",
" <td>316.455696</td>\n",
" <td>um</td>\n",
" <td>2</td>\n",
" </tr>\n",
" <tr>\n",
" <th>9359</th>\n",
" <td>OAT1</td>\n",
" <td>3</td>\n",
" <td>72</td>\n",
" <td>H22</td>\n",
" <td>22</td>\n",
" <td>8</td>\n",
" <td>PF-06740120</td>\n",
" <td>1000.000000</td>\n",
" <td>um</td>\n",
" <td>2</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"<p>9360 rows × 10 columns</p>\n",
"</div>"
],
"text/plain": [
" CellType BiologicalReplicate TimePointHours WellName Column Row \\\n",
"0 HPTEC 1 0 I3 3 9 \n",
"1 HPTEC 1 0 J3 3 10 \n",
"2 HPTEC 1 0 K3 3 11 \n",
"3 HPTEC 1 0 L3 3 12 \n",
"4 HPTEC 1 0 M3 3 13 \n",
"5 HPTEC 1 0 N3 3 14 \n",
"6 HPTEC 1 0 I4 4 9 \n",
"7 HPTEC 1 0 J4 4 10 \n",
"8 HPTEC 1 0 K4 4 11 \n",
"9 HPTEC 1 0 L4 4 12 \n",
"10 HPTEC 1 0 M4 4 13 \n",
"11 HPTEC 1 0 N4 4 14 \n",
"12 HPTEC 1 0 I5 5 9 \n",
"13 HPTEC 1 0 J5 5 10 \n",
"14 HPTEC 1 0 K5 5 11 \n",
"15 HPTEC 1 0 L5 5 12 \n",
"16 HPTEC 1 0 M5 5 13 \n",
"17 HPTEC 1 0 N5 5 14 \n",
"18 HPTEC 1 0 I6 6 9 \n",
"19 HPTEC 1 0 J6 6 10 \n",
"20 HPTEC 1 0 K6 6 11 \n",
"21 HPTEC 1 0 L6 6 12 \n",
"22 HPTEC 1 0 M6 6 13 \n",
"23 HPTEC 1 0 N6 6 14 \n",
"24 HPTEC 1 0 I7 7 9 \n",
"25 HPTEC 1 0 J7 7 10 \n",
"26 HPTEC 1 0 K7 7 11 \n",
"27 HPTEC 1 0 L7 7 12 \n",
"28 HPTEC 1 0 M7 7 13 \n",
"29 HPTEC 1 0 N7 7 14 \n",
"... ... ... ... ... ... ... \n",
"9330 OAT1 3 72 C18 18 3 \n",
"9331 OAT1 3 72 D18 18 4 \n",
"9332 OAT1 3 72 E18 18 5 \n",
"9333 OAT1 3 72 F18 18 6 \n",
"9334 OAT1 3 72 G18 18 7 \n",
"9335 OAT1 3 72 H18 18 8 \n",
"9336 OAT1 3 72 C19 19 3 \n",
"9337 OAT1 3 72 D19 19 4 \n",
"9338 OAT1 3 72 E19 19 5 \n",
"9339 OAT1 3 72 F19 19 6 \n",
"9340 OAT1 3 72 G19 19 7 \n",
"9341 OAT1 3 72 H19 19 8 \n",
"9342 OAT1 3 72 C20 20 3 \n",
"9343 OAT1 3 72 D20 20 4 \n",
"9344 OAT1 3 72 E20 20 5 \n",
"9345 OAT1 3 72 F20 20 6 \n",
"9346 OAT1 3 72 G20 20 7 \n",
"9347 OAT1 3 72 H20 20 8 \n",
"9348 OAT1 3 72 C21 21 3 \n",
"9349 OAT1 3 72 D21 21 4 \n",
"9350 OAT1 3 72 E21 21 5 \n",
"9351 OAT1 3 72 F21 21 6 \n",
"9352 OAT1 3 72 G21 21 7 \n",
"9353 OAT1 3 72 H21 21 8 \n",
"9354 OAT1 3 72 C22 22 3 \n",
"9355 OAT1 3 72 D22 22 4 \n",
"9356 OAT1 3 72 E22 22 5 \n",
"9357 OAT1 3 72 F22 22 6 \n",
"9358 OAT1 3 72 G22 22 7 \n",
"9359 OAT1 3 72 H22 22 8 \n",
"\n",
" pert_iname pert_dose pert_dose_unit pert_replicate \n",
"0 Aspirin 3.173691 um 1 \n",
"1 Aspirin 10.028862 um 1 \n",
"2 Aspirin 31.691205 um 1 \n",
"3 Aspirin 100.144208 um 1 \n",
"4 Aspirin 316.455696 um 1 \n",
"5 Aspirin 1000.000000 um 1 \n",
"6 Aspirin 3.173691 um 2 \n",
"7 Aspirin 10.028862 um 2 \n",
"8 Aspirin 31.691205 um 2 \n",
"9 Aspirin 100.144208 um 2 \n",
"10 Aspirin 316.455696 um 2 \n",
"11 Aspirin 1000.000000 um 2 \n",
"12 Sorbitol 3.173691 um 1 \n",
"13 Sorbitol 10.028862 um 1 \n",
"14 Sorbitol 31.691205 um 1 \n",
"15 Sorbitol 100.144208 um 1 \n",
"16 Sorbitol 316.455696 um 1 \n",
"17 Sorbitol 1000.000000 um 1 \n",
"18 Sorbitol 3.173691 um 2 \n",
"19 Sorbitol 10.028862 um 2 \n",
"20 Sorbitol 31.691205 um 2 \n",
"21 Sorbitol 100.144208 um 2 \n",
"22 Sorbitol 316.455696 um 2 \n",
"23 Sorbitol 1000.000000 um 2 \n",
"24 Acyclovir 3.173691 um 1 \n",
"25 Acyclovir 10.028862 um 1 \n",
"26 Acyclovir 31.691205 um 1 \n",
"27 Acyclovir 100.144208 um 1 \n",
"28 Acyclovir 316.455696 um 1 \n",
"29 Acyclovir 1000.000000 um 1 \n",
"... ... ... ... ... \n",
"9330 PF-05279870 1.586845 um 2 \n",
"9331 PF-05279870 5.014431 um 2 \n",
"9332 PF-05279870 15.845602 um 2 \n",
"9333 PF-05279870 50.072104 um 2 \n",
"9334 PF-05279870 158.227848 um 2 \n",
"9335 PF-05279870 500.000000 um 2 \n",
"9336 PF-06260618 1.586845 um 1 \n",
"9337 PF-06260618 5.014431 um 1 \n",
"9338 PF-06260618 15.845602 um 1 \n",
"9339 PF-06260618 50.072104 um 1 \n",
"9340 PF-06260618 158.227848 um 1 \n",
"9341 PF-06260618 500.000000 um 1 \n",
"9342 PF-06260618 1.586845 um 2 \n",
"9343 PF-06260618 5.014431 um 2 \n",
"9344 PF-06260618 15.845602 um 2 \n",
"9345 PF-06260618 50.072104 um 2 \n",
"9346 PF-06260618 158.227848 um 2 \n",
"9347 PF-06260618 500.000000 um 2 \n",
"9348 PF-06740120 3.173691 um 1 \n",
"9349 PF-06740120 10.028862 um 1 \n",
"9350 PF-06740120 31.691205 um 1 \n",
"9351 PF-06740120 100.144208 um 1 \n",
"9352 PF-06740120 316.455696 um 1 \n",
"9353 PF-06740120 1000.000000 um 1 \n",
"9354 PF-06740120 3.173691 um 2 \n",
"9355 PF-06740120 10.028862 um 2 \n",
"9356 PF-06740120 31.691205 um 2 \n",
"9357 PF-06740120 100.144208 um 2 \n",
"9358 PF-06740120 316.455696 um 2 \n",
"9359 PF-06740120 1000.000000 um 2 \n",
"\n",
"[9360 rows x 10 columns]"
]
},
"execution_count": 14,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"design"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Build list of all data files in sub-subdirectories"
]
},
{
"cell_type": "code",
"execution_count": 15,
"metadata": {
"collapsed": false
},
"outputs": [],
"source": [
"data_paths = sorted(p for p in input_path.glob('**/*.csv'))\n"
]
},
{
"cell_type": "code",
"execution_count": 16,
"metadata": {
"collapsed": false
},
"outputs": [],
"source": [
"data_struct = pd.DataFrame()\n",
"data_func = pd.DataFrame()\n"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Read one data file\n",
"This is just an example of reading and displaying a single data file. The full list is read in below."
]
},
{
"cell_type": "code",
"execution_count": 17,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"p = data_paths[0]"
]
},
{
"cell_type": "code",
"execution_count": 18,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/plain": [
"PosixPath('/Users/jmuhlich/development/ramm_screening_data_processing/input/20170516_hptec_oat1_two_panel/170511_Pfizer_PICS_HPTEC_4batch[5602]/Sim_000001[18614]/2017-05-11T130016-0400[22658]/struct_max_features_DPC_BasicFFC[7211533].result.1.csv')"
]
},
"execution_count": 18,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"p"
]
},
{
"cell_type": "code",
"execution_count": 19,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
" new_data = pd.read_csv(str(p), float_precision='high', encoding='utf-8',\n",
" parse_dates=['MeasurementDate'])\n"
]
},
{
"cell_type": "code",
"execution_count": 20,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
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" <thead>\n",
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" <th></th>\n",
" <th>ScreenName</th>\n",
" <th>ScreenID</th>\n",
" <th>PlateName</th>\n",
" <th>PlateID</th>\n",
" <th>MeasurementDate</th>\n",
" <th>MeasurementID</th>\n",
" <th>WellName</th>\n",
" <th>Row</th>\n",
" <th>Column</th>\n",
" <th>Timepoint</th>\n",
" <th>...</th>\n",
" <th>Nuclei - Texture Lysosomes Cell Texas Red SER Bright 1 px - Mean per Well</th>\n",
" <th>Nuclei - Texture Lysosomes Cell Texas Red SER Dark 1 px - Mean per Well</th>\n",
" <th>Nuclei - Cell Lysosomes Haralick Correlation 1 px - Mean per Well</th>\n",
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" <th>Nuclei - Cell Lysosomes Gabor Min 2 px w2 - Mean per Well</th>\n",
" <th>Nuclei - Cell Lysosomes Gabor Max 2 px w2 - Mean per Well</th>\n",
" <th>Number of Analyzed Fields</th>\n",
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" <tr>\n",
" <th>0</th>\n",
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" <td>18614</td>\n",
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" <td>0.039738</td>\n",
" <td>0.883412</td>\n",
" <td>0.051805</td>\n",
" <td>0.260911</td>\n",
" <td>0.419395</td>\n",
" <td>0.002370</td>\n",
" <td>0.014604</td>\n",
" <td>3</td>\n",
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" <tr>\n",
" <th>3</th>\n",
" <td>170511_Pfizer_PICS_HPTEC_4batch</td>\n",
" <td>5602</td>\n",
" <td>Sim_000001</td>\n",
" <td>18614</td>\n",
" <td>2017-05-11 17:00:16</td>\n",
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" <td>0.039631</td>\n",
" <td>0.885805</td>\n",
" <td>0.050463</td>\n",
" <td>0.253571</td>\n",
" <td>0.430671</td>\n",
" <td>0.002172</td>\n",
" <td>0.013341</td>\n",
" <td>3</td>\n",
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" <td>170511_Pfizer_PICS_HPTEC_4batch</td>\n",
" <td>5602</td>\n",
" <td>Sim_000001</td>\n",
" <td>18614</td>\n",
" <td>2017-05-11 17:00:16</td>\n",
" <td>22658</td>\n",
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" <td>0.040318</td>\n",
" <td>0.886857</td>\n",
" <td>0.053998</td>\n",
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" <td>0.014830</td>\n",
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" <tr>\n",
" <th>5</th>\n",
" <td>170511_Pfizer_PICS_HPTEC_4batch</td>\n",
" <td>5602</td>\n",
" <td>Sim_000001</td>\n",
" <td>18614</td>\n",
" <td>2017-05-11 17:00:16</td>\n",
" <td>22658</td>\n",
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" <td>8</td>\n",
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" <td>http://columbus.hms.harvard.edu/browse/measure...</td>\n",
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" <tr>\n",
" <th>6</th>\n",
" <td>170511_Pfizer_PICS_HPTEC_4batch</td>\n",
" <td>5602</td>\n",
" <td>Sim_000001</td>\n",
" <td>18614</td>\n",
" <td>2017-05-11 17:00:16</td>\n",
" <td>22658</td>\n",
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" <td>9</td>\n",
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" <td>0.041312</td>\n",
" <td>0.876270</td>\n",
" <td>0.059210</td>\n",
" <td>0.274224</td>\n",
" <td>0.414606</td>\n",
" <td>0.002590</td>\n",
" <td>0.015820</td>\n",
" <td>3</td>\n",
" <td>http://columbus.hms.harvard.edu/browse/measure...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>7</th>\n",
" <td>170511_Pfizer_PICS_HPTEC_4batch</td>\n",
" <td>5602</td>\n",
" <td>Sim_000001</td>\n",
" <td>18614</td>\n",
" <td>2017-05-11 17:00:16</td>\n",
" <td>22658</td>\n",
" <td>C10</td>\n",
" <td>3</td>\n",
" <td>10</td>\n",
" <td>1</td>\n",
" <td>...</td>\n",
" <td>0.025357</td>\n",
" <td>0.039461</td>\n",
" <td>0.880322</td>\n",
" <td>0.051778</td>\n",
" <td>0.248820</td>\n",
" <td>0.419539</td>\n",
" <td>0.002490</td>\n",
" <td>0.015299</td>\n",
" <td>3</td>\n",
" <td>http://columbus.hms.harvard.edu/browse/measure...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>8</th>\n",
" <td>170511_Pfizer_PICS_HPTEC_4batch</td>\n",
" <td>5602</td>\n",
" <td>Sim_000001</td>\n",
" <td>18614</td>\n",
" <td>2017-05-11 17:00:16</td>\n",
" <td>22658</td>\n",
" <td>C11</td>\n",
" <td>3</td>\n",
" <td>11</td>\n",
" <td>1</td>\n",
" <td>...</td>\n",
" <td>0.023544</td>\n",
" <td>0.036573</td>\n",
" <td>0.892732</td>\n",
" <td>0.044474</td>\n",
" <td>0.238439</td>\n",
" <td>0.435617</td>\n",
" <td>0.002183</td>\n",
" <td>0.013558</td>\n",
" <td>3</td>\n",
" <td>http://columbus.hms.harvard.edu/browse/measure...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>9</th>\n",
" <td>170511_Pfizer_PICS_HPTEC_4batch</td>\n",
" <td>5602</td>\n",
" <td>Sim_000001</td>\n",
" <td>18614</td>\n",
" <td>2017-05-11 17:00:16</td>\n",
" <td>22658</td>\n",
" <td>C12</td>\n",
" <td>3</td>\n",
" <td>12</td>\n",
" <td>1</td>\n",
" <td>...</td>\n",
" <td>0.025865</td>\n",
" <td>0.040598</td>\n",
" <td>0.877491</td>\n",
" <td>0.054786</td>\n",
" <td>0.257585</td>\n",
" <td>0.420966</td>\n",
" <td>0.002380</td>\n",
" <td>0.014631</td>\n",
" <td>3</td>\n",
" <td>http://columbus.hms.harvard.edu/browse/measure...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>10</th>\n",
" <td>170511_Pfizer_PICS_HPTEC_4batch</td>\n",
" <td>5602</td>\n",
" <td>Sim_000001</td>\n",
" <td>18614</td>\n",
" <td>2017-05-11 17:00:16</td>\n",
" <td>22658</td>\n",
" <td>C13</td>\n",
" <td>3</td>\n",
" <td>13</td>\n",
" <td>1</td>\n",
" <td>...</td>\n",
" <td>0.025107</td>\n",
" <td>0.039503</td>\n",
" <td>0.884573</td>\n",
" <td>0.053206</td>\n",
" <td>0.267229</td>\n",
" <td>0.424678</td>\n",
" <td>0.002350</td>\n",
" <td>0.014464</td>\n",
" <td>3</td>\n",
" <td>http://columbus.hms.harvard.edu/browse/measure...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>11</th>\n",
" <td>170511_Pfizer_PICS_HPTEC_4batch</td>\n",
" <td>5602</td>\n",
" <td>Sim_000001</td>\n",
" <td>18614</td>\n",
" <td>2017-05-11 17:00:16</td>\n",
" <td>22658</td>\n",
" <td>C14</td>\n",
" <td>3</td>\n",
" <td>14</td>\n",
" <td>1</td>\n",
" <td>...</td>\n",
" <td>0.024418</td>\n",
" <td>0.037880</td>\n",
" <td>0.887916</td>\n",
" <td>0.046467</td>\n",
" <td>0.240779</td>\n",
" <td>0.430344</td>\n",
" <td>0.002235</td>\n",
" <td>0.013833</td>\n",
" <td>3</td>\n",
" <td>http://columbus.hms.harvard.edu/browse/measure...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>12</th>\n",
" <td>170511_Pfizer_PICS_HPTEC_4batch</td>\n",
" <td>5602</td>\n",
" <td>Sim_000001</td>\n",
" <td>18614</td>\n",
" <td>2017-05-11 17:00:16</td>\n",
" <td>22658</td>\n",
" <td>C15</td>\n",
" <td>3</td>\n",
" <td>15</td>\n",
" <td>1</td>\n",
" <td>...</td>\n",
" <td>0.019342</td>\n",
" <td>0.028261</td>\n",
" <td>0.883340</td>\n",
" <td>0.034020</td>\n",
" <td>0.179612</td>\n",
" <td>0.458313</td>\n",
" <td>0.002367</td>\n",
" <td>0.014702</td>\n",
" <td>3</td>\n",
" <td>http://columbus.hms.harvard.edu/browse/measure...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>13</th>\n",
" <td>170511_Pfizer_PICS_HPTEC_4batch</td>\n",
" <td>5602</td>\n",
" <td>Sim_000001</td>\n",
" <td>18614</td>\n",
" <td>2017-05-11 17:00:16</td>\n",
" <td>22658</td>\n",
" <td>C16</td>\n",
" <td>3</td>\n",
" <td>16</td>\n",
" <td>1</td>\n",
" <td>...</td>\n",
" <td>0.024373</td>\n",
" <td>0.037548</td>\n",
" <td>0.875849</td>\n",
" <td>0.048003</td>\n",
" <td>0.233630</td>\n",
" <td>0.426251</td>\n",
" <td>0.002330</td>\n",
" <td>0.014470</td>\n",
" <td>3</td>\n",
" <td>http://columbus.hms.harvard.edu/browse/measure...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>14</th>\n",
" <td>170511_Pfizer_PICS_HPTEC_4batch</td>\n",
" <td>5602</td>\n",
" <td>Sim_000001</td>\n",
" <td>18614</td>\n",
" <td>2017-05-11 17:00:16</td>\n",
" <td>22658</td>\n",
" <td>C17</td>\n",
" <td>3</td>\n",
" <td>17</td>\n",
" <td>1</td>\n",
" <td>...</td>\n",
" <td>0.025843</td>\n",
" <td>0.040759</td>\n",
" <td>0.871708</td>\n",
" <td>0.055554</td>\n",
" <td>0.252852</td>\n",
" <td>0.424653</td>\n",
" <td>0.002383</td>\n",
" <td>0.014708</td>\n",
" <td>3</td>\n",
" <td>http://columbus.hms.harvard.edu/browse/measure...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>15</th>\n",
" <td>170511_Pfizer_PICS_HPTEC_4batch</td>\n",
" <td>5602</td>\n",
" <td>Sim_000001</td>\n",
" <td>18614</td>\n",
" <td>2017-05-11 17:00:16</td>\n",
" <td>22658</td>\n",
" <td>C18</td>\n",
" <td>3</td>\n",
" <td>18</td>\n",
" <td>1</td>\n",
" <td>...</td>\n",
" <td>0.026012</td>\n",
" <td>0.040611</td>\n",
" <td>0.867595</td>\n",
" <td>0.053206</td>\n",
" <td>0.233135</td>\n",
" <td>0.411209</td>\n",
" <td>0.002503</td>\n",
" <td>0.015495</td>\n",
" <td>3</td>\n",
" <td>http://columbus.hms.harvard.edu/browse/measure...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>16</th>\n",
" <td>170511_Pfizer_PICS_HPTEC_4batch</td>\n",
" <td>5602</td>\n",
" <td>Sim_000001</td>\n",
" <td>18614</td>\n",
" <td>2017-05-11 17:00:16</td>\n",
" <td>22658</td>\n",
" <td>C19</td>\n",
" <td>3</td>\n",
" <td>19</td>\n",
" <td>1</td>\n",
" <td>...</td>\n",
" <td>0.024514</td>\n",
" <td>0.038226</td>\n",
" <td>0.884716</td>\n",
" <td>0.046878</td>\n",
" <td>0.247199</td>\n",
" <td>0.431919</td>\n",
" <td>0.002212</td>\n",
" <td>0.013695</td>\n",
" <td>3</td>\n",
" <td>http://columbus.hms.harvard.edu/browse/measure...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>17</th>\n",
" <td>170511_Pfizer_PICS_HPTEC_4batch</td>\n",
" <td>5602</td>\n",
" <td>Sim_000001</td>\n",
" <td>18614</td>\n",
" <td>2017-05-11 17:00:16</td>\n",
" <td>22658</td>\n",
" <td>C20</td>\n",
" <td>3</td>\n",
" <td>20</td>\n",
" <td>1</td>\n",
" <td>...</td>\n",
" <td>0.023349</td>\n",
" <td>0.034439</td>\n",
" <td>0.875565</td>\n",
" <td>0.044993</td>\n",
" <td>0.223763</td>\n",
" <td>0.419200</td>\n",
" <td>0.002532</td>\n",
" <td>0.015829</td>\n",
" <td>3</td>\n",
" <td>http://columbus.hms.harvard.edu/browse/measure...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>18</th>\n",
" <td>170511_Pfizer_PICS_HPTEC_4batch</td>\n",
" <td>5602</td>\n",
" <td>Sim_000001</td>\n",
" <td>18614</td>\n",
" <td>2017-05-11 17:00:16</td>\n",
" <td>22658</td>\n",
" <td>C21</td>\n",
" <td>3</td>\n",
" <td>21</td>\n",
" <td>1</td>\n",
" <td>...</td>\n",
" <td>0.024049</td>\n",
" <td>0.037018</td>\n",
" <td>0.891968</td>\n",
" <td>0.043060</td>\n",
" <td>0.241829</td>\n",
" <td>0.424031</td>\n",
" <td>0.002259</td>\n",
" <td>0.014192</td>\n",
" <td>3</td>\n",
" <td>http://columbus.hms.harvard.edu/browse/measure...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>19</th>\n",
" <td>170511_Pfizer_PICS_HPTEC_4batch</td>\n",
" <td>5602</td>\n",
" <td>Sim_000001</td>\n",
" <td>18614</td>\n",
" <td>2017-05-11 17:00:16</td>\n",
" <td>22658</td>\n",
" <td>C22</td>\n",
" <td>3</td>\n",
" <td>22</td>\n",
" <td>1</td>\n",
" <td>...</td>\n",
" <td>0.022633</td>\n",
" <td>0.033373</td>\n",
" <td>0.880241</td>\n",
" <td>0.041985</td>\n",
" <td>0.222954</td>\n",
" <td>0.421580</td>\n",
" <td>0.002528</td>\n",
" <td>0.015832</td>\n",
" <td>3</td>\n",
" <td>http://columbus.hms.harvard.edu/browse/measure...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>20</th>\n",
" <td>170511_Pfizer_PICS_HPTEC_4batch</td>\n",
" <td>5602</td>\n",
" <td>Sim_000001</td>\n",
" <td>18614</td>\n",
" <td>2017-05-11 17:00:16</td>\n",
" <td>22658</td>\n",
" <td>D3</td>\n",
" <td>4</td>\n",
" <td>3</td>\n",
" <td>1</td>\n",
" <td>...</td>\n",
" <td>0.023159</td>\n",
" <td>0.036481</td>\n",
" <td>0.899404</td>\n",
" <td>0.046483</td>\n",
" <td>0.269205</td>\n",
" <td>0.428951</td>\n",
" <td>0.002323</td>\n",
" <td>0.014386</td>\n",
" <td>3</td>\n",
" <td>http://columbus.hms.harvard.edu/browse/measure...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>21</th>\n",
" <td>170511_Pfizer_PICS_HPTEC_4batch</td>\n",
" <td>5602</td>\n",
" <td>Sim_000001</td>\n",
" <td>18614</td>\n",
" <td>2017-05-11 17:00:16</td>\n",
" <td>22658</td>\n",
" <td>D4</td>\n",
" <td>4</td>\n",
" <td>4</td>\n",
" <td>1</td>\n",
" <td>...</td>\n",
" <td>0.024926</td>\n",
" <td>0.039920</td>\n",
" <td>0.896178</td>\n",
" <td>0.051066</td>\n",
" <td>0.290902</td>\n",
" <td>0.412370</td>\n",
" <td>0.002413</td>\n",
" <td>0.015048</td>\n",
" <td>3</td>\n",
" <td>http://columbus.hms.harvard.edu/browse/measure...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>22</th>\n",
" <td>170511_Pfizer_PICS_HPTEC_4batch</td>\n",
" <td>5602</td>\n",
" <td>Sim_000001</td>\n",
" <td>18614</td>\n",
" <td>2017-05-11 17:00:16</td>\n",
" <td>22658</td>\n",
" <td>D5</td>\n",
" <td>4</td>\n",
" <td>5</td>\n",
" <td>1</td>\n",
" <td>...</td>\n",
" <td>0.023903</td>\n",
" <td>0.038052</td>\n",
" <td>0.899046</td>\n",
" <td>0.046888</td>\n",
" <td>0.276939</td>\n",
" <td>0.422884</td>\n",
" <td>0.002332</td>\n",
" <td>0.014479</td>\n",
" <td>3</td>\n",
" <td>http://columbus.hms.harvard.edu/browse/measure...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>23</th>\n",
" <td>170511_Pfizer_PICS_HPTEC_4batch</td>\n",
" <td>5602</td>\n",
" <td>Sim_000001</td>\n",
" <td>18614</td>\n",
" <td>2017-05-11 17:00:16</td>\n",
" <td>22658</td>\n",
" <td>D6</td>\n",
" <td>4</td>\n",
" <td>6</td>\n",
" <td>1</td>\n",
" <td>...</td>\n",
" <td>0.025092</td>\n",
" <td>0.039491</td>\n",
" <td>0.891667</td>\n",
" <td>0.054293</td>\n",
" <td>0.290492</td>\n",
" <td>0.409910</td>\n",
" <td>0.002549</td>\n",
" <td>0.015806</td>\n",
" <td>3</td>\n",
" <td>http://columbus.hms.harvard.edu/browse/measure...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>24</th>\n",
" <td>170511_Pfizer_PICS_HPTEC_4batch</td>\n",
" <td>5602</td>\n",
" <td>Sim_000001</td>\n",
" <td>18614</td>\n",
" <td>2017-05-11 17:00:16</td>\n",
" <td>22658</td>\n",
" <td>D7</td>\n",
" <td>4</td>\n",
" <td>7</td>\n",
" <td>1</td>\n",
" <td>...</td>\n",
" <td>0.024460</td>\n",
" <td>0.037962</td>\n",
" <td>0.886278</td>\n",
" <td>0.051871</td>\n",
" <td>0.262153</td>\n",
" <td>0.422574</td>\n",
" <td>0.002503</td>\n",
" <td>0.015378</td>\n",
" <td>3</td>\n",
" <td>http://columbus.hms.harvard.edu/browse/measure...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>25</th>\n",
" <td>170511_Pfizer_PICS_HPTEC_4batch</td>\n",
" <td>5602</td>\n",
" <td>Sim_000001</td>\n",
" <td>18614</td>\n",
" <td>2017-05-11 17:00:16</td>\n",
" <td>22658</td>\n",
" <td>D8</td>\n",
" <td>4</td>\n",
" <td>8</td>\n",
" <td>1</td>\n",
" <td>...</td>\n",
" <td>0.023976</td>\n",
" <td>0.038074</td>\n",
" <td>0.899227</td>\n",
" <td>0.048638</td>\n",
" <td>0.278205</td>\n",
" <td>0.418891</td>\n",
" <td>0.002441</td>\n",
" <td>0.015179</td>\n",
" <td>3</td>\n",
" <td>http://columbus.hms.harvard.edu/browse/measure...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>26</th>\n",
" <td>170511_Pfizer_PICS_HPTEC_4batch</td>\n",
" <td>5602</td>\n",
" <td>Sim_000001</td>\n",
" <td>18614</td>\n",
" <td>2017-05-11 17:00:16</td>\n",
" <td>22658</td>\n",
" <td>D9</td>\n",
" <td>4</td>\n",
" <td>9</td>\n",
" <td>1</td>\n",
" <td>...</td>\n",
" <td>0.025600</td>\n",
" <td>0.040092</td>\n",
" <td>0.884507</td>\n",
" <td>0.053898</td>\n",
" <td>0.275341</td>\n",
" <td>0.410469</td>\n",
" <td>0.002538</td>\n",
" <td>0.015739</td>\n",
" <td>3</td>\n",
" <td>http://columbus.hms.harvard.edu/browse/measure...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>27</th>\n",
" <td>170511_Pfizer_PICS_HPTEC_4batch</td>\n",
" <td>5602</td>\n",
" <td>Sim_000001</td>\n",
" <td>18614</td>\n",
" <td>2017-05-11 17:00:16</td>\n",
" <td>22658</td>\n",
" <td>D10</td>\n",
" <td>4</td>\n",
" <td>10</td>\n",
" <td>1</td>\n",
" <td>...</td>\n",
" <td>0.025210</td>\n",
" <td>0.039549</td>\n",
" <td>0.877922</td>\n",
" <td>0.056915</td>\n",
" <td>0.274711</td>\n",
" <td>0.407508</td>\n",
" <td>0.002699</td>\n",
" <td>0.016684</td>\n",
" <td>3</td>\n",
" <td>http://columbus.hms.harvard.edu/browse/measure...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>28</th>\n",
" <td>170511_Pfizer_PICS_HPTEC_4batch</td>\n",
" <td>5602</td>\n",
" <td>Sim_000001</td>\n",
" <td>18614</td>\n",
" <td>2017-05-11 17:00:16</td>\n",
" <td>22658</td>\n",
" <td>D11</td>\n",
" <td>4</td>\n",
" <td>11</td>\n",
" <td>1</td>\n",
" <td>...</td>\n",
" <td>0.023366</td>\n",
" <td>0.034602</td>\n",
" <td>0.881070</td>\n",
" <td>0.048314</td>\n",
" <td>0.245975</td>\n",
" <td>0.413988</td>\n",
" <td>0.002668</td>\n",
" <td>0.016552</td>\n",
" <td>3</td>\n",
" <td>http://columbus.hms.harvard.edu/browse/measure...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>29</th>\n",
" <td>170511_Pfizer_PICS_HPTEC_4batch</td>\n",
" <td>5602</td>\n",
" <td>Sim_000001</td>\n",
" <td>18614</td>\n",
" <td>2017-05-11 17:00:16</td>\n",
" <td>22658</td>\n",
" <td>D12</td>\n",
" <td>4</td>\n",
" <td>12</td>\n",
" <td>1</td>\n",
" <td>...</td>\n",
" <td>0.025051</td>\n",
" <td>0.038637</td>\n",
" <td>0.874498</td>\n",
" <td>0.054170</td>\n",
" <td>0.259421</td>\n",
" <td>0.414380</td>\n",
" <td>0.002528</td>\n",
" <td>0.015750</td>\n",
" <td>3</td>\n",
" <td>http://columbus.hms.harvard.edu/browse/measure...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>...</th>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>210</th>\n",
" <td>170511_Pfizer_PICS_HPTEC_4batch</td>\n",
" <td>5602</td>\n",
" <td>Sim_000001</td>\n",
" <td>18614</td>\n",
" <td>2017-05-11 17:00:16</td>\n",
" <td>22658</td>\n",
" <td>M13</td>\n",
" <td>13</td>\n",
" <td>13</td>\n",
" <td>1</td>\n",
" <td>...</td>\n",
" <td>0.020137</td>\n",
" <td>0.028998</td>\n",
" <td>0.901512</td>\n",
" <td>0.033716</td>\n",
" <td>0.210589</td>\n",
" <td>0.443200</td>\n",
" <td>0.002323</td>\n",
" <td>0.014483</td>\n",
" <td>3</td>\n",
" <td>http://columbus.hms.harvard.edu/browse/measure...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>211</th>\n",
" <td>170511_Pfizer_PICS_HPTEC_4batch</td>\n",
" <td>5602</td>\n",
" <td>Sim_000001</td>\n",
" <td>18614</td>\n",
" <td>2017-05-11 17:00:16</td>\n",
" <td>22658</td>\n",
" <td>M14</td>\n",
" <td>13</td>\n",
" <td>14</td>\n",
" <td>1</td>\n",
" <td>...</td>\n",
" <td>0.019943</td>\n",
" <td>0.028722</td>\n",
" <td>0.903380</td>\n",
" <td>0.031592</td>\n",
" <td>0.201278</td>\n",
" <td>0.441867</td>\n",
" <td>0.002340</td>\n",
" <td>0.014607</td>\n",
" <td>3</td>\n",
" <td>http://columbus.hms.harvard.edu/browse/measure...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>212</th>\n",
" <td>170511_Pfizer_PICS_HPTEC_4batch</td>\n",
" <td>5602</td>\n",
" <td>Sim_000001</td>\n",
" <td>18614</td>\n",
" <td>2017-05-11 17:00:16</td>\n",
" <td>22658</td>\n",
" <td>M15</td>\n",
" <td>13</td>\n",
" <td>15</td>\n",
" <td>1</td>\n",
" <td>...</td>\n",
" <td>0.024451</td>\n",
" <td>0.037870</td>\n",
" <td>0.881057</td>\n",
" <td>0.048912</td>\n",
" <td>0.244019</td>\n",
" <td>0.424485</td>\n",
" <td>0.002361</td>\n",
" <td>0.014688</td>\n",
" <td>3</td>\n",
" <td>http://columbus.hms.harvard.edu/browse/measure...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>213</th>\n",
" <td>170511_Pfizer_PICS_HPTEC_4batch</td>\n",
" <td>5602</td>\n",
" <td>Sim_000001</td>\n",
" <td>18614</td>\n",
" <td>2017-05-11 17:00:16</td>\n",
" <td>22658</td>\n",
" <td>M16</td>\n",
" <td>13</td>\n",
" <td>16</td>\n",
" <td>1</td>\n",
" <td>...</td>\n",
" <td>0.023698</td>\n",
" <td>0.036366</td>\n",
" <td>0.885574</td>\n",
" <td>0.042993</td>\n",
" <td>0.226103</td>\n",
" <td>0.430971</td>\n",
" <td>0.002206</td>\n",
" <td>0.013770</td>\n",
" <td>3</td>\n",
" <td>http://columbus.hms.harvard.edu/browse/measure...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>214</th>\n",
" <td>170511_Pfizer_PICS_HPTEC_4batch</td>\n",
" <td>5602</td>\n",
" <td>Sim_000001</td>\n",
" <td>18614</td>\n",
" <td>2017-05-11 17:00:16</td>\n",
" <td>22658</td>\n",
" <td>M17</td>\n",
" <td>13</td>\n",
" <td>17</td>\n",
" <td>1</td>\n",
" <td>...</td>\n",
" <td>0.021039</td>\n",
" <td>0.031967</td>\n",
" <td>0.906546</td>\n",
" <td>0.042127</td>\n",
" <td>0.267935</td>\n",
" <td>0.443116</td>\n",
" <td>0.002287</td>\n",
" <td>0.014287</td>\n",
" <td>3</td>\n",
" <td>http://columbus.hms.harvard.edu/browse/measure...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>215</th>\n",
" <td>170511_Pfizer_PICS_HPTEC_4batch</td>\n",
" <td>5602</td>\n",
" <td>Sim_000001</td>\n",
" <td>18614</td>\n",
" <td>2017-05-11 17:00:16</td>\n",
" <td>22658</td>\n",
" <td>M18</td>\n",
" <td>13</td>\n",
" <td>18</td>\n",
" <td>1</td>\n",
" <td>...</td>\n",
" <td>0.020297</td>\n",
" <td>0.029575</td>\n",
" <td>0.897194</td>\n",
" <td>0.043770</td>\n",
" <td>0.260896</td>\n",
" <td>0.442182</td>\n",
" <td>0.002504</td>\n",
" <td>0.015615</td>\n",
" <td>3</td>\n",
" <td>http://columbus.hms.harvard.edu/browse/measure...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>216</th>\n",
" <td>170511_Pfizer_PICS_HPTEC_4batch</td>\n",
" <td>5602</td>\n",
" <td>Sim_000001</td>\n",
" <td>18614</td>\n",
" <td>2017-05-11 17:00:16</td>\n",
" <td>22658</td>\n",
" <td>M19</td>\n",
" <td>13</td>\n",
" <td>19</td>\n",
" <td>1</td>\n",
" <td>...</td>\n",
" <td>0.024524</td>\n",
" <td>0.037643</td>\n",
" <td>0.881941</td>\n",
" <td>0.046550</td>\n",
" <td>0.234783</td>\n",
" <td>0.422010</td>\n",
" <td>0.002360</td>\n",
" <td>0.014807</td>\n",
" <td>3</td>\n",
" <td>http://columbus.hms.harvard.edu/browse/measure...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>217</th>\n",
" <td>170511_Pfizer_PICS_HPTEC_4batch</td>\n",
" <td>5602</td>\n",
" <td>Sim_000001</td>\n",
" <td>18614</td>\n",
" <td>2017-05-11 17:00:16</td>\n",
" <td>22658</td>\n",
" <td>M20</td>\n",
" <td>13</td>\n",
" <td>20</td>\n",
" <td>1</td>\n",
" <td>...</td>\n",
" <td>0.023390</td>\n",
" <td>0.035260</td>\n",
" <td>0.879411</td>\n",
" <td>0.047469</td>\n",
" <td>0.240944</td>\n",
" <td>0.427377</td>\n",
" <td>0.002408</td>\n",
" <td>0.014989</td>\n",
" <td>3</td>\n",
" <td>http://columbus.hms.harvard.edu/browse/measure...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>218</th>\n",
" <td>170511_Pfizer_PICS_HPTEC_4batch</td>\n",
" <td>5602</td>\n",
" <td>Sim_000001</td>\n",
" <td>18614</td>\n",
" <td>2017-05-11 17:00:16</td>\n",
" <td>22658</td>\n",
" <td>M21</td>\n",
" <td>13</td>\n",
" <td>21</td>\n",
" <td>1</td>\n",
" <td>...</td>\n",
" <td>0.022586</td>\n",
" <td>0.032869</td>\n",
" <td>0.877435</td>\n",
" <td>0.043283</td>\n",
" <td>0.217641</td>\n",
" <td>0.424843</td>\n",
" <td>0.002518</td>\n",
" <td>0.015798</td>\n",
" <td>3</td>\n",
" <td>http://columbus.hms.harvard.edu/browse/measure...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>219</th>\n",
" <td>170511_Pfizer_PICS_HPTEC_4batch</td>\n",
" <td>5602</td>\n",
" <td>Sim_000001</td>\n",
" <td>18614</td>\n",
" <td>2017-05-11 17:00:16</td>\n",
" <td>22658</td>\n",
" <td>M22</td>\n",
" <td>13</td>\n",
" <td>22</td>\n",
" <td>1</td>\n",
" <td>...</td>\n",
" <td>0.022724</td>\n",
" <td>0.033094</td>\n",
" <td>0.877403</td>\n",
" <td>0.044062</td>\n",
" <td>0.220137</td>\n",
" <td>0.420403</td>\n",
" <td>0.002550</td>\n",
" <td>0.016004</td>\n",
" <td>3</td>\n",
" <td>http://columbus.hms.harvard.edu/browse/measure...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>220</th>\n",
" <td>170511_Pfizer_PICS_HPTEC_4batch</td>\n",
" <td>5602</td>\n",
" <td>Sim_000001</td>\n",
" <td>18614</td>\n",
" <td>2017-05-11 17:00:16</td>\n",
" <td>22658</td>\n",
" <td>N3</td>\n",
" <td>14</td>\n",
" <td>3</td>\n",
" <td>1</td>\n",
" <td>...</td>\n",
" <td>0.024896</td>\n",
" <td>0.037856</td>\n",
" <td>0.881585</td>\n",
" <td>0.049779</td>\n",
" <td>0.257941</td>\n",
" <td>0.396120</td>\n",
" <td>0.002858</td>\n",
" <td>0.017746</td>\n",
" <td>3</td>\n",
" <td>http://columbus.hms.harvard.edu/browse/measure...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>221</th>\n",
" <td>170511_Pfizer_PICS_HPTEC_4batch</td>\n",
" <td>5602</td>\n",
" <td>Sim_000001</td>\n",
" <td>18614</td>\n",
" <td>2017-05-11 17:00:16</td>\n",
" <td>22658</td>\n",
" <td>N4</td>\n",
" <td>14</td>\n",
" <td>4</td>\n",
" <td>1</td>\n",
" <td>...</td>\n",
" <td>0.025618</td>\n",
" <td>0.040052</td>\n",
" <td>0.886201</td>\n",
" <td>0.055973</td>\n",
" <td>0.295966</td>\n",
" <td>0.392844</td>\n",
" <td>0.002887</td>\n",
" <td>0.017947</td>\n",
" <td>3</td>\n",
" <td>http://columbus.hms.harvard.edu/browse/measure...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>222</th>\n",
" <td>170511_Pfizer_PICS_HPTEC_4batch</td>\n",
" <td>5602</td>\n",
" <td>Sim_000001</td>\n",
" <td>18614</td>\n",
" <td>2017-05-11 17:00:16</td>\n",
" <td>22658</td>\n",
" <td>N5</td>\n",
" <td>14</td>\n",
" <td>5</td>\n",
" <td>1</td>\n",
" <td>...</td>\n",
" <td>0.025211</td>\n",
" <td>0.039746</td>\n",
" <td>0.885883</td>\n",
" <td>0.052552</td>\n",
" <td>0.275548</td>\n",
" <td>0.400147</td>\n",
" <td>0.002760</td>\n",
" <td>0.017108</td>\n",
" <td>3</td>\n",
" <td>http://columbus.hms.harvard.edu/browse/measure...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>223</th>\n",
" <td>170511_Pfizer_PICS_HPTEC_4batch</td>\n",
" <td>5602</td>\n",
" <td>Sim_000001</td>\n",
" <td>18614</td>\n",
" <td>2017-05-11 17:00:16</td>\n",
" <td>22658</td>\n",
" <td>N6</td>\n",
" <td>14</td>\n",
" <td>6</td>\n",
" <td>1</td>\n",
" <td>...</td>\n",
" <td>0.024944</td>\n",
" <td>0.036893</td>\n",
" <td>0.873574</td>\n",
" <td>0.056881</td>\n",
" <td>0.263325</td>\n",
" <td>0.380339</td>\n",
" <td>0.003237</td>\n",
" <td>0.020105</td>\n",
" <td>3</td>\n",
" <td>http://columbus.hms.harvard.edu/browse/measure...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>224</th>\n",
" <td>170511_Pfizer_PICS_HPTEC_4batch</td>\n",
" <td>5602</td>\n",
" <td>Sim_000001</td>\n",
" <td>18614</td>\n",
" <td>2017-05-11 17:00:16</td>\n",
" <td>22658</td>\n",
" <td>N7</td>\n",
" <td>14</td>\n",
" <td>7</td>\n",
" <td>1</td>\n",
" <td>...</td>\n",
" <td>0.025544</td>\n",
" <td>0.039259</td>\n",
" <td>0.873622</td>\n",
" <td>0.054273</td>\n",
" <td>0.259939</td>\n",
" <td>0.395110</td>\n",
" <td>0.002847</td>\n",
" <td>0.017638</td>\n",
" <td>3</td>\n",
" <td>http://columbus.hms.harvard.edu/browse/measure...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>225</th>\n",
" <td>170511_Pfizer_PICS_HPTEC_4batch</td>\n",
" <td>5602</td>\n",
" <td>Sim_000001</td>\n",
" <td>18614</td>\n",
" <td>2017-05-11 17:00:16</td>\n",
" <td>22658</td>\n",
" <td>N8</td>\n",
" <td>14</td>\n",
" <td>8</td>\n",
" <td>1</td>\n",
" <td>...</td>\n",
" <td>0.024782</td>\n",
" <td>0.038302</td>\n",
" <td>0.878694</td>\n",
" <td>0.053250</td>\n",
" <td>0.269332</td>\n",
" <td>0.400954</td>\n",
" <td>0.002846</td>\n",
" <td>0.017593</td>\n",
" <td>3</td>\n",
" <td>http://columbus.hms.harvard.edu/browse/measure...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>226</th>\n",
" <td>170511_Pfizer_PICS_HPTEC_4batch</td>\n",
" <td>5602</td>\n",
" <td>Sim_000001</td>\n",
" <td>18614</td>\n",
" <td>2017-05-11 17:00:16</td>\n",
" <td>22658</td>\n",
" <td>N9</td>\n",
" <td>14</td>\n",
" <td>9</td>\n",
" <td>1</td>\n",
" <td>...</td>\n",
" <td>0.025060</td>\n",
" <td>0.037902</td>\n",
" <td>0.869723</td>\n",
" <td>0.054831</td>\n",
" <td>0.253384</td>\n",
" <td>0.391293</td>\n",
" <td>0.003005</td>\n",
" <td>0.018664</td>\n",
" <td>3</td>\n",
" <td>http://columbus.hms.harvard.edu/browse/measure...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>227</th>\n",
" <td>170511_Pfizer_PICS_HPTEC_4batch</td>\n",
" <td>5602</td>\n",
" <td>Sim_000001</td>\n",
" <td>18614</td>\n",
" <td>2017-05-11 17:00:16</td>\n",
" <td>22658</td>\n",
" <td>N10</td>\n",
" <td>14</td>\n",
" <td>10</td>\n",
" <td>1</td>\n",
" <td>...</td>\n",
" <td>0.025185</td>\n",
" <td>0.037612</td>\n",
" <td>0.864047</td>\n",
" <td>0.056471</td>\n",
" <td>0.248876</td>\n",
" <td>0.382022</td>\n",
" <td>0.003184</td>\n",
" <td>0.019792</td>\n",
" <td>3</td>\n",
" <td>http://columbus.hms.harvard.edu/browse/measure...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>228</th>\n",
" <td>170511_Pfizer_PICS_HPTEC_4batch</td>\n",
" <td>5602</td>\n",
" <td>Sim_000001</td>\n",
" <td>18614</td>\n",
" <td>2017-05-11 17:00:16</td>\n",
" <td>22658</td>\n",
" <td>N11</td>\n",
" <td>14</td>\n",
" <td>11</td>\n",
" <td>1</td>\n",
" <td>...</td>\n",
" <td>0.021619</td>\n",
" <td>0.031006</td>\n",
" <td>0.889198</td>\n",
" <td>0.042591</td>\n",
" <td>0.236914</td>\n",
" <td>0.400721</td>\n",
" <td>0.003006</td>\n",
" <td>0.018761</td>\n",
" <td>3</td>\n",
" <td>http://columbus.hms.harvard.edu/browse/measure...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>229</th>\n",
" <td>170511_Pfizer_PICS_HPTEC_4batch</td>\n",
" <td>5602</td>\n",
" <td>Sim_000001</td>\n",
" <td>18614</td>\n",
" <td>2017-05-11 17:00:16</td>\n",
" <td>22658</td>\n",
" <td>N12</td>\n",
" <td>14</td>\n",
" <td>12</td>\n",
" <td>1</td>\n",
" <td>...</td>\n",
" <td>0.023554</td>\n",
" <td>0.036511</td>\n",
" <td>0.886336</td>\n",
" <td>0.045864</td>\n",
" <td>0.246295</td>\n",
" <td>0.426091</td>\n",
" <td>0.002370</td>\n",
" <td>0.014728</td>\n",
" <td>3</td>\n",
" <td>http://columbus.hms.harvard.edu/browse/measure...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>230</th>\n",
" <td>170511_Pfizer_PICS_HPTEC_4batch</td>\n",
" <td>5602</td>\n",
" <td>Sim_000001</td>\n",
" <td>18614</td>\n",
" <td>2017-05-11 17:00:16</td>\n",
" <td>22658</td>\n",
" <td>N13</td>\n",
" <td>14</td>\n",
" <td>13</td>\n",
" <td>1</td>\n",
" <td>...</td>\n",
" <td>0.018021</td>\n",
" <td>0.024361</td>\n",
" <td>0.893440</td>\n",
" <td>0.026240</td>\n",
" <td>0.157816</td>\n",
" <td>0.425453</td>\n",
" <td>0.002819</td>\n",
" <td>0.017591</td>\n",
" <td>3</td>\n",
" <td>http://columbus.hms.harvard.edu/browse/measure...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>231</th>\n",
" <td>170511_Pfizer_PICS_HPTEC_4batch</td>\n",
" <td>5602</td>\n",
" <td>Sim_000001</td>\n",
" <td>18614</td>\n",
" <td>2017-05-11 17:00:16</td>\n",
" <td>22658</td>\n",
" <td>N14</td>\n",
" <td>14</td>\n",
" <td>14</td>\n",
" <td>1</td>\n",
" <td>...</td>\n",
" <td>0.019456</td>\n",
" <td>0.026059</td>\n",
" <td>0.884442</td>\n",
" <td>0.029933</td>\n",
" <td>0.158828</td>\n",
" <td>0.397340</td>\n",
" <td>0.003167</td>\n",
" <td>0.019761</td>\n",
" <td>3</td>\n",
" <td>http://columbus.hms.harvard.edu/browse/measure...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>232</th>\n",
" <td>170511_Pfizer_PICS_HPTEC_4batch</td>\n",
" <td>5602</td>\n",
" <td>Sim_000001</td>\n",
" <td>18614</td>\n",
" <td>2017-05-11 17:00:16</td>\n",
" <td>22658</td>\n",
" <td>N15</td>\n",
" <td>14</td>\n",
" <td>15</td>\n",
" <td>1</td>\n",
" <td>...</td>\n",
" <td>0.023994</td>\n",
" <td>0.035877</td>\n",
" <td>0.879783</td>\n",
" <td>0.045512</td>\n",
" <td>0.233954</td>\n",
" <td>0.405180</td>\n",
" <td>0.002701</td>\n",
" <td>0.016816</td>\n",
" <td>3</td>\n",
" <td>http://columbus.hms.harvard.edu/browse/measure...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>233</th>\n",
" <td>170511_Pfizer_PICS_HPTEC_4batch</td>\n",
" <td>5602</td>\n",
" <td>Sim_000001</td>\n",
" <td>18614</td>\n",
" <td>2017-05-11 17:00:16</td>\n",
" <td>22658</td>\n",
" <td>N16</td>\n",
" <td>14</td>\n",
" <td>16</td>\n",
" <td>1</td>\n",
" <td>...</td>\n",
" <td>0.024097</td>\n",
" <td>0.036153</td>\n",
" <td>0.875693</td>\n",
" <td>0.045642</td>\n",
" <td>0.222333</td>\n",
" <td>0.403922</td>\n",
" <td>0.002769</td>\n",
" <td>0.017250</td>\n",
" <td>3</td>\n",
" <td>http://columbus.hms.harvard.edu/browse/measure...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>234</th>\n",
" <td>170511_Pfizer_PICS_HPTEC_4batch</td>\n",
" <td>5602</td>\n",
" <td>Sim_000001</td>\n",
" <td>18614</td>\n",
" <td>2017-05-11 17:00:16</td>\n",
" <td>22658</td>\n",
" <td>N17</td>\n",
" <td>14</td>\n",
" <td>17</td>\n",
" <td>1</td>\n",
" <td>...</td>\n",
" <td>0.018380</td>\n",
" <td>0.028198</td>\n",
" <td>0.916090</td>\n",
" <td>0.049026</td>\n",
" <td>0.397918</td>\n",
" <td>0.412545</td>\n",
" <td>0.003071</td>\n",
" <td>0.019216</td>\n",
" <td>3</td>\n",
" <td>http://columbus.hms.harvard.edu/browse/measure...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>235</th>\n",
" <td>170511_Pfizer_PICS_HPTEC_4batch</td>\n",
" <td>5602</td>\n",
" <td>Sim_000001</td>\n",
" <td>18614</td>\n",
" <td>2017-05-11 17:00:16</td>\n",
" <td>22658</td>\n",
" <td>N18</td>\n",
" <td>14</td>\n",
" <td>18</td>\n",
" <td>1</td>\n",
" <td>...</td>\n",
" <td>0.018462</td>\n",
" <td>0.029761</td>\n",
" <td>0.928694</td>\n",
" <td>0.051590</td>\n",
" <td>0.446623</td>\n",
" <td>0.413638</td>\n",
" <td>0.003010</td>\n",
" <td>0.018774</td>\n",
" <td>3</td>\n",
" <td>http://columbus.hms.harvard.edu/browse/measure...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>236</th>\n",
" <td>170511_Pfizer_PICS_HPTEC_4batch</td>\n",
" <td>5602</td>\n",
" <td>Sim_000001</td>\n",
" <td>18614</td>\n",
" <td>2017-05-11 17:00:16</td>\n",
" <td>22658</td>\n",
" <td>N19</td>\n",
" <td>14</td>\n",
" <td>19</td>\n",
" <td>1</td>\n",
" <td>...</td>\n",
" <td>0.024035</td>\n",
" <td>0.035412</td>\n",
" <td>0.864277</td>\n",
" <td>0.048963</td>\n",
" <td>0.225018</td>\n",
" <td>0.400462</td>\n",
" <td>0.002904</td>\n",
" <td>0.018058</td>\n",
" <td>3</td>\n",
" <td>http://columbus.hms.harvard.edu/browse/measure...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>237</th>\n",
" <td>170511_Pfizer_PICS_HPTEC_4batch</td>\n",
" <td>5602</td>\n",
" <td>Sim_000001</td>\n",
" <td>18614</td>\n",
" <td>2017-05-11 17:00:16</td>\n",
" <td>22658</td>\n",
" <td>N20</td>\n",
" <td>14</td>\n",
" <td>20</td>\n",
" <td>1</td>\n",
" <td>...</td>\n",
" <td>0.024591</td>\n",
" <td>0.037806</td>\n",
" <td>0.875561</td>\n",
" <td>0.050159</td>\n",
" <td>0.248539</td>\n",
" <td>0.410022</td>\n",
" <td>0.002611</td>\n",
" <td>0.016371</td>\n",
" <td>3</td>\n",
" <td>http://columbus.hms.harvard.edu/browse/measure...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>238</th>\n",
" <td>170511_Pfizer_PICS_HPTEC_4batch</td>\n",
" <td>5602</td>\n",
" <td>Sim_000001</td>\n",
" <td>18614</td>\n",
" <td>2017-05-11 17:00:16</td>\n",
" <td>22658</td>\n",
" <td>N21</td>\n",
" <td>14</td>\n",
" <td>21</td>\n",
" <td>1</td>\n",
" <td>...</td>\n",
" <td>0.023336</td>\n",
" <td>0.034819</td>\n",
" <td>0.878887</td>\n",
" <td>0.043985</td>\n",
" <td>0.231720</td>\n",
" <td>0.403556</td>\n",
" <td>0.002789</td>\n",
" <td>0.017389</td>\n",
" <td>3</td>\n",
" <td>http://columbus.hms.harvard.edu/browse/measure...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>239</th>\n",
" <td>170511_Pfizer_PICS_HPTEC_4batch</td>\n",
" <td>5602</td>\n",
" <td>Sim_000001</td>\n",
" <td>18614</td>\n",
" <td>2017-05-11 17:00:16</td>\n",
" <td>22658</td>\n",
" <td>N22</td>\n",
" <td>14</td>\n",
" <td>22</td>\n",
" <td>1</td>\n",
" <td>...</td>\n",
" <td>0.023124</td>\n",
" <td>0.033662</td>\n",
" <td>0.863765</td>\n",
" <td>0.047918</td>\n",
" <td>0.229280</td>\n",
" <td>0.395416</td>\n",
" <td>0.003024</td>\n",
" <td>0.018916</td>\n",
" <td>3</td>\n",
" <td>http://columbus.hms.harvard.edu/browse/measure...</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"<p>240 rows × 525 columns</p>\n",
"</div>"
],
"text/plain": [
" ScreenName ScreenID PlateName PlateID \\\n",
"0 170511_Pfizer_PICS_HPTEC_4batch 5602 Sim_000001 18614 \n",
"1 170511_Pfizer_PICS_HPTEC_4batch 5602 Sim_000001 18614 \n",
"2 170511_Pfizer_PICS_HPTEC_4batch 5602 Sim_000001 18614 \n",
"3 170511_Pfizer_PICS_HPTEC_4batch 5602 Sim_000001 18614 \n",
"4 170511_Pfizer_PICS_HPTEC_4batch 5602 Sim_000001 18614 \n",
"5 170511_Pfizer_PICS_HPTEC_4batch 5602 Sim_000001 18614 \n",
"6 170511_Pfizer_PICS_HPTEC_4batch 5602 Sim_000001 18614 \n",
"7 170511_Pfizer_PICS_HPTEC_4batch 5602 Sim_000001 18614 \n",
"8 170511_Pfizer_PICS_HPTEC_4batch 5602 Sim_000001 18614 \n",
"9 170511_Pfizer_PICS_HPTEC_4batch 5602 Sim_000001 18614 \n",
"10 170511_Pfizer_PICS_HPTEC_4batch 5602 Sim_000001 18614 \n",
"11 170511_Pfizer_PICS_HPTEC_4batch 5602 Sim_000001 18614 \n",
"12 170511_Pfizer_PICS_HPTEC_4batch 5602 Sim_000001 18614 \n",
"13 170511_Pfizer_PICS_HPTEC_4batch 5602 Sim_000001 18614 \n",
"14 170511_Pfizer_PICS_HPTEC_4batch 5602 Sim_000001 18614 \n",
"15 170511_Pfizer_PICS_HPTEC_4batch 5602 Sim_000001 18614 \n",
"16 170511_Pfizer_PICS_HPTEC_4batch 5602 Sim_000001 18614 \n",
"17 170511_Pfizer_PICS_HPTEC_4batch 5602 Sim_000001 18614 \n",
"18 170511_Pfizer_PICS_HPTEC_4batch 5602 Sim_000001 18614 \n",
"19 170511_Pfizer_PICS_HPTEC_4batch 5602 Sim_000001 18614 \n",
"20 170511_Pfizer_PICS_HPTEC_4batch 5602 Sim_000001 18614 \n",
"21 170511_Pfizer_PICS_HPTEC_4batch 5602 Sim_000001 18614 \n",
"22 170511_Pfizer_PICS_HPTEC_4batch 5602 Sim_000001 18614 \n",
"23 170511_Pfizer_PICS_HPTEC_4batch 5602 Sim_000001 18614 \n",
"24 170511_Pfizer_PICS_HPTEC_4batch 5602 Sim_000001 18614 \n",
"25 170511_Pfizer_PICS_HPTEC_4batch 5602 Sim_000001 18614 \n",
"26 170511_Pfizer_PICS_HPTEC_4batch 5602 Sim_000001 18614 \n",
"27 170511_Pfizer_PICS_HPTEC_4batch 5602 Sim_000001 18614 \n",
"28 170511_Pfizer_PICS_HPTEC_4batch 5602 Sim_000001 18614 \n",
"29 170511_Pfizer_PICS_HPTEC_4batch 5602 Sim_000001 18614 \n",
".. ... ... ... ... \n",
"210 170511_Pfizer_PICS_HPTEC_4batch 5602 Sim_000001 18614 \n",
"211 170511_Pfizer_PICS_HPTEC_4batch 5602 Sim_000001 18614 \n",
"212 170511_Pfizer_PICS_HPTEC_4batch 5602 Sim_000001 18614 \n",
"213 170511_Pfizer_PICS_HPTEC_4batch 5602 Sim_000001 18614 \n",
"214 170511_Pfizer_PICS_HPTEC_4batch 5602 Sim_000001 18614 \n",
"215 170511_Pfizer_PICS_HPTEC_4batch 5602 Sim_000001 18614 \n",
"216 170511_Pfizer_PICS_HPTEC_4batch 5602 Sim_000001 18614 \n",
"217 170511_Pfizer_PICS_HPTEC_4batch 5602 Sim_000001 18614 \n",
"218 170511_Pfizer_PICS_HPTEC_4batch 5602 Sim_000001 18614 \n",
"219 170511_Pfizer_PICS_HPTEC_4batch 5602 Sim_000001 18614 \n",
"220 170511_Pfizer_PICS_HPTEC_4batch 5602 Sim_000001 18614 \n",
"221 170511_Pfizer_PICS_HPTEC_4batch 5602 Sim_000001 18614 \n",
"222 170511_Pfizer_PICS_HPTEC_4batch 5602 Sim_000001 18614 \n",
"223 170511_Pfizer_PICS_HPTEC_4batch 5602 Sim_000001 18614 \n",
"224 170511_Pfizer_PICS_HPTEC_4batch 5602 Sim_000001 18614 \n",
"225 170511_Pfizer_PICS_HPTEC_4batch 5602 Sim_000001 18614 \n",
"226 170511_Pfizer_PICS_HPTEC_4batch 5602 Sim_000001 18614 \n",
"227 170511_Pfizer_PICS_HPTEC_4batch 5602 Sim_000001 18614 \n",
"228 170511_Pfizer_PICS_HPTEC_4batch 5602 Sim_000001 18614 \n",
"229 170511_Pfizer_PICS_HPTEC_4batch 5602 Sim_000001 18614 \n",
"230 170511_Pfizer_PICS_HPTEC_4batch 5602 Sim_000001 18614 \n",
"231 170511_Pfizer_PICS_HPTEC_4batch 5602 Sim_000001 18614 \n",
"232 170511_Pfizer_PICS_HPTEC_4batch 5602 Sim_000001 18614 \n",
"233 170511_Pfizer_PICS_HPTEC_4batch 5602 Sim_000001 18614 \n",
"234 170511_Pfizer_PICS_HPTEC_4batch 5602 Sim_000001 18614 \n",
"235 170511_Pfizer_PICS_HPTEC_4batch 5602 Sim_000001 18614 \n",
"236 170511_Pfizer_PICS_HPTEC_4batch 5602 Sim_000001 18614 \n",
"237 170511_Pfizer_PICS_HPTEC_4batch 5602 Sim_000001 18614 \n",
"238 170511_Pfizer_PICS_HPTEC_4batch 5602 Sim_000001 18614 \n",
"239 170511_Pfizer_PICS_HPTEC_4batch 5602 Sim_000001 18614 \n",
"\n",
" MeasurementDate MeasurementID WellName Row Column Timepoint \\\n",
"0 2017-05-11 17:00:16 22658 C3 3 3 1 \n",
"1 2017-05-11 17:00:16 22658 C4 3 4 1 \n",
"2 2017-05-11 17:00:16 22658 C5 3 5 1 \n",
"3 2017-05-11 17:00:16 22658 C6 3 6 1 \n",
"4 2017-05-11 17:00:16 22658 C7 3 7 1 \n",
"5 2017-05-11 17:00:16 22658 C8 3 8 1 \n",
"6 2017-05-11 17:00:16 22658 C9 3 9 1 \n",
"7 2017-05-11 17:00:16 22658 C10 3 10 1 \n",
"8 2017-05-11 17:00:16 22658 C11 3 11 1 \n",
"9 2017-05-11 17:00:16 22658 C12 3 12 1 \n",
"10 2017-05-11 17:00:16 22658 C13 3 13 1 \n",
"11 2017-05-11 17:00:16 22658 C14 3 14 1 \n",
"12 2017-05-11 17:00:16 22658 C15 3 15 1 \n",
"13 2017-05-11 17:00:16 22658 C16 3 16 1 \n",
"14 2017-05-11 17:00:16 22658 C17 3 17 1 \n",
"15 2017-05-11 17:00:16 22658 C18 3 18 1 \n",
"16 2017-05-11 17:00:16 22658 C19 3 19 1 \n",
"17 2017-05-11 17:00:16 22658 C20 3 20 1 \n",
"18 2017-05-11 17:00:16 22658 C21 3 21 1 \n",
"19 2017-05-11 17:00:16 22658 C22 3 22 1 \n",
"20 2017-05-11 17:00:16 22658 D3 4 3 1 \n",
"21 2017-05-11 17:00:16 22658 D4 4 4 1 \n",
"22 2017-05-11 17:00:16 22658 D5 4 5 1 \n",
"23 2017-05-11 17:00:16 22658 D6 4 6 1 \n",
"24 2017-05-11 17:00:16 22658 D7 4 7 1 \n",
"25 2017-05-11 17:00:16 22658 D8 4 8 1 \n",
"26 2017-05-11 17:00:16 22658 D9 4 9 1 \n",
"27 2017-05-11 17:00:16 22658 D10 4 10 1 \n",
"28 2017-05-11 17:00:16 22658 D11 4 11 1 \n",
"29 2017-05-11 17:00:16 22658 D12 4 12 1 \n",
".. ... ... ... ... ... ... \n",
"210 2017-05-11 17:00:16 22658 M13 13 13 1 \n",
"211 2017-05-11 17:00:16 22658 M14 13 14 1 \n",
"212 2017-05-11 17:00:16 22658 M15 13 15 1 \n",
"213 2017-05-11 17:00:16 22658 M16 13 16 1 \n",
"214 2017-05-11 17:00:16 22658 M17 13 17 1 \n",
"215 2017-05-11 17:00:16 22658 M18 13 18 1 \n",
"216 2017-05-11 17:00:16 22658 M19 13 19 1 \n",
"217 2017-05-11 17:00:16 22658 M20 13 20 1 \n",
"218 2017-05-11 17:00:16 22658 M21 13 21 1 \n",
"219 2017-05-11 17:00:16 22658 M22 13 22 1 \n",
"220 2017-05-11 17:00:16 22658 N3 14 3 1 \n",
"221 2017-05-11 17:00:16 22658 N4 14 4 1 \n",
"222 2017-05-11 17:00:16 22658 N5 14 5 1 \n",
"223 2017-05-11 17:00:16 22658 N6 14 6 1 \n",
"224 2017-05-11 17:00:16 22658 N7 14 7 1 \n",
"225 2017-05-11 17:00:16 22658 N8 14 8 1 \n",
"226 2017-05-11 17:00:16 22658 N9 14 9 1 \n",
"227 2017-05-11 17:00:16 22658 N10 14 10 1 \n",
"228 2017-05-11 17:00:16 22658 N11 14 11 1 \n",
"229 2017-05-11 17:00:16 22658 N12 14 12 1 \n",
"230 2017-05-11 17:00:16 22658 N13 14 13 1 \n",
"231 2017-05-11 17:00:16 22658 N14 14 14 1 \n",
"232 2017-05-11 17:00:16 22658 N15 14 15 1 \n",
"233 2017-05-11 17:00:16 22658 N16 14 16 1 \n",
"234 2017-05-11 17:00:16 22658 N17 14 17 1 \n",
"235 2017-05-11 17:00:16 22658 N18 14 18 1 \n",
"236 2017-05-11 17:00:16 22658 N19 14 19 1 \n",
"237 2017-05-11 17:00:16 22658 N20 14 20 1 \n",
"238 2017-05-11 17:00:16 22658 N21 14 21 1 \n",
"239 2017-05-11 17:00:16 22658 N22 14 22 1 \n",
"\n",
" ... \\\n",
"0 ... \n",
"1 ... \n",
"2 ... \n",
"3 ... \n",
"4 ... \n",
"5 ... \n",
"6 ... \n",
"7 ... \n",
"8 ... \n",
"9 ... \n",
"10 ... \n",
"11 ... \n",
"12 ... \n",
"13 ... \n",
"14 ... \n",
"15 ... \n",
"16 ... \n",
"17 ... \n",
"18 ... \n",
"19 ... \n",
"20 ... \n",
"21 ... \n",
"22 ... \n",
"23 ... \n",
"24 ... \n",
"25 ... \n",
"26 ... \n",
"27 ... \n",
"28 ... \n",
"29 ... \n",
".. ... \n",
"210 ... \n",
"211 ... \n",
"212 ... \n",
"213 ... \n",
"214 ... \n",
"215 ... \n",
"216 ... \n",
"217 ... \n",
"218 ... \n",
"219 ... \n",
"220 ... \n",
"221 ... \n",
"222 ... \n",
"223 ... \n",
"224 ... \n",
"225 ... \n",
"226 ... \n",
"227 ... \n",
"228 ... \n",
"229 ... \n",
"230 ... \n",
"231 ... \n",
"232 ... \n",
"233 ... \n",
"234 ... \n",
"235 ... \n",
"236 ... \n",
"237 ... \n",
"238 ... \n",
"239 ... \n",
"\n",
" Nuclei - Texture Lysosomes Cell Texas Red SER Bright 1 px - Mean per Well \\\n",
"0 0.024857 \n",
"1 0.023802 \n",
"2 0.025417 \n",
"3 0.025126 \n",
"4 0.025488 \n",
"5 0.023948 \n",
"6 0.026175 \n",
"7 0.025357 \n",
"8 0.023544 \n",
"9 0.025865 \n",
"10 0.025107 \n",
"11 0.024418 \n",
"12 0.019342 \n",
"13 0.024373 \n",
"14 0.025843 \n",
"15 0.026012 \n",
"16 0.024514 \n",
"17 0.023349 \n",
"18 0.024049 \n",
"19 0.022633 \n",
"20 0.023159 \n",
"21 0.024926 \n",
"22 0.023903 \n",
"23 0.025092 \n",
"24 0.024460 \n",
"25 0.023976 \n",
"26 0.025600 \n",
"27 0.025210 \n",
"28 0.023366 \n",
"29 0.025051 \n",
".. ... \n",
"210 0.020137 \n",
"211 0.019943 \n",
"212 0.024451 \n",
"213 0.023698 \n",
"214 0.021039 \n",
"215 0.020297 \n",
"216 0.024524 \n",
"217 0.023390 \n",
"218 0.022586 \n",
"219 0.022724 \n",
"220 0.024896 \n",
"221 0.025618 \n",
"222 0.025211 \n",
"223 0.024944 \n",
"224 0.025544 \n",
"225 0.024782 \n",
"226 0.025060 \n",
"227 0.025185 \n",
"228 0.021619 \n",
"229 0.023554 \n",
"230 0.018021 \n",
"231 0.019456 \n",
"232 0.023994 \n",
"233 0.024097 \n",
"234 0.018380 \n",
"235 0.018462 \n",
"236 0.024035 \n",
"237 0.024591 \n",
"238 0.023336 \n",
"239 0.023124 \n",
"\n",
" Nuclei - Texture Lysosomes Cell Texas Red SER Dark 1 px - Mean per Well \\\n",
"0 0.039483 \n",
"1 0.037895 \n",
"2 0.039738 \n",
"3 0.039631 \n",
"4 0.040318 \n",
"5 0.036370 \n",
"6 0.041312 \n",
"7 0.039461 \n",
"8 0.036573 \n",
"9 0.040598 \n",
"10 0.039503 \n",
"11 0.037880 \n",
"12 0.028261 \n",
"13 0.037548 \n",
"14 0.040759 \n",
"15 0.040611 \n",
"16 0.038226 \n",
"17 0.034439 \n",
"18 0.037018 \n",
"19 0.033373 \n",
"20 0.036481 \n",
"21 0.039920 \n",
"22 0.038052 \n",
"23 0.039491 \n",
"24 0.037962 \n",
"25 0.038074 \n",
"26 0.040092 \n",
"27 0.039549 \n",
"28 0.034602 \n",
"29 0.038637 \n",
".. ... \n",
"210 0.028998 \n",
"211 0.028722 \n",
"212 0.037870 \n",
"213 0.036366 \n",
"214 0.031967 \n",
"215 0.029575 \n",
"216 0.037643 \n",
"217 0.035260 \n",
"218 0.032869 \n",
"219 0.033094 \n",
"220 0.037856 \n",
"221 0.040052 \n",
"222 0.039746 \n",
"223 0.036893 \n",
"224 0.039259 \n",
"225 0.038302 \n",
"226 0.037902 \n",
"227 0.037612 \n",
"228 0.031006 \n",
"229 0.036511 \n",
"230 0.024361 \n",
"231 0.026059 \n",
"232 0.035877 \n",
"233 0.036153 \n",
"234 0.028198 \n",
"235 0.029761 \n",
"236 0.035412 \n",
"237 0.037806 \n",
"238 0.034819 \n",
"239 0.033662 \n",
"\n",
" Nuclei - Cell Lysosomes Haralick Correlation 1 px - Mean per Well \\\n",
"0 0.891642 \n",
"1 0.896648 \n",
"2 0.883412 \n",
"3 0.885805 \n",
"4 0.886857 \n",
"5 0.883247 \n",
"6 0.876270 \n",
"7 0.880322 \n",
"8 0.892732 \n",
"9 0.877491 \n",
"10 0.884573 \n",
"11 0.887916 \n",
"12 0.883340 \n",
"13 0.875849 \n",
"14 0.871708 \n",
"15 0.867595 \n",
"16 0.884716 \n",
"17 0.875565 \n",
"18 0.891968 \n",
"19 0.880241 \n",
"20 0.899404 \n",
"21 0.896178 \n",
"22 0.899046 \n",
"23 0.891667 \n",
"24 0.886278 \n",
"25 0.899227 \n",
"26 0.884507 \n",
"27 0.877922 \n",
"28 0.881070 \n",
"29 0.874498 \n",
".. ... \n",
"210 0.901512 \n",
"211 0.903380 \n",
"212 0.881057 \n",
"213 0.885574 \n",
"214 0.906546 \n",
"215 0.897194 \n",
"216 0.881941 \n",
"217 0.879411 \n",
"218 0.877435 \n",
"219 0.877403 \n",
"220 0.881585 \n",
"221 0.886201 \n",
"222 0.885883 \n",
"223 0.873574 \n",
"224 0.873622 \n",
"225 0.878694 \n",
"226 0.869723 \n",
"227 0.864047 \n",
"228 0.889198 \n",
"229 0.886336 \n",
"230 0.893440 \n",
"231 0.884442 \n",
"232 0.879783 \n",
"233 0.875693 \n",
"234 0.916090 \n",
"235 0.928694 \n",
"236 0.864277 \n",
"237 0.875561 \n",
"238 0.878887 \n",
"239 0.863765 \n",
"\n",
" Nuclei - Cell Lysosomes Haralick Contrast 1 px - Mean per Well \\\n",
"0 0.056064 \n",
"1 0.046771 \n",
"2 0.051805 \n",
"3 0.050463 \n",
"4 0.053998 \n",
"5 0.048120 \n",
"6 0.059210 \n",
"7 0.051778 \n",
"8 0.044474 \n",
"9 0.054786 \n",
"10 0.053206 \n",
"11 0.046467 \n",
"12 0.034020 \n",
"13 0.048003 \n",
"14 0.055554 \n",
"15 0.053206 \n",
"16 0.046878 \n",
"17 0.044993 \n",
"18 0.043060 \n",
"19 0.041985 \n",
"20 0.046483 \n",
"21 0.051066 \n",
"22 0.046888 \n",
"23 0.054293 \n",
"24 0.051871 \n",
"25 0.048638 \n",
"26 0.053898 \n",
"27 0.056915 \n",
"28 0.048314 \n",
"29 0.054170 \n",
".. ... \n",
"210 0.033716 \n",
"211 0.031592 \n",
"212 0.048912 \n",
"213 0.042993 \n",
"214 0.042127 \n",
"215 0.043770 \n",
"216 0.046550 \n",
"217 0.047469 \n",
"218 0.043283 \n",
"219 0.044062 \n",
"220 0.049779 \n",
"221 0.055973 \n",
"222 0.052552 \n",
"223 0.056881 \n",
"224 0.054273 \n",
"225 0.053250 \n",
"226 0.054831 \n",
"227 0.056471 \n",
"228 0.042591 \n",
"229 0.045864 \n",
"230 0.026240 \n",
"231 0.029933 \n",
"232 0.045512 \n",
"233 0.045642 \n",
"234 0.049026 \n",
"235 0.051590 \n",
"236 0.048963 \n",
"237 0.050159 \n",
"238 0.043985 \n",
"239 0.047918 \n",
"\n",
" Nuclei - Cell Lysosomes Haralick Sum Variance 1 px - Mean per Well \\\n",
"0 0.299416 \n",
"1 0.265830 \n",
"2 0.260911 \n",
"3 0.253571 \n",
"4 0.278559 \n",
"5 0.240669 \n",
"6 0.274224 \n",
"7 0.248820 \n",
"8 0.238439 \n",
"9 0.257585 \n",
"10 0.267229 \n",
"11 0.240779 \n",
"12 0.179612 \n",
"13 0.233630 \n",
"14 0.252852 \n",
"15 0.233135 \n",
"16 0.247199 \n",
"17 0.223763 \n",
"18 0.241829 \n",
"19 0.222954 \n",
"20 0.269205 \n",
"21 0.290902 \n",
"22 0.276939 \n",
"23 0.290492 \n",
"24 0.262153 \n",
"25 0.278205 \n",
"26 0.275341 \n",
"27 0.274711 \n",
"28 0.245975 \n",
"29 0.259421 \n",
".. ... \n",
"210 0.210589 \n",
"211 0.201278 \n",
"212 0.244019 \n",
"213 0.226103 \n",
"214 0.267935 \n",
"215 0.260896 \n",
"216 0.234783 \n",
"217 0.240944 \n",
"218 0.217641 \n",
"219 0.220137 \n",
"220 0.257941 \n",
"221 0.295966 \n",
"222 0.275548 \n",
"223 0.263325 \n",
"224 0.259939 \n",
"225 0.269332 \n",
"226 0.253384 \n",
"227 0.248876 \n",
"228 0.236914 \n",
"229 0.246295 \n",
"230 0.157816 \n",
"231 0.158828 \n",
"232 0.233954 \n",
"233 0.222333 \n",
"234 0.397918 \n",
"235 0.446623 \n",
"236 0.225018 \n",
"237 0.248539 \n",
"238 0.231720 \n",
"239 0.229280 \n",
"\n",
" Nuclei - Cell Lysosomes Haralick Homogeneity 1 px - Mean per Well \\\n",
"0 0.432944 \n",
"1 0.434798 \n",
"2 0.419395 \n",
"3 0.430671 \n",
"4 0.419780 \n",
"5 0.423611 \n",
"6 0.414606 \n",
"7 0.419539 \n",
"8 0.435617 \n",
"9 0.420966 \n",
"10 0.424678 \n",
"11 0.430344 \n",
"12 0.458313 \n",
"13 0.426251 \n",
"14 0.424653 \n",
"15 0.411209 \n",
"16 0.431919 \n",
"17 0.419200 \n",
"18 0.424031 \n",
"19 0.421580 \n",
"20 0.428951 \n",
"21 0.412370 \n",
"22 0.422884 \n",
"23 0.409910 \n",
"24 0.422574 \n",
"25 0.418891 \n",
"26 0.410469 \n",
"27 0.407508 \n",
"28 0.413988 \n",
"29 0.414380 \n",
".. ... \n",
"210 0.443200 \n",
"211 0.441867 \n",
"212 0.424485 \n",
"213 0.430971 \n",
"214 0.443116 \n",
"215 0.442182 \n",
"216 0.422010 \n",
"217 0.427377 \n",
"218 0.424843 \n",
"219 0.420403 \n",
"220 0.396120 \n",
"221 0.392844 \n",
"222 0.400147 \n",
"223 0.380339 \n",
"224 0.395110 \n",
"225 0.400954 \n",
"226 0.391293 \n",
"227 0.382022 \n",
"228 0.400721 \n",
"229 0.426091 \n",
"230 0.425453 \n",
"231 0.397340 \n",
"232 0.405180 \n",
"233 0.403922 \n",
"234 0.412545 \n",
"235 0.413638 \n",
"236 0.400462 \n",
"237 0.410022 \n",
"238 0.403556 \n",
"239 0.395416 \n",
"\n",
" Nuclei - Cell Lysosomes Gabor Min 2 px w2 - Mean per Well \\\n",
"0 0.002249 \n",
"1 0.002213 \n",
"2 0.002370 \n",
"3 0.002172 \n",
"4 0.002407 \n",
"5 0.002447 \n",
"6 0.002590 \n",
"7 0.002490 \n",
"8 0.002183 \n",
"9 0.002380 \n",
"10 0.002350 \n",
"11 0.002235 \n",
"12 0.002367 \n",
"13 0.002330 \n",
"14 0.002383 \n",
"15 0.002503 \n",
"16 0.002212 \n",
"17 0.002532 \n",
"18 0.002259 \n",
"19 0.002528 \n",
"20 0.002323 \n",
"21 0.002413 \n",
"22 0.002332 \n",
"23 0.002549 \n",
"24 0.002503 \n",
"25 0.002441 \n",
"26 0.002538 \n",
"27 0.002699 \n",
"28 0.002668 \n",
"29 0.002528 \n",
".. ... \n",
"210 0.002323 \n",
"211 0.002340 \n",
"212 0.002361 \n",
"213 0.002206 \n",
"214 0.002287 \n",
"215 0.002504 \n",
"216 0.002360 \n",
"217 0.002408 \n",
"218 0.002518 \n",
"219 0.002550 \n",
"220 0.002858 \n",
"221 0.002887 \n",
"222 0.002760 \n",
"223 0.003237 \n",
"224 0.002847 \n",
"225 0.002846 \n",
"226 0.003005 \n",
"227 0.003184 \n",
"228 0.003006 \n",
"229 0.002370 \n",
"230 0.002819 \n",
"231 0.003167 \n",
"232 0.002701 \n",
"233 0.002769 \n",
"234 0.003071 \n",
"235 0.003010 \n",
"236 0.002904 \n",
"237 0.002611 \n",
"238 0.002789 \n",
"239 0.003024 \n",
"\n",
" Nuclei - Cell Lysosomes Gabor Max 2 px w2 - Mean per Well \\\n",
"0 0.013862 \n",
"1 0.013673 \n",
"2 0.014604 \n",
"3 0.013341 \n",
"4 0.014830 \n",
"5 0.015122 \n",
"6 0.015820 \n",
"7 0.015299 \n",
"8 0.013558 \n",
"9 0.014631 \n",
"10 0.014464 \n",
"11 0.013833 \n",
"12 0.014702 \n",
"13 0.014470 \n",
"14 0.014708 \n",
"15 0.015495 \n",
"16 0.013695 \n",
"17 0.015829 \n",
"18 0.014192 \n",
"19 0.015832 \n",
"20 0.014386 \n",
"21 0.015048 \n",
"22 0.014479 \n",
"23 0.015806 \n",
"24 0.015378 \n",
"25 0.015179 \n",
"26 0.015739 \n",
"27 0.016684 \n",
"28 0.016552 \n",
"29 0.015750 \n",
".. ... \n",
"210 0.014483 \n",
"211 0.014607 \n",
"212 0.014688 \n",
"213 0.013770 \n",
"214 0.014287 \n",
"215 0.015615 \n",
"216 0.014807 \n",
"217 0.014989 \n",
"218 0.015798 \n",
"219 0.016004 \n",
"220 0.017746 \n",
"221 0.017947 \n",
"222 0.017108 \n",
"223 0.020105 \n",
"224 0.017638 \n",
"225 0.017593 \n",
"226 0.018664 \n",
"227 0.019792 \n",
"228 0.018761 \n",
"229 0.014728 \n",
"230 0.017591 \n",
"231 0.019761 \n",
"232 0.016816 \n",
"233 0.017250 \n",
"234 0.019216 \n",
"235 0.018774 \n",
"236 0.018058 \n",
"237 0.016371 \n",
"238 0.017389 \n",
"239 0.018916 \n",
"\n",
" Number of Analyzed Fields \\\n",
"0 3 \n",
"1 3 \n",
"2 3 \n",
"3 3 \n",
"4 3 \n",
"5 3 \n",
"6 3 \n",
"7 3 \n",
"8 3 \n",
"9 3 \n",
"10 3 \n",
"11 3 \n",
"12 3 \n",
"13 3 \n",
"14 3 \n",
"15 3 \n",
"16 3 \n",
"17 3 \n",
"18 3 \n",
"19 3 \n",
"20 3 \n",
"21 3 \n",
"22 3 \n",
"23 3 \n",
"24 3 \n",
"25 3 \n",
"26 3 \n",
"27 3 \n",
"28 3 \n",
"29 3 \n",
".. ... \n",
"210 3 \n",
"211 3 \n",
"212 3 \n",
"213 3 \n",
"214 3 \n",
"215 3 \n",
"216 3 \n",
"217 3 \n",
"218 3 \n",
"219 3 \n",
"220 3 \n",
"221 3 \n",
"222 3 \n",
"223 3 \n",
"224 3 \n",
"225 3 \n",
"226 3 \n",
"227 3 \n",
"228 3 \n",
"229 3 \n",
"230 3 \n",
"231 3 \n",
"232 3 \n",
"233 3 \n",
"234 3 \n",
"235 3 \n",
"236 3 \n",
"237 3 \n",
"238 3 \n",
"239 3 \n",
"\n",
" Link \n",
"0 http://columbus.hms.harvard.edu/browse/measure... \n",
"1 http://columbus.hms.harvard.edu/browse/measure... \n",
"2 http://columbus.hms.harvard.edu/browse/measure... \n",
"3 http://columbus.hms.harvard.edu/browse/measure... \n",
"4 http://columbus.hms.harvard.edu/browse/measure... \n",
"5 http://columbus.hms.harvard.edu/browse/measure... \n",
"6 http://columbus.hms.harvard.edu/browse/measure... \n",
"7 http://columbus.hms.harvard.edu/browse/measure... \n",
"8 http://columbus.hms.harvard.edu/browse/measure... \n",
"9 http://columbus.hms.harvard.edu/browse/measure... \n",
"10 http://columbus.hms.harvard.edu/browse/measure... \n",
"11 http://columbus.hms.harvard.edu/browse/measure... \n",
"12 http://columbus.hms.harvard.edu/browse/measure... \n",
"13 http://columbus.hms.harvard.edu/browse/measure... \n",
"14 http://columbus.hms.harvard.edu/browse/measure... \n",
"15 http://columbus.hms.harvard.edu/browse/measure... \n",
"16 http://columbus.hms.harvard.edu/browse/measure... \n",
"17 http://columbus.hms.harvard.edu/browse/measure... \n",
"18 http://columbus.hms.harvard.edu/browse/measure... \n",
"19 http://columbus.hms.harvard.edu/browse/measure... \n",
"20 http://columbus.hms.harvard.edu/browse/measure... \n",
"21 http://columbus.hms.harvard.edu/browse/measure... \n",
"22 http://columbus.hms.harvard.edu/browse/measure... \n",
"23 http://columbus.hms.harvard.edu/browse/measure... \n",
"24 http://columbus.hms.harvard.edu/browse/measure... \n",
"25 http://columbus.hms.harvard.edu/browse/measure... \n",
"26 http://columbus.hms.harvard.edu/browse/measure... \n",
"27 http://columbus.hms.harvard.edu/browse/measure... \n",
"28 http://columbus.hms.harvard.edu/browse/measure... \n",
"29 http://columbus.hms.harvard.edu/browse/measure... \n",
".. ... \n",
"210 http://columbus.hms.harvard.edu/browse/measure... \n",
"211 http://columbus.hms.harvard.edu/browse/measure... \n",
"212 http://columbus.hms.harvard.edu/browse/measure... \n",
"213 http://columbus.hms.harvard.edu/browse/measure... \n",
"214 http://columbus.hms.harvard.edu/browse/measure... \n",
"215 http://columbus.hms.harvard.edu/browse/measure... \n",
"216 http://columbus.hms.harvard.edu/browse/measure... \n",
"217 http://columbus.hms.harvard.edu/browse/measure... \n",
"218 http://columbus.hms.harvard.edu/browse/measure... \n",
"219 http://columbus.hms.harvard.edu/browse/measure... \n",
"220 http://columbus.hms.harvard.edu/browse/measure... \n",
"221 http://columbus.hms.harvard.edu/browse/measure... \n",
"222 http://columbus.hms.harvard.edu/browse/measure... \n",
"223 http://columbus.hms.harvard.edu/browse/measure... \n",
"224 http://columbus.hms.harvard.edu/browse/measure... \n",
"225 http://columbus.hms.harvard.edu/browse/measure... \n",
"226 http://columbus.hms.harvard.edu/browse/measure... \n",
"227 http://columbus.hms.harvard.edu/browse/measure... \n",
"228 http://columbus.hms.harvard.edu/browse/measure... \n",
"229 http://columbus.hms.harvard.edu/browse/measure... \n",
"230 http://columbus.hms.harvard.edu/browse/measure... \n",
"231 http://columbus.hms.harvard.edu/browse/measure... \n",
"232 http://columbus.hms.harvard.edu/browse/measure... \n",
"233 http://columbus.hms.harvard.edu/browse/measure... \n",
"234 http://columbus.hms.harvard.edu/browse/measure... \n",
"235 http://columbus.hms.harvard.edu/browse/measure... \n",
"236 http://columbus.hms.harvard.edu/browse/measure... \n",
"237 http://columbus.hms.harvard.edu/browse/measure... \n",
"238 http://columbus.hms.harvard.edu/browse/measure... \n",
"239 http://columbus.hms.harvard.edu/browse/measure... \n",
"\n",
"[240 rows x 525 columns]"
]
},
"execution_count": 20,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"new_data"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Read all data into separate struct and func dataframes"
]
},
{
"cell_type": "code",
"execution_count": 21,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"for p in data_paths:\n",
" new_data = pd.read_csv(str(p), float_precision='high', encoding='utf-8',\n",
" parse_dates=['MeasurementDate'])\n",
" assert len(new_data.PlateName.unique()) == 1, 'Multiple plates in file'\n",
" assert new_data.PlateName.str.contains(r'Sim_00000[1-6]').all(), \\\n",
" 'Bad plate name'\n",
" sim_num = int(new_data.PlateName.iloc[0][-1])\n",
" if sim_num in (1, 2, 3):\n",
" new_data['BiologicalReplicate'] = sim_num\n",
" data_struct = data_struct.append(new_data, ignore_index=True)\n",
" elif sim_num in (4, 5, 6):\n",
" new_data['BiologicalReplicate'] = sim_num - 3\n",
" data_func = data_func.append(new_data, ignore_index=True)\n",
" else:\n",
" assert False, 'Unexpected plate (sim) number'\n",
" #columns.update(OrderedDict.fromkeys(new_data.columns))\n"
]
},
{
"cell_type": "code",
"execution_count": 22,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/plain": [
"(9360, 163)"
]
},
"execution_count": 22,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"data_func.shape"
]
},
{
"cell_type": "code",
"execution_count": 23,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/plain": [
"(9351, 526)"
]
},
"execution_count": 23,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"data_struct.shape"
]
},
{
"cell_type": "code",
"execution_count": 24,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/plain": [
"0 170511_Pfizer_PICS_HPTEC_4batch\n",
"1 170511_Pfizer_PICS_HPTEC_4batch\n",
"2 170511_Pfizer_PICS_HPTEC_4batch\n",
"3 170511_Pfizer_PICS_HPTEC_4batch\n",
"4 170511_Pfizer_PICS_HPTEC_4batch\n",
"5 170511_Pfizer_PICS_HPTEC_4batch\n",
"6 170511_Pfizer_PICS_HPTEC_4batch\n",
"7 170511_Pfizer_PICS_HPTEC_4batch\n",
"8 170511_Pfizer_PICS_HPTEC_4batch\n",
"9 170511_Pfizer_PICS_HPTEC_4batch\n",
"10 170511_Pfizer_PICS_HPTEC_4batch\n",
"11 170511_Pfizer_PICS_HPTEC_4batch\n",
"12 170511_Pfizer_PICS_HPTEC_4batch\n",
"13 170511_Pfizer_PICS_HPTEC_4batch\n",
"14 170511_Pfizer_PICS_HPTEC_4batch\n",
"15 170511_Pfizer_PICS_HPTEC_4batch\n",
"16 170511_Pfizer_PICS_HPTEC_4batch\n",
"17 170511_Pfizer_PICS_HPTEC_4batch\n",
"18 170511_Pfizer_PICS_HPTEC_4batch\n",
"19 170511_Pfizer_PICS_HPTEC_4batch\n",
"20 170511_Pfizer_PICS_HPTEC_4batch\n",
"21 170511_Pfizer_PICS_HPTEC_4batch\n",
"22 170511_Pfizer_PICS_HPTEC_4batch\n",
"23 170511_Pfizer_PICS_HPTEC_4batch\n",
"24 170511_Pfizer_PICS_HPTEC_4batch\n",
"25 170511_Pfizer_PICS_HPTEC_4batch\n",
"26 170511_Pfizer_PICS_HPTEC_4batch\n",
"27 170511_Pfizer_PICS_HPTEC_4batch\n",
"28 170511_Pfizer_PICS_HPTEC_4batch\n",
"29 170511_Pfizer_PICS_HPTEC_4batch\n",
" ... \n",
"9321 170516_Pfizer_PICS_OAT1_4batch\n",
"9322 170516_Pfizer_PICS_OAT1_4batch\n",
"9323 170516_Pfizer_PICS_OAT1_4batch\n",
"9324 170516_Pfizer_PICS_OAT1_4batch\n",
"9325 170516_Pfizer_PICS_OAT1_4batch\n",
"9326 170516_Pfizer_PICS_OAT1_4batch\n",
"9327 170516_Pfizer_PICS_OAT1_4batch\n",
"9328 170516_Pfizer_PICS_OAT1_4batch\n",
"9329 170516_Pfizer_PICS_OAT1_4batch\n",
"9330 170516_Pfizer_PICS_OAT1_4batch\n",
"9331 170516_Pfizer_PICS_OAT1_4batch\n",
"9332 170516_Pfizer_PICS_OAT1_4batch\n",
"9333 170516_Pfizer_PICS_OAT1_4batch\n",
"9334 170516_Pfizer_PICS_OAT1_4batch\n",
"9335 170516_Pfizer_PICS_OAT1_4batch\n",
"9336 170516_Pfizer_PICS_OAT1_4batch\n",
"9337 170516_Pfizer_PICS_OAT1_4batch\n",
"9338 170516_Pfizer_PICS_OAT1_4batch\n",
"9339 170516_Pfizer_PICS_OAT1_4batch\n",
"9340 170516_Pfizer_PICS_OAT1_4batch\n",
"9341 170516_Pfizer_PICS_OAT1_4batch\n",
"9342 170516_Pfizer_PICS_OAT1_4batch\n",
"9343 170516_Pfizer_PICS_OAT1_4batch\n",
"9344 170516_Pfizer_PICS_OAT1_4batch\n",
"9345 170516_Pfizer_PICS_OAT1_4batch\n",
"9346 170516_Pfizer_PICS_OAT1_4batch\n",
"9347 170516_Pfizer_PICS_OAT1_4batch\n",
"9348 170516_Pfizer_PICS_OAT1_4batch\n",
"9349 170516_Pfizer_PICS_OAT1_4batch\n",
"9350 170516_Pfizer_PICS_OAT1_4batch\n",
"Name: ScreenName, dtype: object"
]
},
"execution_count": 24,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"data_struct.ScreenName"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Extract cell type out of ScreenName column"
]
},
{
"cell_type": "code",
"execution_count": 25,
"metadata": {
"collapsed": false
},
"outputs": [],
"source": [
"cell_type = data_struct.ScreenName.str.extract(r'(HPTEC|OAT1)', expand=False)\n",
"cell_type.name = 'CellType'\n",
"data_struct = pd.concat([cell_type, data_struct], axis=1)\n"
]
},
{
"cell_type": "code",
"execution_count": 26,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"cell_type = data_func.ScreenName.str.extract(r'(HPTEC|OAT1)', expand=False)\n",
"cell_type.name = 'CellType'\n",
"data_func = pd.concat([cell_type, data_func], axis=1)\n"
]
},
{
"cell_type": "code",
"execution_count": 27,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/html": [
"<div>\n",
"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
" <th>CellType</th>\n",
" <th>ScreenName</th>\n",
" <th>ScreenID</th>\n",
" <th>PlateName</th>\n",
" <th>PlateID</th>\n",
" <th>MeasurementDate</th>\n",
" <th>MeasurementID</th>\n",
" <th>WellName</th>\n",
" <th>Row</th>\n",
" <th>Column</th>\n",
" <th>...</th>\n",
" <th>Nuclei - Texture Lysosomes Cell Texas Red SER Dark 1 px - Mean per Well</th>\n",
" <th>Nuclei - Cell Lysosomes Haralick Correlation 1 px - Mean per Well</th>\n",
" <th>Nuclei - Cell Lysosomes Haralick Contrast 1 px - Mean per Well</th>\n",
" <th>Nuclei - Cell Lysosomes Haralick Sum Variance 1 px - Mean per Well</th>\n",
" <th>Nuclei - Cell Lysosomes Haralick Homogeneity 1 px - Mean per Well</th>\n",
" <th>Nuclei - Cell Lysosomes Gabor Min 2 px w2 - Mean per Well</th>\n",
" <th>Nuclei - Cell Lysosomes Gabor Max 2 px w2 - Mean per Well</th>\n",
" <th>Number of Analyzed Fields</th>\n",
" <th>Link</th>\n",
" <th>BiologicalReplicate</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
" <td>HPTEC</td>\n",
" <td>170511_Pfizer_PICS_HPTEC_4batch</td>\n",
" <td>5602</td>\n",
" <td>Sim_000001</td>\n",
" <td>18614</td>\n",
" <td>2017-05-11 17:00:16</td>\n",
" <td>22658</td>\n",
" <td>C3</td>\n",
" <td>3</td>\n",
" <td>3</td>\n",
" <td>...</td>\n",
" <td>0.039483</td>\n",
" <td>0.891642</td>\n",
" <td>0.056064</td>\n",
" <td>0.299416</td>\n",
" <td>0.432944</td>\n",
" <td>0.002249</td>\n",
" <td>0.013862</td>\n",
" <td>3</td>\n",
" <td>http://columbus.hms.harvard.edu/browse/measure...</td>\n",
" <td>1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
" <td>HPTEC</td>\n",
" <td>170511_Pfizer_PICS_HPTEC_4batch</td>\n",
" <td>5602</td>\n",
" <td>Sim_000001</td>\n",
" <td>18614</td>\n",
" <td>2017-05-11 17:00:16</td>\n",
" <td>22658</td>\n",
" <td>C4</td>\n",
" <td>3</td>\n",
" <td>4</td>\n",
" <td>...</td>\n",
" <td>0.037895</td>\n",
" <td>0.896648</td>\n",
" <td>0.046771</td>\n",
" <td>0.265830</td>\n",
" <td>0.434798</td>\n",
" <td>0.002213</td>\n",
" <td>0.013673</td>\n",
" <td>3</td>\n",
" <td>http://columbus.hms.harvard.edu/browse/measure...</td>\n",
" <td>1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>2</th>\n",
" <td>HPTEC</td>\n",
" <td>170511_Pfizer_PICS_HPTEC_4batch</td>\n",
" <td>5602</td>\n",
" <td>Sim_000001</td>\n",
" <td>18614</td>\n",
" <td>2017-05-11 17:00:16</td>\n",
" <td>22658</td>\n",
" <td>C5</td>\n",
" <td>3</td>\n",
" <td>5</td>\n",
" <td>...</td>\n",
" <td>0.039738</td>\n",
" <td>0.883412</td>\n",
" <td>0.051805</td>\n",
" <td>0.260911</td>\n",
" <td>0.419395</td>\n",
" <td>0.002370</td>\n",
" <td>0.014604</td>\n",
" <td>3</td>\n",
" <td>http://columbus.hms.harvard.edu/browse/measure...</td>\n",
" <td>1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>3</th>\n",
" <td>HPTEC</td>\n",
" <td>170511_Pfizer_PICS_HPTEC_4batch</td>\n",
" <td>5602</td>\n",
" <td>Sim_000001</td>\n",
" <td>18614</td>\n",
" <td>2017-05-11 17:00:16</td>\n",
" <td>22658</td>\n",
" <td>C6</td>\n",
" <td>3</td>\n",
" <td>6</td>\n",
" <td>...</td>\n",
" <td>0.039631</td>\n",
" <td>0.885805</td>\n",
" <td>0.050463</td>\n",
" <td>0.253571</td>\n",
" <td>0.430671</td>\n",
" <td>0.002172</td>\n",
" <td>0.013341</td>\n",
" <td>3</td>\n",
" <td>http://columbus.hms.harvard.edu/browse/measure...</td>\n",
" <td>1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>4</th>\n",
" <td>HPTEC</td>\n",
" <td>170511_Pfizer_PICS_HPTEC_4batch</td>\n",
" <td>5602</td>\n",
" <td>Sim_000001</td>\n",
" <td>18614</td>\n",
" <td>2017-05-11 17:00:16</td>\n",
" <td>22658</td>\n",
" <td>C7</td>\n",
" <td>3</td>\n",
" <td>7</td>\n",
" <td>...</td>\n",
" <td>0.040318</td>\n",
" <td>0.886857</td>\n",
" <td>0.053998</td>\n",
" <td>0.278559</td>\n",
" <td>0.419780</td>\n",
" <td>0.002407</td>\n",
" <td>0.014830</td>\n",
" <td>3</td>\n",
" <td>http://columbus.hms.harvard.edu/browse/measure...</td>\n",
" <td>1</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"<p>5 rows × 527 columns</p>\n",
"</div>"
],
"text/plain": [
" CellType ScreenName ScreenID PlateName PlateID \\\n",
"0 HPTEC 170511_Pfizer_PICS_HPTEC_4batch 5602 Sim_000001 18614 \n",
"1 HPTEC 170511_Pfizer_PICS_HPTEC_4batch 5602 Sim_000001 18614 \n",
"2 HPTEC 170511_Pfizer_PICS_HPTEC_4batch 5602 Sim_000001 18614 \n",
"3 HPTEC 170511_Pfizer_PICS_HPTEC_4batch 5602 Sim_000001 18614 \n",
"4 HPTEC 170511_Pfizer_PICS_HPTEC_4batch 5602 Sim_000001 18614 \n",
"\n",
" MeasurementDate MeasurementID WellName Row Column \\\n",
"0 2017-05-11 17:00:16 22658 C3 3 3 \n",
"1 2017-05-11 17:00:16 22658 C4 3 4 \n",
"2 2017-05-11 17:00:16 22658 C5 3 5 \n",
"3 2017-05-11 17:00:16 22658 C6 3 6 \n",
"4 2017-05-11 17:00:16 22658 C7 3 7 \n",
"\n",
" ... \\\n",
"0 ... \n",
"1 ... \n",
"2 ... \n",
"3 ... \n",
"4 ... \n",
"\n",
" Nuclei - Texture Lysosomes Cell Texas Red SER Dark 1 px - Mean per Well \\\n",
"0 0.039483 \n",
"1 0.037895 \n",
"2 0.039738 \n",
"3 0.039631 \n",
"4 0.040318 \n",
"\n",
" Nuclei - Cell Lysosomes Haralick Correlation 1 px - Mean per Well \\\n",
"0 0.891642 \n",
"1 0.896648 \n",
"2 0.883412 \n",
"3 0.885805 \n",
"4 0.886857 \n",
"\n",
" Nuclei - Cell Lysosomes Haralick Contrast 1 px - Mean per Well \\\n",
"0 0.056064 \n",
"1 0.046771 \n",
"2 0.051805 \n",
"3 0.050463 \n",
"4 0.053998 \n",
"\n",
" Nuclei - Cell Lysosomes Haralick Sum Variance 1 px - Mean per Well \\\n",
"0 0.299416 \n",
"1 0.265830 \n",
"2 0.260911 \n",
"3 0.253571 \n",
"4 0.278559 \n",
"\n",
" Nuclei - Cell Lysosomes Haralick Homogeneity 1 px - Mean per Well \\\n",
"0 0.432944 \n",
"1 0.434798 \n",
"2 0.419395 \n",
"3 0.430671 \n",
"4 0.419780 \n",
"\n",
" Nuclei - Cell Lysosomes Gabor Min 2 px w2 - Mean per Well \\\n",
"0 0.002249 \n",
"1 0.002213 \n",
"2 0.002370 \n",
"3 0.002172 \n",
"4 0.002407 \n",
"\n",
" Nuclei - Cell Lysosomes Gabor Max 2 px w2 - Mean per Well \\\n",
"0 0.013862 \n",
"1 0.013673 \n",
"2 0.014604 \n",
"3 0.013341 \n",
"4 0.014830 \n",
"\n",
" Number of Analyzed Fields \\\n",
"0 3 \n",
"1 3 \n",
"2 3 \n",
"3 3 \n",
"4 3 \n",
"\n",
" Link BiologicalReplicate \n",
"0 http://columbus.hms.harvard.edu/browse/measure... 1 \n",
"1 http://columbus.hms.harvard.edu/browse/measure... 1 \n",
"2 http://columbus.hms.harvard.edu/browse/measure... 1 \n",
"3 http://columbus.hms.harvard.edu/browse/measure... 1 \n",
"4 http://columbus.hms.harvard.edu/browse/measure... 1 \n",
"\n",
"[5 rows x 527 columns]"
]
},
"execution_count": 27,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"data_struct.head()"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Compute TimePointHours column from MeasurementDate timestamps"
]
},
{
"cell_type": "code",
"execution_count": 28,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"for df in data_struct, data_func:\n",
" time_info = df[['PlateID', 'MeasurementDate']].set_index('PlateID')\n",
" t0 = df.groupby('PlateID').MeasurementDate.min()\n",
" time_info['t0'] = t0\n",
" hours = (time_info.MeasurementDate - time_info.t0).dt.round('6h') / pd.to_timedelta('1h')\n",
" hours = hours.astype('int').reset_index(drop=True)\n",
" df['TimePointHours'] = hours"
]
},
{
"cell_type": "code",
"execution_count": 29,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
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"</table>\n",
"<p>9360 rows × 2 columns</p>\n",
"</div>"
],
"text/plain": [
" MeasurementDate t0\n",
"PlateID \n",
"18619 2017-05-11 20:21:39 2017-05-11 20:21:39\n",
"18619 2017-05-11 20:21:39 2017-05-11 20:21:39\n",
"18619 2017-05-11 20:21:39 2017-05-11 20:21:39\n",
"18619 2017-05-11 20:21:39 2017-05-11 20:21:39\n",
"18619 2017-05-11 20:21:39 2017-05-11 20:21:39\n",
"18619 2017-05-11 20:21:39 2017-05-11 20:21:39\n",
"18619 2017-05-11 20:21:39 2017-05-11 20:21:39\n",
"18619 2017-05-11 20:21:39 2017-05-11 20:21:39\n",
"18619 2017-05-11 20:21:39 2017-05-11 20:21:39\n",
"18619 2017-05-11 20:21:39 2017-05-11 20:21:39\n",
"18619 2017-05-11 20:21:39 2017-05-11 20:21:39\n",
"18619 2017-05-11 20:21:39 2017-05-11 20:21:39\n",
"18619 2017-05-11 20:21:39 2017-05-11 20:21:39\n",
"18619 2017-05-11 20:21:39 2017-05-11 20:21:39\n",
"18619 2017-05-11 20:21:39 2017-05-11 20:21:39\n",
"18619 2017-05-11 20:21:39 2017-05-11 20:21:39\n",
"18619 2017-05-11 20:21:39 2017-05-11 20:21:39\n",
"18619 2017-05-11 20:21:39 2017-05-11 20:21:39\n",
"18619 2017-05-11 20:21:39 2017-05-11 20:21:39\n",
"18619 2017-05-11 20:21:39 2017-05-11 20:21:39\n",
"18619 2017-05-11 20:21:39 2017-05-11 20:21:39\n",
"18619 2017-05-11 20:21:39 2017-05-11 20:21:39\n",
"18619 2017-05-11 20:21:39 2017-05-11 20:21:39\n",
"18619 2017-05-11 20:21:39 2017-05-11 20:21:39\n",
"18619 2017-05-11 20:21:39 2017-05-11 20:21:39\n",
"18619 2017-05-11 20:21:39 2017-05-11 20:21:39\n",
"18619 2017-05-11 20:21:39 2017-05-11 20:21:39\n",
"18619 2017-05-11 20:21:39 2017-05-11 20:21:39\n",
"18619 2017-05-11 20:21:39 2017-05-11 20:21:39\n",
"18619 2017-05-11 20:21:39 2017-05-11 20:21:39\n",
"... ... ...\n",
"18663 2017-05-20 02:07:38 2017-05-17 00:17:02\n",
"18663 2017-05-20 02:07:38 2017-05-17 00:17:02\n",
"18663 2017-05-20 02:07:38 2017-05-17 00:17:02\n",
"18663 2017-05-20 02:07:38 2017-05-17 00:17:02\n",
"18663 2017-05-20 02:07:38 2017-05-17 00:17:02\n",
"18663 2017-05-20 02:07:38 2017-05-17 00:17:02\n",
"18663 2017-05-20 02:07:38 2017-05-17 00:17:02\n",
"18663 2017-05-20 02:07:38 2017-05-17 00:17:02\n",
"18663 2017-05-20 02:07:38 2017-05-17 00:17:02\n",
"18663 2017-05-20 02:07:38 2017-05-17 00:17:02\n",
"18663 2017-05-20 02:07:38 2017-05-17 00:17:02\n",
"18663 2017-05-20 02:07:38 2017-05-17 00:17:02\n",
"18663 2017-05-20 02:07:38 2017-05-17 00:17:02\n",
"18663 2017-05-20 02:07:38 2017-05-17 00:17:02\n",
"18663 2017-05-20 02:07:38 2017-05-17 00:17:02\n",
"18663 2017-05-20 02:07:38 2017-05-17 00:17:02\n",
"18663 2017-05-20 02:07:38 2017-05-17 00:17:02\n",
"18663 2017-05-20 02:07:38 2017-05-17 00:17:02\n",
"18663 2017-05-20 02:07:38 2017-05-17 00:17:02\n",
"18663 2017-05-20 02:07:38 2017-05-17 00:17:02\n",
"18663 2017-05-20 02:07:38 2017-05-17 00:17:02\n",
"18663 2017-05-20 02:07:38 2017-05-17 00:17:02\n",
"18663 2017-05-20 02:07:38 2017-05-17 00:17:02\n",
"18663 2017-05-20 02:07:38 2017-05-17 00:17:02\n",
"18663 2017-05-20 02:07:38 2017-05-17 00:17:02\n",
"18663 2017-05-20 02:07:38 2017-05-17 00:17:02\n",
"18663 2017-05-20 02:07:38 2017-05-17 00:17:02\n",
"18663 2017-05-20 02:07:38 2017-05-17 00:17:02\n",
"18663 2017-05-20 02:07:38 2017-05-17 00:17:02\n",
"18663 2017-05-20 02:07:38 2017-05-17 00:17:02\n",
"\n",
"[9360 rows x 2 columns]"
]
},
"execution_count": 29,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"time_info"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Drop some redundant or useless columns"
]
},
{
"cell_type": "code",
"execution_count": 30,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"for df in data_struct, data_func:\n",
" df.drop(['Row', 'Column', 'Timepoint'], axis=1, inplace=True)\n"
]
},
{
"cell_type": "code",
"execution_count": 31,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/plain": [
"Index(['CellType', 'BiologicalReplicate', 'TimePointHours', 'WellName',\n",
" 'Column', 'Row', 'pert_iname', 'pert_dose', 'pert_dose_unit',\n",
" 'pert_replicate'],\n",
" dtype='object')"
]
},
"execution_count": 31,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"design.columns"
]
},
{
"cell_type": "code",
"execution_count": 32,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/plain": [
"Index(['CellType', 'ScreenName', 'ScreenID', 'PlateName', 'PlateID',\n",
" 'MeasurementDate', 'MeasurementID', 'WellName', 'Plane',\n",
" 'Nuclei - Number of Objects',\n",
" ...\n",
" 'Nuclei - Cell Lysosomes Haralick Correlation 1 px - Mean per Well',\n",
" 'Nuclei - Cell Lysosomes Haralick Contrast 1 px - Mean per Well',\n",
" 'Nuclei - Cell Lysosomes Haralick Sum Variance 1 px - Mean per Well',\n",
" 'Nuclei - Cell Lysosomes Haralick Homogeneity 1 px - Mean per Well',\n",
" 'Nuclei - Cell Lysosomes Gabor Min 2 px w2 - Mean per Well',\n",
" 'Nuclei - Cell Lysosomes Gabor Max 2 px w2 - Mean per Well',\n",
" 'Number of Analyzed Fields', 'Link', 'BiologicalReplicate',\n",
" 'TimePointHours'],\n",
" dtype='object', length=525)"
]
},
"execution_count": 32,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"data_struct.columns"
]
},
{
"cell_type": "code",
"execution_count": 33,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/plain": [
"(9360, 10)"
]
},
"execution_count": 33,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"design.shape"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Merge design and data into a single dataframe"
]
},
{
"cell_type": "code",
"execution_count": 34,
"metadata": {
"collapsed": false
},
"outputs": [],
"source": [
"data = pd.merge(\n",
" design, data_struct,\n",
" on=['CellType', 'BiologicalReplicate', 'TimePointHours', 'WellName'],\n",
" how='left', indicator=True\n",
")\n"
]
},
{
"cell_type": "code",
"execution_count": 35,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/html": [
"<div>\n",
"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
" <th>CellType</th>\n",
" <th>BiologicalReplicate</th>\n",
" <th>TimePointHours</th>\n",
" <th>WellName</th>\n",
" <th>Column</th>\n",
" <th>Row</th>\n",
" <th>pert_iname</th>\n",
" <th>pert_dose</th>\n",
" <th>pert_dose_unit</th>\n",
" <th>pert_replicate</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
" <td>HPTEC</td>\n",
" <td>1</td>\n",
" <td>0</td>\n",
" <td>I3</td>\n",
" <td>3</td>\n",
" <td>9</td>\n",
" <td>Aspirin</td>\n",
" <td>3.173691</td>\n",
" <td>um</td>\n",
" <td>1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
" <td>HPTEC</td>\n",
" <td>1</td>\n",
" <td>0</td>\n",
" <td>J3</td>\n",
" <td>3</td>\n",
" <td>10</td>\n",
" <td>Aspirin</td>\n",
" <td>10.028862</td>\n",
" <td>um</td>\n",
" <td>1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>2</th>\n",
" <td>HPTEC</td>\n",
" <td>1</td>\n",
" <td>0</td>\n",
" <td>K3</td>\n",
" <td>3</td>\n",
" <td>11</td>\n",
" <td>Aspirin</td>\n",
" <td>31.691205</td>\n",
" <td>um</td>\n",
" <td>1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>3</th>\n",
" <td>HPTEC</td>\n",
" <td>1</td>\n",
" <td>0</td>\n",
" <td>L3</td>\n",
" <td>3</td>\n",
" <td>12</td>\n",
" <td>Aspirin</td>\n",
" <td>100.144208</td>\n",
" <td>um</td>\n",
" <td>1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>4</th>\n",
" <td>HPTEC</td>\n",
" <td>1</td>\n",
" <td>0</td>\n",
" <td>M3</td>\n",
" <td>3</td>\n",
" <td>13</td>\n",
" <td>Aspirin</td>\n",
" <td>316.455696</td>\n",
" <td>um</td>\n",
" <td>1</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"</div>"
],
"text/plain": [
" CellType BiologicalReplicate TimePointHours WellName Column Row \\\n",
"0 HPTEC 1 0 I3 3 9 \n",
"1 HPTEC 1 0 J3 3 10 \n",
"2 HPTEC 1 0 K3 3 11 \n",
"3 HPTEC 1 0 L3 3 12 \n",
"4 HPTEC 1 0 M3 3 13 \n",
"\n",
" pert_iname pert_dose pert_dose_unit pert_replicate \n",
"0 Aspirin 3.173691 um 1 \n",
"1 Aspirin 10.028862 um 1 \n",
"2 Aspirin 31.691205 um 1 \n",
"3 Aspirin 100.144208 um 1 \n",
"4 Aspirin 316.455696 um 1 "
]
},
"execution_count": 35,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"design.head()"
]
},
{
"cell_type": "code",
"execution_count": 36,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
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" <th>CellType</th>\n",
" <th>ScreenName</th>\n",
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" <th>MeasurementDate</th>\n",
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" <th>WellName</th>\n",
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" <th>Number of Analyzed Fields</th>\n",
" <th>Link</th>\n",
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" <td>1</td>\n",
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" <tr>\n",
" <th>1</th>\n",
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" <td>5602</td>\n",
" <td>Sim_000001</td>\n",
" <td>18614</td>\n",
" <td>2017-05-11 17:00:16</td>\n",
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" <td>2345</td>\n",
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" <td>0.046771</td>\n",
" <td>0.265830</td>\n",
" <td>0.434798</td>\n",
" <td>0.002213</td>\n",
" <td>0.013673</td>\n",
" <td>3</td>\n",
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" <td>1</td>\n",
" <td>0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>2</th>\n",
" <td>HPTEC</td>\n",
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" <td>18614</td>\n",
" <td>2017-05-11 17:00:16</td>\n",
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" <td>2249</td>\n",
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" <td>0.883412</td>\n",
" <td>0.051805</td>\n",
" <td>0.260911</td>\n",
" <td>0.419395</td>\n",
" <td>0.002370</td>\n",
" <td>0.014604</td>\n",
" <td>3</td>\n",
" <td>http://columbus.hms.harvard.edu/browse/measure...</td>\n",
" <td>1</td>\n",
" <td>0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>3</th>\n",
" <td>HPTEC</td>\n",
" <td>170511_Pfizer_PICS_HPTEC_4batch</td>\n",
" <td>5602</td>\n",
" <td>Sim_000001</td>\n",
" <td>18614</td>\n",
" <td>2017-05-11 17:00:16</td>\n",
" <td>22658</td>\n",
" <td>C6</td>\n",
" <td>1</td>\n",
" <td>2426</td>\n",
" <td>...</td>\n",
" <td>0.885805</td>\n",
" <td>0.050463</td>\n",
" <td>0.253571</td>\n",
" <td>0.430671</td>\n",
" <td>0.002172</td>\n",
" <td>0.013341</td>\n",
" <td>3</td>\n",
" <td>http://columbus.hms.harvard.edu/browse/measure...</td>\n",
" <td>1</td>\n",
" <td>0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>4</th>\n",
" <td>HPTEC</td>\n",
" <td>170511_Pfizer_PICS_HPTEC_4batch</td>\n",
" <td>5602</td>\n",
" <td>Sim_000001</td>\n",
" <td>18614</td>\n",
" <td>2017-05-11 17:00:16</td>\n",
" <td>22658</td>\n",
" <td>C7</td>\n",
" <td>1</td>\n",
" <td>2384</td>\n",
" <td>...</td>\n",
" <td>0.886857</td>\n",
" <td>0.053998</td>\n",
" <td>0.278559</td>\n",
" <td>0.419780</td>\n",
" <td>0.002407</td>\n",
" <td>0.014830</td>\n",
" <td>3</td>\n",
" <td>http://columbus.hms.harvard.edu/browse/measure...</td>\n",
" <td>1</td>\n",
" <td>0</td>\n",
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"</table>\n",
"<p>5 rows × 525 columns</p>\n",
"</div>"
],
"text/plain": [
" CellType ScreenName ScreenID PlateName PlateID \\\n",
"0 HPTEC 170511_Pfizer_PICS_HPTEC_4batch 5602 Sim_000001 18614 \n",
"1 HPTEC 170511_Pfizer_PICS_HPTEC_4batch 5602 Sim_000001 18614 \n",
"2 HPTEC 170511_Pfizer_PICS_HPTEC_4batch 5602 Sim_000001 18614 \n",
"3 HPTEC 170511_Pfizer_PICS_HPTEC_4batch 5602 Sim_000001 18614 \n",
"4 HPTEC 170511_Pfizer_PICS_HPTEC_4batch 5602 Sim_000001 18614 \n",
"\n",
" MeasurementDate MeasurementID WellName Plane \\\n",
"0 2017-05-11 17:00:16 22658 C3 1 \n",
"1 2017-05-11 17:00:16 22658 C4 1 \n",
"2 2017-05-11 17:00:16 22658 C5 1 \n",
"3 2017-05-11 17:00:16 22658 C6 1 \n",
"4 2017-05-11 17:00:16 22658 C7 1 \n",
"\n",
" Nuclei - Number of Objects ... \\\n",
"0 2200 ... \n",
"1 2345 ... \n",
"2 2249 ... \n",
"3 2426 ... \n",
"4 2384 ... \n",
"\n",
" Nuclei - Cell Lysosomes Haralick Correlation 1 px - Mean per Well \\\n",
"0 0.891642 \n",
"1 0.896648 \n",
"2 0.883412 \n",
"3 0.885805 \n",
"4 0.886857 \n",
"\n",
" Nuclei - Cell Lysosomes Haralick Contrast 1 px - Mean per Well \\\n",
"0 0.056064 \n",
"1 0.046771 \n",
"2 0.051805 \n",
"3 0.050463 \n",
"4 0.053998 \n",
"\n",
" Nuclei - Cell Lysosomes Haralick Sum Variance 1 px - Mean per Well \\\n",
"0 0.299416 \n",
"1 0.265830 \n",
"2 0.260911 \n",
"3 0.253571 \n",
"4 0.278559 \n",
"\n",
" Nuclei - Cell Lysosomes Haralick Homogeneity 1 px - Mean per Well \\\n",
"0 0.432944 \n",
"1 0.434798 \n",
"2 0.419395 \n",
"3 0.430671 \n",
"4 0.419780 \n",
"\n",
" Nuclei - Cell Lysosomes Gabor Min 2 px w2 - Mean per Well \\\n",
"0 0.002249 \n",
"1 0.002213 \n",
"2 0.002370 \n",
"3 0.002172 \n",
"4 0.002407 \n",
"\n",
" Nuclei - Cell Lysosomes Gabor Max 2 px w2 - Mean per Well \\\n",
"0 0.013862 \n",
"1 0.013673 \n",
"2 0.014604 \n",
"3 0.013341 \n",
"4 0.014830 \n",
"\n",
" Number of Analyzed Fields \\\n",
"0 3 \n",
"1 3 \n",
"2 3 \n",
"3 3 \n",
"4 3 \n",
"\n",
" Link BiologicalReplicate \\\n",
"0 http://columbus.hms.harvard.edu/browse/measure... 1 \n",
"1 http://columbus.hms.harvard.edu/browse/measure... 1 \n",
"2 http://columbus.hms.harvard.edu/browse/measure... 1 \n",
"3 http://columbus.hms.harvard.edu/browse/measure... 1 \n",
"4 http://columbus.hms.harvard.edu/browse/measure... 1 \n",
"\n",
" TimePointHours \n",
"0 0 \n",
"1 0 \n",
"2 0 \n",
"3 0 \n",
"4 0 \n",
"\n",
"[5 rows x 525 columns]"
]
},
"execution_count": 36,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"data_struct.head()"
]
},
{
"cell_type": "code",
"execution_count": 37,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
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" <th>...</th>\n",
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" <th>Nuclei - Cell Lysosomes Haralick Contrast 1 px - Mean per Well</th>\n",
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" <th>Number of Analyzed Fields</th>\n",
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" <th>_merge</th>\n",
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" </thead>\n",
" <tbody>\n",
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" <td>0.284172</td>\n",
" <td>0.434552</td>\n",
" <td>0.002335</td>\n",
" <td>0.014509</td>\n",
" <td>3.0</td>\n",
" <td>http://columbus.hms.harvard.edu/browse/measure...</td>\n",
" <td>both</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
" <td>HPTEC</td>\n",
" <td>1</td>\n",
" <td>0</td>\n",
" <td>J3</td>\n",
" <td>3</td>\n",
" <td>10</td>\n",
" <td>Aspirin</td>\n",
" <td>10.028862</td>\n",
" <td>um</td>\n",
" <td>1</td>\n",
" <td>...</td>\n",
" <td>0.034961</td>\n",
" <td>0.901297</td>\n",
" <td>0.043992</td>\n",
" <td>0.257642</td>\n",
" <td>0.437758</td>\n",
" <td>0.002191</td>\n",
" <td>0.013646</td>\n",
" <td>3.0</td>\n",
" <td>http://columbus.hms.harvard.edu/browse/measure...</td>\n",
" <td>both</td>\n",
" </tr>\n",
" <tr>\n",
" <th>2</th>\n",
" <td>HPTEC</td>\n",
" <td>1</td>\n",
" <td>0</td>\n",
" <td>K3</td>\n",
" <td>3</td>\n",
" <td>11</td>\n",
" <td>Aspirin</td>\n",
" <td>31.691205</td>\n",
" <td>um</td>\n",
" <td>1</td>\n",
" <td>...</td>\n",
" <td>0.038099</td>\n",
" <td>0.903263</td>\n",
" <td>0.046459</td>\n",
" <td>0.281722</td>\n",
" <td>0.436832</td>\n",
" <td>0.002040</td>\n",
" <td>0.012778</td>\n",
" <td>3.0</td>\n",
" <td>http://columbus.hms.harvard.edu/browse/measure...</td>\n",
" <td>both</td>\n",
" </tr>\n",
" <tr>\n",
" <th>3</th>\n",
" <td>HPTEC</td>\n",
" <td>1</td>\n",
" <td>0</td>\n",
" <td>L3</td>\n",
" <td>3</td>\n",
" <td>12</td>\n",
" <td>Aspirin</td>\n",
" <td>100.144208</td>\n",
" <td>um</td>\n",
" <td>1</td>\n",
" <td>...</td>\n",
" <td>0.038625</td>\n",
" <td>0.897676</td>\n",
" <td>0.049467</td>\n",
" <td>0.281461</td>\n",
" <td>0.430197</td>\n",
" <td>0.002189</td>\n",
" <td>0.013637</td>\n",
" <td>3.0</td>\n",
" <td>http://columbus.hms.harvard.edu/browse/measure...</td>\n",
" <td>both</td>\n",
" </tr>\n",
" <tr>\n",
" <th>4</th>\n",
" <td>HPTEC</td>\n",
" <td>1</td>\n",
" <td>0</td>\n",
" <td>M3</td>\n",
" <td>3</td>\n",
" <td>13</td>\n",
" <td>Aspirin</td>\n",
" <td>316.455696</td>\n",
" <td>um</td>\n",
" <td>1</td>\n",
" <td>...</td>\n",
" <td>0.035713</td>\n",
" <td>0.894964</td>\n",
" <td>0.043462</td>\n",
" <td>0.243228</td>\n",
" <td>0.429876</td>\n",
" <td>0.002308</td>\n",
" <td>0.014368</td>\n",
" <td>3.0</td>\n",
" <td>http://columbus.hms.harvard.edu/browse/measure...</td>\n",
" <td>both</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"<p>5 rows × 532 columns</p>\n",
"</div>"
],
"text/plain": [
" CellType BiologicalReplicate TimePointHours WellName Column Row \\\n",
"0 HPTEC 1 0 I3 3 9 \n",
"1 HPTEC 1 0 J3 3 10 \n",
"2 HPTEC 1 0 K3 3 11 \n",
"3 HPTEC 1 0 L3 3 12 \n",
"4 HPTEC 1 0 M3 3 13 \n",
"\n",
" pert_iname pert_dose pert_dose_unit pert_replicate ... \\\n",
"0 Aspirin 3.173691 um 1 ... \n",
"1 Aspirin 10.028862 um 1 ... \n",
"2 Aspirin 31.691205 um 1 ... \n",
"3 Aspirin 100.144208 um 1 ... \n",
"4 Aspirin 316.455696 um 1 ... \n",
"\n",
" Nuclei - Texture Lysosomes Cell Texas Red SER Dark 1 px - Mean per Well \\\n",
"0 0.033588 \n",
"1 0.034961 \n",
"2 0.038099 \n",
"3 0.038625 \n",
"4 0.035713 \n",
"\n",
" Nuclei - Cell Lysosomes Haralick Correlation 1 px - Mean per Well \\\n",
"0 0.907915 \n",
"1 0.901297 \n",
"2 0.903263 \n",
"3 0.897676 \n",
"4 0.894964 \n",
"\n",
" Nuclei - Cell Lysosomes Haralick Contrast 1 px - Mean per Well \\\n",
"0 0.043857 \n",
"1 0.043992 \n",
"2 0.046459 \n",
"3 0.049467 \n",
"4 0.043462 \n",
"\n",
" Nuclei - Cell Lysosomes Haralick Sum Variance 1 px - Mean per Well \\\n",
"0 0.284172 \n",
"1 0.257642 \n",
"2 0.281722 \n",
"3 0.281461 \n",
"4 0.243228 \n",
"\n",
" Nuclei - Cell Lysosomes Haralick Homogeneity 1 px - Mean per Well \\\n",
"0 0.434552 \n",
"1 0.437758 \n",
"2 0.436832 \n",
"3 0.430197 \n",
"4 0.429876 \n",
"\n",
" Nuclei - Cell Lysosomes Gabor Min 2 px w2 - Mean per Well \\\n",
"0 0.002335 \n",
"1 0.002191 \n",
"2 0.002040 \n",
"3 0.002189 \n",
"4 0.002308 \n",
"\n",
" Nuclei - Cell Lysosomes Gabor Max 2 px w2 - Mean per Well \\\n",
"0 0.014509 \n",
"1 0.013646 \n",
"2 0.012778 \n",
"3 0.013637 \n",
"4 0.014368 \n",
"\n",
" Number of Analyzed Fields \\\n",
"0 3.0 \n",
"1 3.0 \n",
"2 3.0 \n",
"3 3.0 \n",
"4 3.0 \n",
"\n",
" Link _merge \n",
"0 http://columbus.hms.harvard.edu/browse/measure... both \n",
"1 http://columbus.hms.harvard.edu/browse/measure... both \n",
"2 http://columbus.hms.harvard.edu/browse/measure... both \n",
"3 http://columbus.hms.harvard.edu/browse/measure... both \n",
"4 http://columbus.hms.harvard.edu/browse/measure... both \n",
"\n",
"[5 rows x 532 columns]"
]
},
"execution_count": 37,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"data.head()"
]
},
{
"cell_type": "code",
"execution_count": 38,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/plain": [
"(9360, 532)"
]
},
"execution_count": 38,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"data.shape"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Identify wells with missing data by examing the merge indicator column"
]
},
{
"cell_type": "code",
"execution_count": 39,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/html": [
"<div>\n",
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" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
" <th>CellType</th>\n",
" <th>BiologicalReplicate</th>\n",
" <th>TimePointHours</th>\n",
" <th>WellName</th>\n",
" <th>Column</th>\n",
" <th>Row</th>\n",
" <th>pert_iname</th>\n",
" <th>pert_dose</th>\n",
" <th>pert_dose_unit</th>\n",
" <th>pert_replicate</th>\n",
" <th>...</th>\n",
" <th>Nuclei - Texture Lysosomes Cell Texas Red SER Dark 1 px - Mean per Well</th>\n",
" <th>Nuclei - Cell Lysosomes Haralick Correlation 1 px - Mean per Well</th>\n",
" <th>Nuclei - Cell Lysosomes Haralick Contrast 1 px - Mean per Well</th>\n",
" <th>Nuclei - Cell Lysosomes Haralick Sum Variance 1 px - Mean per Well</th>\n",
" <th>Nuclei - Cell Lysosomes Haralick Homogeneity 1 px - Mean per Well</th>\n",
" <th>Nuclei - Cell Lysosomes Gabor Min 2 px w2 - Mean per Well</th>\n",
" <th>Nuclei - Cell Lysosomes Gabor Max 2 px w2 - Mean per Well</th>\n",
" <th>Number of Analyzed Fields</th>\n",
" <th>Link</th>\n",
" <th>_merge</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>5525</th>\n",
" <td>OAT1</td>\n",
" <td>1</td>\n",
" <td>48</td>\n",
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" <td>3</td>\n",
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" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>left_only</td>\n",
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" <tr>\n",
" <th>5765</th>\n",
" <td>OAT1</td>\n",
" <td>1</td>\n",
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" <td>N3</td>\n",
" <td>3</td>\n",
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" <td>1000.000000</td>\n",
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" <td>1</td>\n",
" <td>...</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
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" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>left_only</td>\n",
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" <tr>\n",
" <th>6004</th>\n",
" <td>OAT1</td>\n",
" <td>2</td>\n",
" <td>0</td>\n",
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" <td>3</td>\n",
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" <td>Aspirin</td>\n",
" <td>316.455696</td>\n",
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" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>left_only</td>\n",
" </tr>\n",
" <tr>\n",
" <th>6005</th>\n",
" <td>OAT1</td>\n",
" <td>2</td>\n",
" <td>0</td>\n",
" <td>N3</td>\n",
" <td>3</td>\n",
" <td>14</td>\n",
" <td>Aspirin</td>\n",
" <td>1000.000000</td>\n",
" <td>um</td>\n",
" <td>1</td>\n",
" <td>...</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>left_only</td>\n",
" </tr>\n",
" <tr>\n",
" <th>6485</th>\n",
" <td>OAT1</td>\n",
" <td>2</td>\n",
" <td>12</td>\n",
" <td>N3</td>\n",
" <td>3</td>\n",
" <td>14</td>\n",
" <td>Aspirin</td>\n",
" <td>1000.000000</td>\n",
" <td>um</td>\n",
" <td>1</td>\n",
" <td>...</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>left_only</td>\n",
" </tr>\n",
" <tr>\n",
" <th>7683</th>\n",
" <td>OAT1</td>\n",
" <td>3</td>\n",
" <td>0</td>\n",
" <td>L3</td>\n",
" <td>3</td>\n",
" <td>12</td>\n",
" <td>Aspirin</td>\n",
" <td>100.144208</td>\n",
" <td>um</td>\n",
" <td>1</td>\n",
" <td>...</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>left_only</td>\n",
" </tr>\n",
" <tr>\n",
" <th>7684</th>\n",
" <td>OAT1</td>\n",
" <td>3</td>\n",
" <td>0</td>\n",
" <td>M3</td>\n",
" <td>3</td>\n",
" <td>13</td>\n",
" <td>Aspirin</td>\n",
" <td>316.455696</td>\n",
" <td>um</td>\n",
" <td>1</td>\n",
" <td>...</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>left_only</td>\n",
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" <tr>\n",
" <th>7685</th>\n",
" <td>OAT1</td>\n",
" <td>3</td>\n",
" <td>0</td>\n",
" <td>N3</td>\n",
" <td>3</td>\n",
" <td>14</td>\n",
" <td>Aspirin</td>\n",
" <td>1000.000000</td>\n",
" <td>um</td>\n",
" <td>1</td>\n",
" <td>...</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>left_only</td>\n",
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" <tr>\n",
" <th>8405</th>\n",
" <td>OAT1</td>\n",
" <td>3</td>\n",
" <td>18</td>\n",
" <td>N3</td>\n",
" <td>3</td>\n",
" <td>14</td>\n",
" <td>Aspirin</td>\n",
" <td>1000.000000</td>\n",
" <td>um</td>\n",
" <td>1</td>\n",
" <td>...</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>left_only</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"<p>9 rows × 532 columns</p>\n",
"</div>"
],
"text/plain": [
" CellType BiologicalReplicate TimePointHours WellName Column Row \\\n",
"5525 OAT1 1 48 N3 3 14 \n",
"5765 OAT1 1 72 N3 3 14 \n",
"6004 OAT1 2 0 M3 3 13 \n",
"6005 OAT1 2 0 N3 3 14 \n",
"6485 OAT1 2 12 N3 3 14 \n",
"7683 OAT1 3 0 L3 3 12 \n",
"7684 OAT1 3 0 M3 3 13 \n",
"7685 OAT1 3 0 N3 3 14 \n",
"8405 OAT1 3 18 N3 3 14 \n",
"\n",
" pert_iname pert_dose pert_dose_unit pert_replicate ... \\\n",
"5525 Aspirin 1000.000000 um 1 ... \n",
"5765 Aspirin 1000.000000 um 1 ... \n",
"6004 Aspirin 316.455696 um 1 ... \n",
"6005 Aspirin 1000.000000 um 1 ... \n",
"6485 Aspirin 1000.000000 um 1 ... \n",
"7683 Aspirin 100.144208 um 1 ... \n",
"7684 Aspirin 316.455696 um 1 ... \n",
"7685 Aspirin 1000.000000 um 1 ... \n",
"8405 Aspirin 1000.000000 um 1 ... \n",
"\n",
" Nuclei - Texture Lysosomes Cell Texas Red SER Dark 1 px - Mean per Well \\\n",
"5525 NaN \n",
"5765 NaN \n",
"6004 NaN \n",
"6005 NaN \n",
"6485 NaN \n",
"7683 NaN \n",
"7684 NaN \n",
"7685 NaN \n",
"8405 NaN \n",
"\n",
" Nuclei - Cell Lysosomes Haralick Correlation 1 px - Mean per Well \\\n",
"5525 NaN \n",
"5765 NaN \n",
"6004 NaN \n",
"6005 NaN \n",
"6485 NaN \n",
"7683 NaN \n",
"7684 NaN \n",
"7685 NaN \n",
"8405 NaN \n",
"\n",
" Nuclei - Cell Lysosomes Haralick Contrast 1 px - Mean per Well \\\n",
"5525 NaN \n",
"5765 NaN \n",
"6004 NaN \n",
"6005 NaN \n",
"6485 NaN \n",
"7683 NaN \n",
"7684 NaN \n",
"7685 NaN \n",
"8405 NaN \n",
"\n",
" Nuclei - Cell Lysosomes Haralick Sum Variance 1 px - Mean per Well \\\n",
"5525 NaN \n",
"5765 NaN \n",
"6004 NaN \n",
"6005 NaN \n",
"6485 NaN \n",
"7683 NaN \n",
"7684 NaN \n",
"7685 NaN \n",
"8405 NaN \n",
"\n",
" Nuclei - Cell Lysosomes Haralick Homogeneity 1 px - Mean per Well \\\n",
"5525 NaN \n",
"5765 NaN \n",
"6004 NaN \n",
"6005 NaN \n",
"6485 NaN \n",
"7683 NaN \n",
"7684 NaN \n",
"7685 NaN \n",
"8405 NaN \n",
"\n",
" Nuclei - Cell Lysosomes Gabor Min 2 px w2 - Mean per Well \\\n",
"5525 NaN \n",
"5765 NaN \n",
"6004 NaN \n",
"6005 NaN \n",
"6485 NaN \n",
"7683 NaN \n",
"7684 NaN \n",
"7685 NaN \n",
"8405 NaN \n",
"\n",
" Nuclei - Cell Lysosomes Gabor Max 2 px w2 - Mean per Well \\\n",
"5525 NaN \n",
"5765 NaN \n",
"6004 NaN \n",
"6005 NaN \n",
"6485 NaN \n",
"7683 NaN \n",
"7684 NaN \n",
"7685 NaN \n",
"8405 NaN \n",
"\n",
" Number of Analyzed Fields Link _merge \n",
"5525 NaN NaN left_only \n",
"5765 NaN NaN left_only \n",
"6004 NaN NaN left_only \n",
"6005 NaN NaN left_only \n",
"6485 NaN NaN left_only \n",
"7683 NaN NaN left_only \n",
"7684 NaN NaN left_only \n",
"7685 NaN NaN left_only \n",
"8405 NaN NaN left_only \n",
"\n",
"[9 rows x 532 columns]"
]
},
"execution_count": 39,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"data[data._merge=='left_only']"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"(The original code goes on to fill in missing data from the corresponding technical replicate and perform the z-score normalization.)"
]
}
],
"metadata": {
"anaconda-cloud": {},
"kernelspec": {
"display_name": "Python 3",
"language": "python",
"name": "python3"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.5.2"
}
},
"nbformat": 4,
"nbformat_minor": 1
}
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