5.2) Whole Slide Scoring - Prediction Confidence Segmentation.ipynb

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  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### 5.2 Whole Slide Scoring - Prediction Confidence Segmentation\n",
    "\n",
    "Prediction confidence heatmaps were segmented to generate the CNN model-based whole-slide scores. \n",
    "\n",
    "First, a CNN confidence threshold was applied to the heatmaps, with only prediction confidences higher than the threshold retained, indicating the existences of plaques predicted with high confidence. Morphological opening and closing operations were then performed to smooth the masks, and prediction areas exceeding a size threshold set to eliminate CNN-noise provided the predicted quantities of Aβ pathologies (ie. cored plaque, diffuse plaque, and CAA). \n",
    "\n",
    "These two hyperparameters, CNN confidence threshold (core: 0.1; diffuse: 0.95; CAA: 0.9) and size threshold (cored: 100; diffuse: 1; CAA: 200), were optimized exclusively by statistical analysis on the combined training and validation sets (32 WSIs). These were then used on the hold-out test set with 30 unseen WSIs to show the generalizability. "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "import csv\n",
    "import glob, os\n",
    "\n",
    "import cv2\n",
    "import numpy as np\n",
    "import pandas as pd\n",
    "import matplotlib.pyplot as plt\n",
    "from skimage import measure\n",
    "from scipy import stats\n",
    "\n",
    "from tqdm import tqdm"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "CSV_DIR = 'data/outputs/CNNscore/WSI_CERAD_AREA.csv'\n",
    "HEATMAP_DIR = 'data/outputs/heatmaps'\n",
    "SAVE_DIR = 'data/outputs/CNNscore/'"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "if not os.path.exists(SAVE_DIR):\n",
    "        os.makedirs(SAVE_DIR)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "file = pd.read_csv(CSV_DIR)\n",
    "filenames = list(file['WSI_ID'])\n",
    "img_class = ['cored', 'diffuse', 'caa']\n",
    "\n",
    "# two hyperparameters\n",
    "confidence_thresholds = [0.1, 0.95, 0.9]\n",
    "pixel_thresholds = [100, 1, 200]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "def count_blobs(mask,\n",
    "               threshold=1500):\n",
    "    labels = measure.label(mask, neighbors=8, background=0)\n",
    "    new_mask = np.zeros(mask.shape, dtype='uint8')\n",
    "    sizes = []\n",
    "    \n",
    "    # loop over the unique components\n",
    "    for label in np.unique(labels):\n",
    "        # if this is the background label, ignore it\n",
    "        if label == 0:\n",
    "            continue\n",
    "        # otherwise, construct the label mask and count the\n",
    "        # number of pixels \n",
    "        labelMask = np.zeros(mask.shape, dtype=\"uint8\")\n",
    "        labelMask[labels == label] = 255\n",
    "        numPixels = cv2.countNonZero(labelMask)\n",
    "        \n",
    "        # if the number of pixels in the component is sufficiently\n",
    "        # large, then add it to our mask of \"large blobs\"\n",
    "        if numPixels > threshold:\n",
    "            sizes.append(numPixels)\n",
    "            new_mask = cv2.add(new_mask, labelMask)\n",
    "\n",
    "    return sizes, new_mask"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
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      "62it [07:13,  6.99s/it]\n",
      "0it [00:00, ?it/s]"
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     "text": [
      "0.1 100\n"
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     "text": [
      "62it [20:42, 20.05s/it]\n",
      "0it [00:00, ?it/s]"
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     "text": [
      "0.95 1\n"
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      "62it [01:14,  1.21s/it]"
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      "0.9 200\n"
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   "source": [
    "new_file = file\n",
    "for index in [0,1,2]:\n",
    "    preds = np.zeros(len(file))\n",
    "    confidence_threshold = confidence_thresholds[index]\n",
    "    pixel_threshold = pixel_thresholds[index]\n",
    "\n",
    "    for i, WSIname in tqdm(enumerate(filenames)):\n",
    "        try:\n",
    "            heatmap_path = HEATMAP_DIR+'new_WSI_heatmap_{}.npy'.format(WSIname)\n",
    "            h = np.load(heatmap_path)\n",
    "\n",
    "        except:\n",
    "            heatmap_path = HEATMAP_DIR+'{}.npy'.format(WSIname)\n",
    "            h = np.load(heatmap_path)\n",
    "\n",
    "        mask = h[index] > confidence_threshold\n",
    "        mask = mask.astype(np.float32)\n",
    "\n",
    "        kernel = cv2.getStructuringElement(cv2.MORPH_CROSS,(5,5))\n",
    "\n",
    "        # Apply morphological closing, then opening operations \n",
    "        opening = cv2.morphologyEx(mask, cv2.MORPH_OPEN, kernel)\n",
    "        closing = cv2.morphologyEx(opening, cv2.MORPH_CLOSE, kernel)\n",
    "\n",
    "        a, m = count_blobs(closing, threshold=pixel_threshold)\n",
    "\n",
    "        preds[i] = len(a)\n",
    "\n",
    "    print(confidence_threshold, pixel_threshold)\n",
    "\n",
    "    new_file['CNN_{}_count'.format(img_class[index])] = preds\n",
    "\n",
    "new_file.to_csv(SAVE_DIR+'CNN_vs_CERAD.csv', index=False)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {
    "scrolled": false
   },
   "outputs": [
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       "      <td>2.0</td>\n",
       "      <td>3.0</td>\n",
       "      <td>2730917</td>\n",
       "      <td>7.0</td>\n",
       "      <td>410.0</td>\n",
       "      <td>595.0</td>\n",
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       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>NA5003_2AB</td>\n",
       "      <td>train</td>\n",
       "      <td>sparse</td>\n",
       "      <td>1.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>2.0</td>\n",
       "      <td>4108923</td>\n",
       "      <td>55.0</td>\n",
       "      <td>109.0</td>\n",
       "      <td>117.0</td>\n",
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       "      <td>train</td>\n",
       "      <td>sparse</td>\n",
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       "      <td>3.0</td>\n",
       "      <td>0.0</td>\n",
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       "      <td>train</td>\n",
       "      <td>moderate</td>\n",
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       "      <td>2.0</td>\n",
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       "      <td>861.0</td>\n",
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       "      <td>64.0</td>\n",
       "      <td>183.0</td>\n",
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       "      <td>5578344</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
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       "      <td>train</td>\n",
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       "      <td>0.0</td>\n",
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       "      <td>train</td>\n",
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       "      <td>validation</td>\n",
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       "      <td>train</td>\n",
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       "      <td>3.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>4664757</td>\n",
       "      <td>646.0</td>\n",
       "      <td>3539.0</td>\n",
       "      <td>4.0</td>\n",
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       "    <tr>\n",
       "      <th>18</th>\n",
       "      <td>NA5005-02_AB</td>\n",
       "      <td>train</td>\n",
       "      <td>moderate</td>\n",
       "      <td>1.0</td>\n",
       "      <td>3.0</td>\n",
       "      <td>2.0</td>\n",
       "      <td>5329063</td>\n",
       "      <td>306.0</td>\n",
       "      <td>3886.0</td>\n",
       "      <td>36.0</td>\n",
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       "    <tr>\n",
       "      <th>19</th>\n",
       "      <td>NA_4882_02_AB</td>\n",
       "      <td>train</td>\n",
       "      <td>frequent</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>5409483</td>\n",
       "      <td>1.0</td>\n",
       "      <td>2.0</td>\n",
       "      <td>0.0</td>\n",
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       "    <tr>\n",
       "      <th>20</th>\n",
       "      <td>NA4229-02_AB</td>\n",
       "      <td>train</td>\n",
       "      <td>frequent</td>\n",
       "      <td>2.0</td>\n",
       "      <td>2.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>3125837</td>\n",
       "      <td>300.0</td>\n",
       "      <td>1910.0</td>\n",
       "      <td>1.0</td>\n",
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       "    <tr>\n",
       "      <th>21</th>\n",
       "      <td>NA4312-02_AB</td>\n",
       "      <td>train</td>\n",
       "      <td>frequent</td>\n",
       "      <td>2.0</td>\n",
       "      <td>3.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>5241430</td>\n",
       "      <td>569.0</td>\n",
       "      <td>255.0</td>\n",
       "      <td>13.0</td>\n",
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       "    <tr>\n",
       "      <th>22</th>\n",
       "      <td>NA4619-02_AB</td>\n",
       "      <td>train</td>\n",
       "      <td>frequent</td>\n",
       "      <td>2.0</td>\n",
       "      <td>3.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>7319038</td>\n",
       "      <td>1053.0</td>\n",
       "      <td>3934.0</td>\n",
       "      <td>43.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>23</th>\n",
       "      <td>NA4711-02_AB</td>\n",
       "      <td>train</td>\n",
       "      <td>frequent</td>\n",
       "      <td>3.0</td>\n",
       "      <td>2.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>4355835</td>\n",
       "      <td>922.0</td>\n",
       "      <td>1066.0</td>\n",
       "      <td>0.0</td>\n",
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       "    <tr>\n",
       "      <th>24</th>\n",
       "      <td>NA4751-02_AB</td>\n",
       "      <td>train</td>\n",
       "      <td>frequent</td>\n",
       "      <td>3.0</td>\n",
       "      <td>2.0</td>\n",
       "      <td>3.0</td>\n",
       "      <td>7192057</td>\n",
       "      <td>1143.0</td>\n",
       "      <td>572.0</td>\n",
       "      <td>218.0</td>\n",
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       "    <tr>\n",
       "      <th>25</th>\n",
       "      <td>NA4757-02_AB</td>\n",
       "      <td>train</td>\n",
       "      <td>frequent</td>\n",
       "      <td>3.0</td>\n",
       "      <td>2.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>6443660</td>\n",
       "      <td>1277.0</td>\n",
       "      <td>575.0</td>\n",
       "      <td>19.0</td>\n",
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       "    <tr>\n",
       "      <th>26</th>\n",
       "      <td>NA4885-02_AB17-24</td>\n",
       "      <td>train</td>\n",
       "      <td>frequent</td>\n",
       "      <td>2.0</td>\n",
       "      <td>3.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>5716866</td>\n",
       "      <td>289.0</td>\n",
       "      <td>3650.0</td>\n",
       "      <td>10.0</td>\n",
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       "    <tr>\n",
       "      <th>27</th>\n",
       "      <td>NA_4888_02_AB17-24</td>\n",
       "      <td>train</td>\n",
       "      <td>frequent</td>\n",
       "      <td>1.0</td>\n",
       "      <td>3.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>5527030</td>\n",
       "      <td>316.0</td>\n",
       "      <td>5387.0</td>\n",
       "      <td>6.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>28</th>\n",
       "      <td>NA_4896_02_AB17-24</td>\n",
       "      <td>validation</td>\n",
       "      <td>frequent</td>\n",
       "      <td>2.0</td>\n",
       "      <td>3.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>5631393</td>\n",
       "      <td>582.0</td>\n",
       "      <td>3874.0</td>\n",
       "      <td>35.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>29</th>\n",
       "      <td>NA_4928_02_AB17-24</td>\n",
       "      <td>validation</td>\n",
       "      <td>frequent</td>\n",
       "      <td>2.0</td>\n",
       "      <td>3.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>5076420</td>\n",
       "      <td>501.0</td>\n",
       "      <td>1832.0</td>\n",
       "      <td>17.0</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>32</th>\n",
       "      <td>NA4256-02_AB</td>\n",
       "      <td>hold out</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>8346087</td>\n",
       "      <td>755.0</td>\n",
       "      <td>3108.0</td>\n",
       "      <td>237.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>33</th>\n",
       "      <td>NA4130-02_AB</td>\n",
       "      <td>hold out</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>4669976</td>\n",
       "      <td>481.0</td>\n",
       "      <td>1458.0</td>\n",
       "      <td>49.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>34</th>\n",
       "      <td>NA4582-02_AB</td>\n",
       "      <td>hold out</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>7540112</td>\n",
       "      <td>3.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>35</th>\n",
       "      <td>NA4291-02_AB</td>\n",
       "      <td>hold out</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>6502760</td>\n",
       "      <td>87.0</td>\n",
       "      <td>296.0</td>\n",
       "      <td>5.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>36</th>\n",
       "      <td>NA4944-02_AB17-24</td>\n",
       "      <td>hold out</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>4195695</td>\n",
       "      <td>3.0</td>\n",
       "      <td>60.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>37</th>\n",
       "      <td>NA4195-02_AB</td>\n",
       "      <td>hold out</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>5459332</td>\n",
       "      <td>470.0</td>\n",
       "      <td>637.0</td>\n",
       "      <td>8.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>38</th>\n",
       "      <td>NA4621-02_AB-001</td>\n",
       "      <td>hold out</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>6352683</td>\n",
       "      <td>4.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>39</th>\n",
       "      <td>NA4370-02_AB</td>\n",
       "      <td>hold out</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>5358120</td>\n",
       "      <td>544.0</td>\n",
       "      <td>2441.0</td>\n",
       "      <td>3.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>40</th>\n",
       "      <td>NA4727-02_AB</td>\n",
       "      <td>hold out</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>5829525</td>\n",
       "      <td>146.0</td>\n",
       "      <td>29.0</td>\n",
       "      <td>1.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>41</th>\n",
       "      <td>NA4945-02_AB17-24</td>\n",
       "      <td>hold out</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>4165097</td>\n",
       "      <td>8.0</td>\n",
       "      <td>2741.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>42</th>\n",
       "      <td>NA4695-02_AB</td>\n",
       "      <td>hold out</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>5671085</td>\n",
       "      <td>328.0</td>\n",
       "      <td>2631.0</td>\n",
       "      <td>16.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>43</th>\n",
       "      <td>NA4675-02_AB</td>\n",
       "      <td>hold out</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>6231302</td>\n",
       "      <td>1014.0</td>\n",
       "      <td>1348.0</td>\n",
       "      <td>6.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>44</th>\n",
       "      <td>NA4963-02_AB17-24</td>\n",
       "      <td>hold out</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>4051948</td>\n",
       "      <td>422.0</td>\n",
       "      <td>2422.0</td>\n",
       "      <td>3.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>45</th>\n",
       "      <td>NA4542-02_AB</td>\n",
       "      <td>hold out</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>8087607</td>\n",
       "      <td>112.0</td>\n",
       "      <td>3949.0</td>\n",
       "      <td>98.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>46</th>\n",
       "      <td>NA4691-02_AB</td>\n",
       "      <td>hold out</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>5408936</td>\n",
       "      <td>195.0</td>\n",
       "      <td>1678.0</td>\n",
       "      <td>15.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>47</th>\n",
       "      <td>NA4669-02_AB</td>\n",
       "      <td>hold out</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>5392129</td>\n",
       "      <td>627.0</td>\n",
       "      <td>1930.0</td>\n",
       "      <td>47.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>48</th>\n",
       "      <td>NA4955-02_AB17-24</td>\n",
       "      <td>hold out</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>3634198</td>\n",
       "      <td>70.0</td>\n",
       "      <td>1925.0</td>\n",
       "      <td>4.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>49</th>\n",
       "      <td>NA4659-02_AB</td>\n",
       "      <td>hold out</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>5933379</td>\n",
       "      <td>578.0</td>\n",
       "      <td>768.0</td>\n",
       "      <td>33.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>50</th>\n",
       "      <td>NA4684-02_AB</td>\n",
       "      <td>hold out</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>5518926</td>\n",
       "      <td>512.0</td>\n",
       "      <td>981.0</td>\n",
       "      <td>1.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>51</th>\n",
       "      <td>NA4653-02_AB</td>\n",
       "      <td>hold out</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>5801814</td>\n",
       "      <td>294.0</td>\n",
       "      <td>672.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>52</th>\n",
       "      <td>NA4129-2_AB</td>\n",
       "      <td>hold out</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>7585823</td>\n",
       "      <td>655.0</td>\n",
       "      <td>1603.0</td>\n",
       "      <td>2.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>53</th>\n",
       "      <td>NA4974-02_AB17-24</td>\n",
       "      <td>hold out</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>3969426</td>\n",
       "      <td>346.0</td>\n",
       "      <td>325.0</td>\n",
       "      <td>24.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>54</th>\n",
       "      <td>NA4156-2_AB</td>\n",
       "      <td>hold out</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>8249458</td>\n",
       "      <td>569.0</td>\n",
       "      <td>3465.0</td>\n",
       "      <td>2.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>55</th>\n",
       "      <td>NA4053-02_AB</td>\n",
       "      <td>hold out</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>8139975</td>\n",
       "      <td>791.0</td>\n",
       "      <td>5360.0</td>\n",
       "      <td>1.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>56</th>\n",
       "      <td>NA4133_2_AB</td>\n",
       "      <td>hold out</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>5552099</td>\n",
       "      <td>839.0</td>\n",
       "      <td>2589.0</td>\n",
       "      <td>20.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>57</th>\n",
       "      <td>NA4167-2_AB</td>\n",
       "      <td>hold out</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>7715256</td>\n",
       "      <td>993.0</td>\n",
       "      <td>3715.0</td>\n",
       "      <td>3.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>58</th>\n",
       "      <td>NA4853-02_AB17-24</td>\n",
       "      <td>hold out</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>2346820</td>\n",
       "      <td>197.0</td>\n",
       "      <td>2364.0</td>\n",
       "      <td>16.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>59</th>\n",
       "      <td>NA4953-02_AB17-24</td>\n",
       "      <td>hold out</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>3350368</td>\n",
       "      <td>165.0</td>\n",
       "      <td>2216.0</td>\n",
       "      <td>2.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>60</th>\n",
       "      <td>NA4954-02_AB17-24</td>\n",
       "      <td>hold out</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>4930841</td>\n",
       "      <td>66.0</td>\n",
       "      <td>2918.0</td>\n",
       "      <td>1.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>61</th>\n",
       "      <td>NA4964-02_AB17-24</td>\n",
       "      <td>hold out</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>3197480</td>\n",
       "      <td>107.0</td>\n",
       "      <td>1641.0</td>\n",
       "      <td>12.0</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>62 rows × 10 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                WSI_ID       Group     CERAD  Cored_MTG  Diffuse_MTG  CAA_MTG  \\\n",
       "0         NA4009-02_AB       train      none        1.0          2.0      0.0   \n",
       "1   NA_4933_02_AB17-24  validation      none        0.0          1.0      0.0   \n",
       "2         NA4137-02_AB       train    sparse        0.0          1.0      0.0   \n",
       "3    NA_4865_02_AB1-40       train    sparse        0.0          0.0      0.0   \n",
       "4        NA_4871_02_AB       train    sparse        0.0          0.0      0.0   \n",
       "5           NA5001_2AB       train    sparse        1.0          2.0      3.0   \n",
       "6           NA5003_2AB       train    sparse        1.0          1.0      2.0   \n",
       "7         NA4144-02_AB       train    sparse        0.0          3.0      0.0   \n",
       "8         NA4072-02_AB       train  moderate        1.0          2.0      0.0   \n",
       "9         NA4185-02_AB       train  moderate        2.0          2.0      0.0   \n",
       "10        NA4471-02_AB       train  moderate        2.0          3.0      0.0   \n",
       "11        NA4722-02_AB       train  moderate        0.0          2.0      3.0   \n",
       "12        NA4749-02_AB       train  moderate        2.0          2.0      1.0   \n",
       "13       NA_4883_02_AB       train  moderate        0.0          0.0      0.0   \n",
       "14   NA4898-02_AB17-24       train  moderate        1.0          3.0      0.0   \n",
       "15   NA4918-02_AB17-24       train  moderate        1.0          3.0      0.0   \n",
       "16  NA_4930_02_AB14-24  validation  moderate        2.0          3.0      1.0   \n",
       "17        NA5004_02_AB       train  moderate        1.0          3.0      0.0   \n",
       "18        NA5005-02_AB       train  moderate        1.0          3.0      2.0   \n",
       "19       NA_4882_02_AB       train  frequent        0.0          0.0      0.0   \n",
       "20        NA4229-02_AB       train  frequent        2.0          2.0      0.0   \n",
       "21        NA4312-02_AB       train  frequent        2.0          3.0      0.0   \n",
       "22        NA4619-02_AB       train  frequent        2.0          3.0      1.0   \n",
       "23        NA4711-02_AB       train  frequent        3.0          2.0      0.0   \n",
       "24        NA4751-02_AB       train  frequent        3.0          2.0      3.0   \n",
       "25        NA4757-02_AB       train  frequent        3.0          2.0      1.0   \n",
       "26   NA4885-02_AB17-24       train  frequent        2.0          3.0      0.0   \n",
       "27  NA_4888_02_AB17-24       train  frequent        1.0          3.0      0.0   \n",
       "28  NA_4896_02_AB17-24  validation  frequent        2.0          3.0      1.0   \n",
       "29  NA_4928_02_AB17-24  validation  frequent        2.0          3.0      1.0   \n",
       "..                 ...         ...       ...        ...          ...      ...   \n",
       "32        NA4256-02_AB    hold out       NaN        NaN          NaN      NaN   \n",
       "33        NA4130-02_AB    hold out       NaN        NaN          NaN      NaN   \n",
       "34        NA4582-02_AB    hold out       NaN        NaN          NaN      NaN   \n",
       "35        NA4291-02_AB    hold out       NaN        NaN          NaN      NaN   \n",
       "36   NA4944-02_AB17-24    hold out       NaN        NaN          NaN      NaN   \n",
       "37        NA4195-02_AB    hold out       NaN        NaN          NaN      NaN   \n",
       "38    NA4621-02_AB-001    hold out       NaN        NaN          NaN      NaN   \n",
       "39        NA4370-02_AB    hold out       NaN        NaN          NaN      NaN   \n",
       "40        NA4727-02_AB    hold out       NaN        NaN          NaN      NaN   \n",
       "41   NA4945-02_AB17-24    hold out       NaN        NaN          NaN      NaN   \n",
       "42        NA4695-02_AB    hold out       NaN        NaN          NaN      NaN   \n",
       "43        NA4675-02_AB    hold out       NaN        NaN          NaN      NaN   \n",
       "44   NA4963-02_AB17-24    hold out       NaN        NaN          NaN      NaN   \n",
       "45        NA4542-02_AB    hold out       NaN        NaN          NaN      NaN   \n",
       "46        NA4691-02_AB    hold out       NaN        NaN          NaN      NaN   \n",
       "47        NA4669-02_AB    hold out       NaN        NaN          NaN      NaN   \n",
       "48   NA4955-02_AB17-24    hold out       NaN        NaN          NaN      NaN   \n",
       "49        NA4659-02_AB    hold out       NaN        NaN          NaN      NaN   \n",
       "50        NA4684-02_AB    hold out       NaN        NaN          NaN      NaN   \n",
       "51        NA4653-02_AB    hold out       NaN        NaN          NaN      NaN   \n",
       "52         NA4129-2_AB    hold out       NaN        NaN          NaN      NaN   \n",
       "53   NA4974-02_AB17-24    hold out       NaN        NaN          NaN      NaN   \n",
       "54         NA4156-2_AB    hold out       NaN        NaN          NaN      NaN   \n",
       "55        NA4053-02_AB    hold out       NaN        NaN          NaN      NaN   \n",
       "56         NA4133_2_AB    hold out       NaN        NaN          NaN      NaN   \n",
       "57         NA4167-2_AB    hold out       NaN        NaN          NaN      NaN   \n",
       "58   NA4853-02_AB17-24    hold out       NaN        NaN          NaN      NaN   \n",
       "59   NA4953-02_AB17-24    hold out       NaN        NaN          NaN      NaN   \n",
       "60   NA4954-02_AB17-24    hold out       NaN        NaN          NaN      NaN   \n",
       "61   NA4964-02_AB17-24    hold out       NaN        NaN          NaN      NaN   \n",
       "\n",
       "       Area  CNN_cored_count  CNN_diffuse_count  CNN_caa_count  \n",
       "0   5863952             96.0             4296.0           38.0  \n",
       "1   3786178             27.0               29.0            1.0  \n",
       "2   5976867             15.0               22.0            2.0  \n",
       "3   5093794              0.0                0.0            0.0  \n",
       "4   3997928              0.0                0.0            2.0  \n",
       "5   2730917              7.0              410.0          595.0  \n",
       "6   4108923             55.0              109.0          117.0  \n",
       "7   6054061             50.0             4390.0            4.0  \n",
       "8   8362154             40.0                9.0            0.0  \n",
       "9   6191811            861.0             1113.0            4.0  \n",
       "10  5916577             69.0              157.0           29.0  \n",
       "11  7357867             64.0              183.0          191.0  \n",
       "12  6603841            742.0             1415.0            1.0  \n",
       "13  5578344              0.0                0.0            1.0  \n",
       "14  5952251            112.0             1206.0           22.0  \n",
       "15  3423404            125.0              874.0            1.0  \n",
       "16  4243631            367.0             1496.0           10.0  \n",
       "17  4664757            646.0             3539.0            4.0  \n",
       "18  5329063            306.0             3886.0           36.0  \n",
       "19  5409483              1.0                2.0            0.0  \n",
       "20  3125837            300.0             1910.0            1.0  \n",
       "21  5241430            569.0              255.0           13.0  \n",
       "22  7319038           1053.0             3934.0           43.0  \n",
       "23  4355835            922.0             1066.0            0.0  \n",
       "24  7192057           1143.0              572.0          218.0  \n",
       "25  6443660           1277.0              575.0           19.0  \n",
       "26  5716866            289.0             3650.0           10.0  \n",
       "27  5527030            316.0             5387.0            6.0  \n",
       "28  5631393            582.0             3874.0           35.0  \n",
       "29  5076420            501.0             1832.0           17.0  \n",
       "..      ...              ...                ...            ...  \n",
       "32  8346087            755.0             3108.0          237.0  \n",
       "33  4669976            481.0             1458.0           49.0  \n",
       "34  7540112              3.0                0.0            0.0  \n",
       "35  6502760             87.0              296.0            5.0  \n",
       "36  4195695              3.0               60.0            0.0  \n",
       "37  5459332            470.0              637.0            8.0  \n",
       "38  6352683              4.0                0.0            0.0  \n",
       "39  5358120            544.0             2441.0            3.0  \n",
       "40  5829525            146.0               29.0            1.0  \n",
       "41  4165097              8.0             2741.0            0.0  \n",
       "42  5671085            328.0             2631.0           16.0  \n",
       "43  6231302           1014.0             1348.0            6.0  \n",
       "44  4051948            422.0             2422.0            3.0  \n",
       "45  8087607            112.0             3949.0           98.0  \n",
       "46  5408936            195.0             1678.0           15.0  \n",
       "47  5392129            627.0             1930.0           47.0  \n",
       "48  3634198             70.0             1925.0            4.0  \n",
       "49  5933379            578.0              768.0           33.0  \n",
       "50  5518926            512.0              981.0            1.0  \n",
       "51  5801814            294.0              672.0            0.0  \n",
       "52  7585823            655.0             1603.0            2.0  \n",
       "53  3969426            346.0              325.0           24.0  \n",
       "54  8249458            569.0             3465.0            2.0  \n",
       "55  8139975            791.0             5360.0            1.0  \n",
       "56  5552099            839.0             2589.0           20.0  \n",
       "57  7715256            993.0             3715.0            3.0  \n",
       "58  2346820            197.0             2364.0           16.0  \n",
       "59  3350368            165.0             2216.0            2.0  \n",
       "60  4930841             66.0             2918.0            1.0  \n",
       "61  3197480            107.0             1641.0           12.0  \n",
       "\n",
       "[62 rows x 10 columns]"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "new_file"
   ]
  }
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